Genome annotation, comparative genomics and evolution of the model grass genus brachypodium: (poaceae)

• Autores: Rubén Sancho Cohen
• Directores de la Tesis: Pilar Catalán Rodríguez (dir. tes.), Bruno Contreras Moreira (dir. tes.)
• Lectura: En la Universidad de Zaragoza ( España ) en 2018
• Idioma: inglés
• Tribunal Calificador de la Tesis: Isabel Marques (presid.), José Antonio Manzaneda (secret.), Javier Terol Alcayde (voc.)
• Programa de doctorado: Programa de Doctorado en Ciencias Agrarias y del Medio Natural por la Universidad de Zaragoza
• Materias:
  • Ciencias de la vida
    • Biología vegetal (botánica)
• Texto completo no disponible (Saber más ...)
• Resumen

  • INTRODUCCIÓN En esta Tesis Doctoral se han llevado a cabo estudios evolutivos, biogeográficos, genómicos, transcriptómicos y de expresión génica en los taxones que integran el género Brachypodium (Poaceae) con el objetivo de descifrar los eventos de especiación que han dado lugar a las especies de dicho género. La tesis está constituida por cuatro capítulos con sus respectivos cuatro apéndices.

    DESARROLLO TEÓRICO Capítulo 1. Reconstrucción de los orígenes y la biogeografía de los genomas de las especies del género modelo de gramíneas Brachypodium, altamente reticulado y rico en especies alopoliploides, mediante métodos de evolución mínima, coalescencia y máxima verosimilitud (Reconstructing the origins and the biogeography of species’ genomes in the highly reticulate allopolyploid-rich model grass genus Brachypodium using minimum evolution, coalescence and maximum likelihood approaches).

    Se ha reconstruido la filogenia y la historia biogeográfica de las especies reconocidas de Brachypodium mediante el análisis evolutivo del gen nuclear copia simple GIGANTEA (GI), y de otros genes tanto nucleares (ITS, ETS) como plastídicos (ndhF, trnL-F). Para ello se han desarrollado análisis de redes haplotípicas, de mapeo de los alelos poliploides en el árbol de especies diploides por evolución mínima y de construcción del árbol de especies (de genomas y subgenomas), así como la reconstrucción biogeográfica y el cálculo de los tiempos de divergencia de los subgenomas homeólogos por métodos máximo verosímiles y bayesianos, respectivamente, y la estimación por coalescencia de los posibles tiempos en los que se produjeron los eventos de hibridación que dieron lugar a las especies alopoliploides.

    Nuestros resultados apoyan la naturaleza alopoliploide de las especies poliploides del género, así como un escenario espacio-temporal de diversas divergencias y fusiones de los genomas en las diferentes áreas ancestrales, mostrando un claro predominio de la dispersión de los genomas diploides frente a los alopoliploides. También han sido inferidos los tiempos de divergencia de todas los linajes estudiados, desde el más ancestral, B. stacei (6,8 Ma) hasta los más recientes del “core perennial” (0,7-0,3 Ma).

    Capítulo 2. Mapeos sinténicos contra genomas de referencia y estudios filogenómicos basados en análisis multigénicos revelan los ancestros de los subgenomas homeologos de especies alopoliploides del género Brachypodium. (Reference-genome syntenic mapping and multigene-based phylogenomics reveal the ancestry of homeologous subgenomes in grass Brachypodium allopolyploids).

    Se llevaron a cabo mapeos sinténicos de datos transcriptómicos y de genotipado genómico (GBS) contra los genomas de referencia de Brachypodium desarrollando nuestros propios algoritmos y herramientas bioinformáticas. Con esos datos se ha reconstruido la filogenia y se han datado los orígenes de los genomas y subgenomas presentes en especies diploides y alopoliploides de Brachypodium empleando métodos bayesianos y de máxima verosimilitud. Adicionalmente, se ha obtenido y analizado el pan-transcriptoma de las especies estudiadas, identificando genes potencialmente exclusivos de determinados grupos de especies.

    Los análisis filogenéticos basados en datos transcriptómicos junto con la obtención de tamaños genómicos nos ha permitido elucidar complejos escenarios de hibridación para los subgenomas homeologos de las seis especies alopoliploides de Brachypodium estudiadas, mostrando distintos eventos de hibridación que implican únicamente a genomas ancestrales, a genomas ancestrales y recientes, y únicamente a genomas recientes. Nuestros resultados apoyan el origen ancestral de B. mexicanum, el intermedio de B. boissieri y B. retusum, y la rápida radiación de las especies del “core perennial”.

    Los capítulos 1 y 2 suponen un completo análisis del género Brachypodium, en especial de las especies alopoliploides, cuyos resultados apoyan y datan los eventos evolutivos que han dado lugar a la compleja y reticulada historia evolutiva que presenta dicho género así como los posibles linajes progenitores de las especies alopoliploides.

    Capítulo 3. Genómica comparada del plastoma y filogenómica de Brachypodium: improntas de los tiempos de floración, introgresión y recombinación en los ecotipos recientemente evolucionados. (Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes).

    Se han ensamblado, anotado y analizado los genomas organulares (plastomas) de un amplio número de ecotipos de las especies anuales de Brachypodium, y se ha reconstruido su filogenia, comparándola con la de sus genomas nucleares. Se ha dilucidado la diversificación de los ecotipos y su relación con factores de tiempos de floración y geográficos. El estudio comparativo de los 57 genomas cloroplásticos ensamblados y anotados, 53 B. distachyon, 3 B. hybridum y 1 B. stacei, ha revelado reordenamientos genómicos, como la inserción de 1161 pb y la deleción de una de las copias del gen rps19, característicos de las especies B. stacei y B. hybridum (plastoma tipo stacei), respecto de las líneas de B. distachyon. Se han estimado sus orígenes mediante datación anidada dentro del marco evolutivo de las gramíneas y, para las líneas de B. distachyon, se ha comparado la filogenia plastómica con la nuclear, detectándose una divergencia clara de dos linajes intra-específicos, relacionada con sus tiempos de floración, y una subestructuración más reciente relacionada con su geografía, así como la evidencia de capturas cloroplásticas e introgresión entre clados distantes. Estos datos apoyan que la tendencia a la microespeciación se ve frenada por procesos de introgresión recurrente.

    Capítulo 4. Características de las redes de co-expresión y los genes diferencialmente expresados explican los patrones de respuesta a sequía en la gramínea modelo Brachypodium distachyon. (Co-expression network features and differentially expressed genes explain drought-response patterns in the model grass Brachypodium distachyon).

    Se han identificado y analizado genes funcionales implicados en la respuesta ambiental a estrés hídrico mediante el análisis de redes de co-expresión génica y de genes diferencialmente expresados en diversos ecotipos de la planta modelo Brachypodium distachyon.

    Se han analizado tanto la topología de dichas redes como los genes e isoformas más interconectadas, detectando 38 módulos en la red de co-expresión bajo condiciones de sequía, con 628 genes altamente interconectados (820 transcritos), y 30 módulos en la red de co-expresión en condiciones de riego con 839 genes altamente interconectados (1072 transcritos). Además se han identificado los procesos biológicos en los que están implicados los genes co-expresados, encontrando cinco módulos exclusivos de la red bajo condiciones de sequía de los cuales tres están directamente relacionados con procesos de respuesta a estrés hídrico. Estos resultados han sido correlacionados con datos pan-genómicos observando que la mayoría de los genes co-expresados son genes “core”, conservados en todos la líneas estudiadas, o “soft-core”, conservados en más del 90% de las líneas estudiadas.

    CONCLUSIONES 1-Los análisis evolutivos y biogeográficos de los 20 taxones reconocidos del género Brachypodium empleando cinco genes (tres nucleares y dos plastídicos) indican que aproximadamente la mitad de las especies son diploides y la otra mitad alopoliploides. El análisis de evolución mínima de “injerto” de alelos alopoliploides en las ramas del árbol diploide recobra los linajes homeólogos (subgenomas) de los alopoliploides. Las sucesivas divergencias de los linajes de las diploides anuales (B. stacei, B. distachyon) tuvieron lugar durante el Mioceno tardío-Plioceno en la cuenca Mediterránea, mientras que las de los linajes de las diploides perennes (B. arbuscula, B. genuense, B. sylvaticum, B. glaucovirens, B. pinnatum-2x y B. rupestre-2x) ocurrieron durante el Cuaternario en las regiones Mediterránea y Euroasiática, con colonizaciones esporádicas de otros continentes. Las respectivas divergencias de los linajes homeólogos de los alopoliploides tuvieron lugar en distintos tiempos evolutivos. Nuestro escenario biogeográfico apoya la existencia de dispersiones a larga distancia únicamente en los linajes diploides, mientras que todos los eventos de hibridación y duplicación genómica ocurrieron dentro de las áreas ancestrales progenitoras más recientes, sin posteriores expansiones de área.

    2- Los análisis filogenómicos mediante datos de RNA-seq y GBS han identificado a B. mexicanum como la especie alopoliploide más antigua mostrando subgenomas de tipo ancestral (A) y materno de tipo stacei (B) (Mioceno medio-tardío). Los alopoliploides de elevado nivel de ploidía, B. boissieri y B. retusum, muestran tres y cuatro subgenomas respectivamente. Ambas especies presentan subgenomas A y B así como el subgenoma intermedio tipo distachyon (C) (Mioceno-Plioceno) (heredado maternalmente en B. boissieri). B. retusum también presenta un subgenoma materno tipo core perennial recientemente evolucionado (D) (Cuaternario). Los alotetraploides del clado core perennial B. rupestre y B. phoenicoides muestran únicamente subgenomas recientemente evolucionados tipo C y D (Cuaternario), siendo los diploides perennes B. pinnatum y B. sylvaticum sus respectivos progenitores maternos. El reciente alopoliploide B. hybridum se formó repetidamente y mediante cruzamientos bidireccionales durante el Cuaternario y es el único alopoliploide del que se conocen ambos progenitores diploides actuales, B. distachyon y B. stacei.

    3- Los análisis pan-transcriptómicos de 5202 conjuntos de tránscritos del género Brachypodium muestran genes expresados exclusivamente en los grupos de especies perennes (30), anuales (49), poliploides (14), alopoliploides más antiguos (143), especies ancestrales (14) y especies recientemente evolucionadas (52). Los tránscritos exclusivos de los alopoliploides antiguos podrían estar asociados con su genoma ancestral tipo A. Los tránscritos anotados como subunidad ARN polimerasa, encontrados únicamente en todas las especies anuales de Brachypodium, podrían indicar la existencia de diferencias en los niveles de expresión de las ARN polimerasas entre las especies anuales y perennes, o la pérdida de copias ancestrales en las especies perennes más recientemente evolucionadas.

    4- Los análisis pan-genómicos de los plastomas de 53 ecotipos de B. distachyon, 3 de B. hybridum y 1 de B. stacei han detectado una inserción (1161 pb) y una deleción en una de las copias del gen rps19 que diferencian a los plastomas de B. stacei y B. hybridum con respecto a los de B. distachyon, sin que se haya observado variación en el contenido génico entre los plastomas de B. distachyon.

    5- El árbol filogenómico de los plastomas de B. distachyon muestra la divergencia de dos linajes principales, correspondientes a los clados Extremely Delayed Flowering (EDF+) y Spanish (S+) – Turkish (T+), sugiriendo que el tiempo de floración es un factor decisivo en la divergencia intra-específica de B. distachyon. La comparación topológica entre las filogenias nucleares y plastídicas de esta especie revela nueve eventos de captura cloroplástica y dos de introgresión y micro-recombinación entre esos clados, apoyando la existencia de flujo génico entre linajes previamente aislados. Los intercambios de plastomas entre los tres grupos, EDF+, T+, S+, probablemente hayan sido el resultado de retro-cruzamientos aleatorios seguidos de estabilización por presión selectiva.

    6- Los análisis mediante redes ponderadas de co-expresión génica llevados a cabo en 33 ecotipos de B. distachyon bajo condiciones de sequía y riego identificaron cinco módulos exclusivos de la red de sequía, incluyendo 465 isoformas y 11 genes altamente interconectados (hubs). El análisis seleccionó genes candidatos y factores de transcripción (bHLH, ABF1, MADS box) potencialmente implicados en la regulación de la respuesta a sequía, tales como la síntesis de prolina y las respuestas a carencias de agua o fosfato, así como a estímulos por temperatura. Los análisis de expresión diferencial de genes en los ecotipos han detectado 4941 tránscritos, de los cuales dos terceras partes están sobre-expresados en las plantas en condiciones de sequía con respecto a las sometidas a condiciones de riego. Los análisis pan-transcriptómicos muestran que la mayoría de los genes expresados en ambas condiciones son genes del core, presentes en todos los ecotipos estudiados, mientras que una fracción de los genes hub corresponden a genes soft-core y shell, encontrados únicamente en algunos ecotipos.

      BIBLIOGRAFÍA Abe, F., Saito, K., Miura, K., & Toriyama, K. (2002) A single nucleotide polymorphism in the alternative oxidase gene among rice varieties differing in low temperature tolerance. FEBS Letters, 527, 181–185.

    Acosta, M., Moscone, E., & Cocucci, A. (2015) Using chromosomal data in the phylogenetic and molecular dating framework: Karyotype evolution and diversification in Nierembergia (Solanaceae) influenced by historical changes in sea level. Plant Biology, 18, 514–526.

    Agrawal, P.K., Babu, B.K., & Saini, N. (2015) Omics of Model Plants. PlantOmics: The Omics of Plant Science (ed. by D. Barh, M.S. Khan, and E. Davies), pp. 1–32. Springer, New Delhi, India.

    Albert, R., Jeong, H., & Barabási, A.-L. (2000) Error and Attack Tolerance of Complex Networks. Nature, 406, 378–382.

    Amrine, K.C.H., Blanco-Ulate, B., & Cantu, D. (2015) Discovery of Core Biotic Stress Responsive Genes in Arabidopsis by Weighted Gene Co-Expression Network Analysis. PLoS ONE, 10, e0118731.

    Andrews, S. (2010) FastQC: a quality control tool for high throughput sequence data. .

    Aoki, K., Ogata, Y., & Shibata, D. (2007) Approaches for Extracting Practical Information from Gene Co-expression Networks in Plant Biology. Plant Cell Physiology, 48, 381–390.

    Aoki, Y., Okamura, Y., Tadaka, S., Kinoshita, K., & Obayashi, T. (2016) ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression. Plants and Cell Physiology, 57, e5(1–9).

    Arenas, M. (2015) Trends in substitution models of molecular evolution. Frontiers in Genetics, 6, 1–9.

    Arthan, W., McKain, M.R., Traiperm, P., Welker, C.A.D., Teisher, J.K., & Kellogg, E.A. (2017) Phylogenomics of Andropogoneae (Panicoideae: Poaceae) of Mainland Southeast Asia. Systematic Botany, 42, 418–431.

    Baek, D., Chun, H.J., Yun, D.-J., & Kim, M.C. (2017) Cross-talk between Phosphate Starvation and Other Environmental Stress Signaling Pathways in Plants. Molecules and Cells, 40, 697–705.

    Bakker, E.G., Montgomery, B., Nguyen, T., Eide, K., Chang, J., Mockler, T.C., Liston, A., Seabloom, E.W., & Borer, E.T. (2009) Strong population structure characterizes weediness gene evolution in the invasive grass species Brachypodium distachyon. Molecular Ecology, 18, 2588–2601.

    Baltisberger, M. & Hörandl, E. (2016) Karyotype evolution supports the molecular phylogeny in the genus Ranunculus (Ranunculaceae). Journal of PPEES Sources, 18, 1–14.

    Bareither, N., Scheffel, A., & Metz, J. (2017) Distribution of polyploid plants in the common annual Brachypodium distachyon (s.l.) in Israel is not linearly correlated with aridity. Israel Journal of Plant Sciences, 1–10.

    Barker, N.P., Linder, H.P., & Harley, E.H. (1995) Polyphyly of Arundinoideae (Poaceae): Evidence from rbcL Sequence Data. Systematic Botany, 20, 423–435.

    Barres, L., Sanmartín, I., Anderson, C.L., Susanna, A., Buerki, S., Galbany-Casals, M., & Vilatersana, R. (2013) Reconstructing the evolution and biogeographic history of tribe Cardueae (Compositae). American Journal of Botany, 100, 867–882.

    Batley, J. (2015) Plant Genotyping. Methods and Protocols. Springer Science+Business Media, New York.

    Beerling, D.J. & Royer, D.L. (2011) Convergent Cenozoic CO2 history. Nature Geoscience, 4, 418–420.

    Beissinger, T.M., Hirsch, C.N., Sekhon, R.S., Foerster, J.M., Johnson, J.M., Muttoni, G., Vaillancourt, B., Buell, C.R., Kaeppler, S.M., & Leon, N. De (2013) Marker Density and Read Depth for Genotyping Populations Using Genotyping-by-Sequencing. Genetics, 193, 1073–1081.

    Betekhtin, A., Jenkins, G., & Hasterok, R. (2014) Reconstructing the Evolution of Brachypodium Genomes Using Comparative Chromosome Painting. PLoS ONE, 9, e115108.

    Bhattacharya, A. & Knoll, J.E. (2012) Conventional and molecular breeding for improvement of biofuel crops. Past, present, and future. Handbook of Bioenergy Crop Plants (ed. by C. Kole, C.P. Joshi, and D.R. Shonnard), pp. 874. CRC Press, Boca Raton, FL.

    Blair, J., Nippert, J., & Briggs, J. (2014) Grassland Ecology. Ecology and the Environment, The Plant Sciences 8 (ed. by R. Monson), pp. 389–423. Springer Science+Business Media, New York, NY.

    Blattner, F.R. (2006) Multiple intercontinental dispersals shaped the distribution area of Hordeum (Poaceae ). New Phytologist, 169, 603–614.

    Boetzer, M., Henkel, C. V., Jansen, H.J., Butler, D., & Pirovano, W. (2011) Scaffolding pre-assembled contigs using SSPACE. Bioinformatics, 27, 578–579.

    Boetzer, M. & Pirovano, W. (2012) Toward almost closed genomes with GapFiller. Genome biology, 13, R56.

    Bohnert, H.J., Nelson, D.E., & Jensenayb, R.G. (1995) Adaptations to Environmental Stresses. The Plant Cell, 7, 1099–1111.

    Bolger, A.M., Lohse, M., & Usadel, B. (2014) Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114–2120.

    Bombarely, A., Coate, J.E., & Doyle, J.J. (2014) Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex. PeerJ, 2, e391.

    Borah, P., Sharma, E., Kaur, A., Chandel, G., Mohapatra, T., Kapoor, S., & Khurana, J. (2017) Analysis of drought-responsive signalling network in two contrasting rice cultivars using transcriptome-based approach. Scientific Report, 42131, 1–21.

    Borsch, T. & Quandt, D. (2009) Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA. Plant Systematics and Evolution, 282, 169–199.

    Bortiri, E., Coleman-Derr, D., Lazo, G.R., Anderson, O.D., & Gu, Y.Q. (2008) The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes. BMC Research Notes, 1, 61.

    Bouchenak-Khelladi, Y., Salamin, N., Savolainen, V., Forest, F., van der Bank, M., Chase, M.W., & Hodkinson, T.R. (2008) Large multi-gene phylogenetic trees of the grasses (Poaceae): Progress towards complete tribal and generic level sampling. Molecular Phylogenetics and Evolution, 47, 488–505.

    Bouchenak-Khelladi, Y., Verboom, G.A., Hodkinson, T.R., Salamin, N., Francois§, O., Ní Chonghaile, G., & Savolainen, V. (2009) The origins and diversification of C4 grasses and savanna-adapted ungulates. Global Change Biology, 15, 2397–2417.

    Bouchenak-Khelladi, Y., Verboom, G.A., Savolainen, V., & Hodkinson, T.R. (2010) Biogeography of the grasses (Poaceae): A phylogenetic approach to reveal evolutionary history in geographical space and geological time. Botanical Journal of the Linnean Society, 162, 543–557.

    Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M.A., Rambaut, A., & Drummond, A.J. (2014) BEAST 2: A Software Platform for Bayesian Evolutionary Analysis. PloS Computational Biology, 10, e1003537.

    Boutet, E., Lieberherr, D., Tognolli, M., Schneider, M., Bansal, P., Bridge, A.J., Poux, S., Bougueleret, L., & Xenarios, I. (2016) UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View. Plant Bioinformatics: Methods and Protocols (ed. by D. Edwards), pp. 23–54. Springer New York, New York, NY.

    Bradshaw, J.E. (2017) Plant breeding: past, present and future. Euphytica, 213, 1–12.

    Brassac, J. & Blattner, F.R. (2015) Species-Level Phylogeny and Polyploid Relationships in Hordeum (Poaceae) Inferred by Next-Generation Sequencing and In Silico Cloning of Multiple Nuclear Loci. Systematic Biology, 64, 792–808.

    Bray, N.L., Pimentel, H., Melsted, P., & Pachter, L. (2016) Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology, 34, 525–527.

    Bremer, K. (2002) Gondwanan Evolution of the Grass Alliance of Families (Poales). Evolution, 56, 1374–1387.

    Brkljacic, J., Grotewold, E., Scholl, R., et al. (2011) Brachypodium as a Model for the Grasses: Today and the Future. Plant Physiology, 157, 3–13.

    Brummer, E.C., Bouton, J.H., Casler, M.D., McCaslin, M.H., & Waldron, B.L. (2009) Grasses and Legumes: Genetics and Plant Breeding. Grassland: Quietness and Strength for a New American Agriculture (ed. by W.F. Wedin and S.L. Fales), pp. 157–171. ASA, CSSA, SSSA, Madison, WI.

    Brysting, A.K., Oxelman, B., Huber, K.T., Moulton, V., & Brochmann, C. (2007) Untangling Complex Histories of Genome Mergings in High Polyploids. Systematic Biology, 56, 467–476.

    Buerki, S., Forest, F., Alvarez, N., Nylander, J.A.A., Arrigo, N., & Sanmartín, I. (2011) An evaluation of new parsimony-based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae. Journal of Biogeography, 38, 531–550.

    Buermans, H.P.J. & den Dunnen, J.T. (2014) Next generation sequencing technology: Advances and applications. Biochimica et Biophysica Acta - Molecular Basis of Disease, 1842, 1932–1941.

    Buggs, R.J.A., Renny-Byfield, S., Chester, M., Jordon-Thaden, I.E., Viccini, L.F., Chamala, S., Leitch, A.R., Schnable, P.S., Bradley Barbazuk, W., Soltis, P.S., & Soltis, D.E. (2012) Next-generation sequencing and genome evolution in allopolyploids. American Journal of Botany, 99, 372–382.

    Byars, S.G., Parsons, Y., & Hoffmann, A.A. (2009) Effect of altitude on the genetic structure of an Alpine grass , Poa hiemata. Annals of Botany, 103, 885–899.

    Cai, D., Rodríguez, F., Teng, Y., Ané, C., Bonierbale, M., Mueller, L.A., & Spooner, D.M. (2012) Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota). BMC evolutionary biology, 12, 1–16.

    Camacho, C. (2013) BLAST+. https://www.ncbi.nlm.nih.gov/books/NBK131777/.

    Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T.L. (2009) BLAST+: Architecture and applications. BMC Bioinformatics, 10, 1–9.

    Cantalapiedra, C.P., García-pereira, M.J., Gracia, M.P., Igartua, E., Casas, A.M., & Contreras-Moreira, B. (2017) Large Differences in Gene Expression Responses to Drought and Heat Stress between Elite Barley Cultivar Scarlett and a Spanish Landrace. Frontiers in plant science, 8, 647.

    Capella-Gutiérrez, S., Silla-Martínez, J.M., & Gabaldón, T. (2009) trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25, 1972–1973.

    Carbon, S., Ireland, A., Mungall, C.J., Shu, S., Marshall, B., Lewis, S., Hub, A., & Presence, W. (2009) AmiGO: online access to ontology and annotation data. Bioinformatics, 25, 288–289.

    Carbonell-Caballero, J., Alonso, R., Ibañez, V., Terol, J., Talon, M., & Dopazo, J. (2015) A phylogenetic analysis of 34 chloroplast genomes elucidates the relationships between wild and domestic species within the genus Citrus. Molecular biology and evolution, 32, msv082–.

    Carlsen, T., Bleeker, W., Hurka, H., Elven, R., & Brochmann, C. (2009) Biogeography and phylogeny of Cardamine (Brassicaceae). Annals of the Missouri Botanical Garden, 96, 215–236.

    Carlson, M.R.J., Zhang, B., Fang, Z., Mischel, P.S., Horvath, S., & Nelson, S.F. (2006) Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks. BMC genomics, 7, 1–15.

    Castilhos, G., Lazzarotto, F., Spagnolo-Fonini, L., Helena, M., & Margis-Pinheiro, M. (2014) Possible roles of basic helix-loop-helix transcription factors in adaptation to drought. Plant Science, 223, 1–7.

    Catalán, P., Chalhoub, B., Chochois, V., Garvin, D.F., Hasterok, R., Manzaneda, A.J., Mur, L.A.J., Pecchioni, N., Rasmussen, S.K., Vogel, J.P., & Voxeur, A. (2014) Update on the genomics and basic biology of Brachypodium. Trends in Plant Science, 19, 414–418.

    Catalán, P., Kellogg, E.A., & Olmstead, R.G. (1997) Phylogeny of Poaceae subfamily Pooideae based on chloroplast ndhF gene sequences. Molecular phylogenetics and evolution, 8, 150–166.

    Catalán, P., López-Alvarez, D., Bellosta, C., & Villar, L. (2016a) Updated taxonomic descriptions, iconography, and habitat preferences of Brachypodium distachyon, B. stacei, and B. hybridum (Poaceae). Anales del Jardín Botánico de Madrid, 73, 1–14.

    Catalán, P., López-Alvarez, D., Díaz-Pérez, A., Sancho, R., & López-Herranz, M.L. (2016b) Phylogeny and Evolution of the Genus Brachypodium. Genetics and genomics of Brachypodium. Plant Genetics and Genomics: Crops Models (ed. by J.P. Vogel), pp. 9–38. Springer.

    Catalán, P., Müller, J., Hasterok, R., Jenkins, G., Mur, L.A., Langdon, T., Betekhtin, A., Siwinska, D., Pimentel, M., & López-Alvarez, D. (2012) Evolution and taxonomic split of the model grass Brachypodium distachyon. Annals of Botany, 109, 385–405.

    Catalán, P. & Olmstead, R.G. (2000) Phylogenetic reconstruction of the genus Brachypodium P. Beauv. (Poaceae) from combined sequences of chloroplast ndhF gene and nuclear ITS. Plant Systematics and Evolution, 220, 1–19.

    Chaves, M.M., Maroco, J.P., & Pereira, J.S. (2003) Understanding plant responses to drought — from genes to whole plant. Functional Plant Biology, 30, 239–264.

    Chaw, S.M., Chang, C.C., Chen, H.L., & Li, W.H. (2004) Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. Journal of Molecular Evolution, 58, 424–441.

    Cheng, F., Wu, J., Cai, X., Liang, J., Freeling, M., & Wang, X. (2018) Gene retention, fractionation and subgenome differences in polyploid plants. Nature Plants, 4, 258–268.

    Chernomor, O., von Haeseler, A., & Minh, B.Q. (2016) Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices. Systematic Biology, 65, 997–1008.

    Childs, K.L., Davidson, R.M., & Buell, C.R. (2011) Gene Coexpression Network Analysis as a Source of Functional Annotation for Rice Genes. PLoS ONE, 6, e22196.

    Christin, P.A., Spriggs, E., Osborne, C.P., Strömberg, C.A.E., Salamin, N., & Edwards, E.J. (2014) Molecular dating, evolutionary rates, and the age of the grasses. Systematic Biology, 63, 153–165.

    Christmann, A. & Grill, E. (2018) Peptide signal alerts plants to drought. Nature, 556, 178–179.

    Clark, L.G., Zhang, W., & Wendel, J.F. (1995) A Phylogeny of the Grass Family (Poaceae) Based on ndhF Sequence. Systematic Botany, 20, 436–460.

    Clement, M., Posada, D., & Crandall, K.A. (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657–1660.

    Clement, M., Snell, Q., Walker, P., Posada, D., & Crandall, K. (2002) TCS: Estimating Gene Genealogies. Proceeding 16th International Parallel Distributed Processing Symposium, 184.

    Clevenger, J., Chavarro, C., Pearl, S.A., Ozias-akins, P., & Jackson, S.A. (2015) Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations. Molecular Plant, 8, 831–846.

    Colton-Gagnon, K., Ali-Benali, M.A., Mayer, B.F., Dionne, R., Bertrand, A., Do Carmo, S., & Charron, J.B. (2014) Comparative analysis of the cold acclimation and freezing tolerance capacities of seven diploid Brachypodium distachyon accessions. Annals of Botany, 113, 681–693.

    Contreras-Moreira, B., Cantalapiedra, C.P., García-Pereira, M.J., Gordon, S.P., Vogel, J.P., Igartua, E., Casas, A.M., & Vinuesa, P. (2017) Analysis of Plant Pan-Genomes and Transcriptomes with GET _ HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species. Frontiers in Genetics, 8, 1–16.

    Contreras-Moreira, B., Castro-Mondragon, J.A., Rioualen, C., Cantalapiedra, C.P., & van Helden, J. (2016) RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes. Plant synthetic promoters (ed. by R. Hehl), pp. 279–295. Springer Science+Business Media, New York.

    Corley, S.M., MacKenzie, K.L., Beverdam, A., Roddam, L.F., & Wilkins, M.R. (2017) Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols. BMC Genomics, 18, 1–13.

    CPWG (2001) Phylogeny and subfamilial classification of the grasses (Poaceae). Annals of the Missouri Botanical Garden, 88, 373–457.

    Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., Depristo, M.A., Handsaker, R.E., Lunter, G., Marth, G.T., Sherry, S.T., Mcvean, G., Durbin, R., Project, G., & Vcf, T. (2011) The variant call format and VCFtools. Bioinformatics, 27, 2156–2158.

    Daniell, H., Lin, C.-S., Yu, M., & Chang, W.-J. (2016) Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biology, 17, 134.

    Darlington, C.D. (1937) Recent advances in cytology. Blakiston’s Son & Co, Philadelphia.

    Darriba, D., Taboada, G.L., Doallo, R., & Posada, D. (2012) jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9, 772.

    Davey, J.W., Hohenlohe, P.A., Etter, P.D., Boone, J.Q., Catchen, J.M., & Blaxter, M.L. (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature reviews. Genetics, 12, 499–510.

    Davidson, R.M., Gowda, M., Moghe, G., Lin, H., Vaillancourt, B., Shiu, S., Jiang, N., & Buell, C.R. (2012) Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution. The Plant Journal, 71, 492–502.

    Davis, J.I. (1997) Evolution, Evidence, and the Role of Species Concepts in Phylogenetics. Systematic Botany, 22, 373–403.

    Davis, J.I. & Soreng, R.J. (1993) Phylogenetic structure in the grass family (Poaceae) as inferred from chloroplast DNA restriction site variation. American Journal of Botany, 80, 1444–1454.

    Davis, J.I. & Soreng, R.J. (2007) A preliminary phylogenetic analysis of the grass subfamily Pooideae (Poaceae), with attention to structural features of the plastid and nuclear genomes, including an intron loss in GBSSI. Aliso: A Journal of Systematics and Evolutionary Botany, 23, 335–348.

    Delsuc, F., Brinkmann, H., & Philippe, H. (2005) Phylogenomics and the reconstruction of the tree of life. Nature reviews. Genetics, 6, 361–375.

    Deschamps, S., Llaca, V., & May, G.D. (2012) Genotyping-by-Sequencing in Plants. Biology, 1, 460–483.

    Des Marais, D.L., Guerrero, R.F., Lasky, J.R., & Scarpino, S. V (2017a) Topological features of gene regulatory networks predict patterns of natural diversity in environmental response. Proceedings of the Royal Society B: Biological Sciences, 284, .

    Des Marais, D.L. & Juenger, T.E. (2016) Brachypodium and the Abiotic Environment. Genetics and genomics of Brachypodium. Plant Genetics and Genomics: Crops Models, volume 18 (ed. by J.P. Vogel), pp. 291–311. Springer, Switzerland.

    Des Marais, D.L., Lasky, J.R., Verslues, P.E., Chang, T.Z., & Juenger, T.E. (2017b) Interactive effects of water limitation and elevated temperature on the physiology, development and fitness of diverse accessions of Brachypodium distachyon. New Phytologist, 214, 132–144.

    Des Marais, D.L., Mckay, J.K., Richards, J.H., Sen, S., Wayne, T., & Juenger, T.E. (2012) Physiological Genomics of Response to Soil Drying in Diverse Arabidopsis Accessions. The plant Cell, 24, 893–914.

    Desper, R. & Gascuel, O. (2002) Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. Journal of Computational Biology, 9, 687–705.

    Díaz-Pérez, A.J., Sharifi-Tehrani, M., Inda, L.A., & Catalán, P. (2014) Molecular Phylogenetics and Evolution Polyphyly, gene-duplication and extensive allopolyploidy framed the evolution of the ephemeral Vulpia grasses and other fine-leaved Loliinae (Poaceae). Molecular phylogenetics and evolution, 79, 92–105.

    Dierckxsens, N., Mardulyn, P., & Smits, G. (2017) NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic acids research, 45, e18.

    Dijk, E.L. Van, Jaszczyszyn, Y., & Thermes, C. (2014) Library preparation methods for next-generation sequencing: Tone down the bias. Experimental Cell Research, 322, 12–20.

    Dinh Thi, V.H., Coriton, O., Le Clainche, I., Arnaud, D., Gordon, S.P., Linc, G., Catalán, P., Hasterok, R., Vogel, J.P., Jahier, J., & Chalhoub, B. (2016) Recreating Stable Brachypodium hybridum Allotetraploids by Uniting the Divergent Genomes of B. distachyon and B. stacei. PloS one, 11, e0167171.

    Dolezel, J., Greilhuber, J., Lucretti, S., Meister, A., Lysákt, M.A., Nardi, L., & Obermayer, R. (1998) Plant Genome Size Estimation by Flow Cytometry: Inter-laboratory Comparison*. Annals of Botany, 82, 17–26.

    Dolezel, J., Sgorbati, S., & Lucretti, S. (1992) Comparison of three DNA fluorochromes for flow cytometric estimation of nuclear DNA content in plants. Physiologia Plantarum, 85, 625–631.

    Dong, J. & Horvath, S. (2007) Understanding network concepts in modules. BMC Systems Biology, 1, 1–20.

    Döring, E., Schneider, J., Hilu, K.W., Röser, M., Hilu, W., Rserl, M., & Doringl, E. (2007) Phylogenetic relationships in the Aveneae/Poeae complex (Pooideae, Poaceae ). Kew Bulletin, 62, 407–424.

    Draper, J., Mur, L.A.J., Jenkins, G., Ghosh-Biswas, G.C., Bablak, P., Hasterok, R., & Routledge, A.P.M. (2001) Brachypodium distachyon. A New Model System for Functional Genomics in Grasses. Plant physiology, 127, 1539–1555.

    Drummond, A.J., Suchard, M.A., Xie, D., & Rambaut, A. (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, 29, 1969–1973.

    Duitama, J., Quintero, J.C., Cruz, D.F., Quintero, C., Hubmann, G., Foulquié-Moreno, M.R., Verstrepen, K.J., Thevelein, J.M., & Tohme, J. (2014) An integrated framework for discovery and genotyping of genomic variants from high- throughput sequencing. Nucleic Acids Research, 42, e44.

    Earl, D.A. & vonHoldt, B.M. (2012) STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4, 359–361.

    Edwards, E.J., Osborne, C.P., Stromberg, C.A.E., et al. (2010) The Origins of C4 Grasslands: Integrating Evolutionary and Ecosystem Science. Science, 328, 587–591.

    Eisen, J.A. (1998) Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis. Genome Research, 8, 163–167.

    Elshire, R.J., Glaubitz, J.C., Sun, Q., Poland, J.A., Kawamoto, K., Buckler, E.S., & Mitchell, S.E. (2011) A Robust , Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species. PLoS ONE, 6, e19379.

    Escudero, M., Eaton, D.A.R., Hahn, M., & Hipp, A.L. (2014) Molecular Phylogenetics and Evolution Genotyping-by-sequencing as a tool to infer phylogeny and ancestral hybridization: A case study in Carex (Cyperaceae). Molecular Phylogenetics and Evolution, 79, 359–367.

    Estep, M.C., Mckain, M.R., Vela Díaz, D., Zhong, J., Hodge, J.G., Hodkinson, T.R., Layton, D.J., Malcomber, S.T., Pasquet, R., & Kellogg, E.A. (2014) Allopolyploidy, diversification, and the Miocene grassland expansion. Proceedings of the National Academy of Sciences of the United States of America, 111, 15149–15154.

    Evanno, G., Regnaut, S., & Goudet, J. (2005) Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology, 14, 2611–2620.

    Farris, J.S. (1983) The Logical Basis of Phylogenetic Analysis. Advances in Cladistics (ed. by N. Platnick and V. Funk), pp. 1–36. Columbia University Press, New York.

    Fedurco, M., Romieu, A., Williams, S., Lawrence, I., & Turcatti, G. (2006) BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Research, 34, .

    Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17, 368–376.

    Feschotte, C. & Pritham, E.J. (2007) DNA Transposons and the Evolution of Eukaryotic Genomes. Annual Review of Genetics, 41, 331–368.

    Filiz, E., Ozdemir, B.S., Budak, F., Vogel, J.P., Tuna, M., & Budak, H. (2009) Molecular, morphological, and cytological analysis of diverse Brachypodium distachyon inbred lines. Genome, 52, 876–890.

    Finn, R.D., Coggill, P., Eberhardt, R.Y., Eddy, S.R., Mistry, J., Mitchell, A.L., Potter, S.C., Punta, M., Qureshi, M., Sangrador-vegas, A., Salazar, G.A., Tate, J., & Bateman, A. (2016) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Research, 44, 279–285.

    Fisher, L.H., Han, J., Corke, F.M., Akinyemi, A., Didion, T., Nielsen, K.K., Doonan, J.H., Mur, L.A., & Bosch, M. (2016) Linking Dynamic Phenotyping with Metabolite Analysis to Study Natural Variation in Drought Responses of Brachypodium distachyon. Frontiers in plant science, 7, 1–15.

    Fitch, W.M. (1971) Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology. Systematic Zoology, 20, 406–416.

    Fjellheim, S., Boden, S., & Trevaskis, B. (2014) The role of seasonal flowering responses in adaptation of grasses to temperate climates. 5, 1–15.

    Fougére-Danezan, M., Joly, S., Bruneau, A., Gao, X., & Zhang, L. (2015) Phylogeny and biogeography of wild roses with specific attention to polyploids. Annals of Botany, 115, 275–291.

    Garvin, D.F. (2007) Brachypodium distachyon: A New Model System for Structural and Functional Analysis of Grass Genomes. Model Plants and Crop Improvement (ed. by R.K. Varshney and R.M.D. Koebner), pp. 109–123.

    Garvin, D.F., Gu, Y.Q., Hasterok, R., Hazen, S.P., Jenkins, G., Mockler, T.C., Mur, L.A.J., & Vogel, J.P. (2008) Development of genetic and genomic research resources for Brachypodium distachyon, a new model system for grass crop research. Crop Science, S69–S84.

    Gaut, B.S. & Doebley, J.F. (1997) DNA sequence evidence for the segmental allotetraploid origin of maize. Proceedings of the National Academy of Sciences of the United States of America, 94, 6809–6814.

    Ge, S., Li, A., Lu, B.R., Zhang, S.Z., & Hong, D.Y. (2002) A phylogeny of the rice tribe Oryzeae (Poaceae) based on matK sequence data. American Journal of Botany, 89, 1967–1972.

    Gehrke, B. & Linder, H.P. (2009) The scramble for Africa: pan-temperate elements on the African high mountains. Proceedings of the Royal Society B, 276, 2657–2665.

    Gibson, G. (2016) On the Evaluation of Module Preservation. Cell Systems, 3, 17–19.

    Gladman, S. & Seemann, T. (2012) VelvetOptimiser. http://www.vicbioinformatics.com/software.velvetoptimiser.shtml.

    Goodstein, D.M., Shu, S., Howson, R., Neupane, R., Hayes, R.D., Fazo, J., Mitros, T., Dirks, W., Hellsten, U., Putnam, N., & Rokhsar, D.S. (2012) Phytozome: a comparative platform for green plant genomics. Nucleic acids research, 40, 1178–1186.

    Goodwin, S., Mcpherson, J.D., & McCombie, W.R. (2016) Coming of age: ten years of next- generation sequencing technologies. Nature Publishing Group, 17, 333–351.

    Gordon, S.P., Contreras-Moreira, B., Woods, D.P., et al. (2017) Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nature Communications, 8, 1-13.

    Gordon, S.P., Liu, L., & Vogel, J.P. (2016) The Genus Brachypodium as a Model for Perenniality and Polyploidy. Genetics and genomics of Brachypodium. Plant Genetics and Genomics: Crops Models (ed. by J. Vogel), pp. 313–326. Springer, Switzerland.

    Gottlieb, A., Müller, H.G., Massa, A.N., Wanjugi, H., Deal, K.R., You, F.M., Xu, X., Gu, Y.Q., Luo, M.C., Anderson, O.D., Chan, A.P., Rabinowicz, P., Devos, K.M., & Dvorak, J. (2013) Insular Organization of Gene Space in Grass Genomes. PLoS ONE, 8, e54101.

    Gouy, M., Guindon, S., & Gascuel, O. (2010) SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular biology and evolution, 27, 221–224.

    Grabherr, M.G., Haas, B.J., Yassour, M., et al. (2011) Trinity: reconstructing a full-length transcrptome without a genome from RNA-Seq data. Nature Biotechnology, 29, 644–652.

    Grass Phylogeny Working Group (2012) New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins. New Phytologist, 193, 304–312.

    Griffith, M., Walker, J.R., Spies, N.C., Ainscough, B.J., & Griffith, O.L. (2015) Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud. PLoS Computational Biology, 11, 1–20.

    Gruenstaeudl, M., Carstens, B.C., Santos-Guerra, A., & Jansen, R.K. (2017) Statistical hybrid detection and the inference of ancestral distribution areas. Biological Journal of the Linnean Society, 121, 133–149.

    Guggisberg, A., Mansion, G., Kelso, S., & Conti, E. (2006) Evolution of biogeographic patterns, ploidy levels , and breeding systems in a diploid – polyploid species complex of Primula. New Phytologist, 171, 617–632.

    Guindon, S. & Gascuel, O. (2003) A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood. Systematic Biology, 52, 696–704.

    Guo, Y.L. & Ge, S. (2005) Molecular phylogeny of Oryzeae (Poaceae) based on DNA sequences from chloroplast, mitochondrial, and nuclear genomes. American Journal of Botany, 92, 1548–1558.

    Hall, T.A. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95–98.

    Hamon, P., Grover, C.E., Davis, A.P., Rakotomalala, J., Nathalie, E., Albert, V.A., Sreenath, H.L., Stoffelen, P., Mitchell, S.E., Hamon, S., Kochko, A. De, Crouzillat, D., Rigoreau, M., Sumirat, U., Akaffou, S., & Guyot, R. (2017) Molecular Phylogenetics and Evolution Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species. GBS coffee phylogeny and the evolution of caffeine content. Molecular Phylogenetics and Evolution, 109, 351–361.

    Hapke, A. & Thiele, D. (2016) GIbPSs: a toolkit for fast and accurate analyses of genotyping-by-sequencing data without a reference genome. Molecular Ecology Resources, 16, 979–990.

    Hayano-Kanashiro, C., Calderón-Vázquez, C., Ibarra-Laclette, E., Herrera-Estrella, L., & Simpson, J. (2009) Analysis of Gene Expression and Physiological Responses in Three Mexican Maize Landraces under Drought Stress and Recovery Irrigation. PLoS ONE, 4, e7531.

    He, F. & Maslov, S. (2016) Pan- and core- network analysis of co-expression genes in a model plant. Scientific Report, 6, 1–11.

    He, J., Zhao, X., Laroche, A., Lu, Z., Liu, H., & Li, Z. (2014) Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Frontiers in plant science, 5, 1–8.

    Head, S.R., Komori, H.K., LaMere, S.A., Whisenant, T., Van Nieuwerburgh, F., R, S.D., & Phillip, O. (2014) Library construction for next-generation sequencing: Overviews and challenges. Biotechniques, 56, 61.

    Heather, J.M. & Chain, B. (2016) The sequence of sequencers: The history of sequencing DNA. Genomics, 107, 1–8.

    Heled, J. & Drummond, A.J. (2012) Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation. Systematic Biology, 61, 138–149.

    Hewitt, G. (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907–913.

    Hey, J. & Nielsen, R. (2004) Multilocus Methods for Estimating Population Sizes, Migration Rates and Divergence Time, With Applications to the Divergence of Drosophila pseudoobscura and D. persimilis. Genetics, 167, 747–760.

    Hilu, K.W., Alice, L.A., & Liang, H. (1999) Phylogeny of Poaceae inferred from matK sequences. Annals of the Missouri Botanical Garden, 86, 835–851.

    Hochbach, A., Schneider, J., & Röser, M. (2015) A multi-locus analysis of phylogenetic relationships within grass subfamily Pooideae (Poaceae) inferred from sequences of nuclear single copy gene regions compared with plastid DNA. Molecular Phylogenetics and Evolution, 87, 14–27.

    Horvath, S. & Dong, J. (2008) Geometric Interpretation of Gene Coexpression Network Analysis. PloS Computational Biology, 4, e1000117.

    Hou, Z., Jiang, P., Swanson, S.A., Elwell, A.L., Nguyen, B.K.S., Bolin, J.M., Stewart, R., & Thomson, J.A. (2015) A cost-effective RNA sequencing protocol for large-scale gene expression studies. Scientific Reports, 5, 1–5.

    Hsiao, C., Chatterton, N.J., Asay, K.H., & Jensen, K.B. (1995) Molecular phylogeny of the Pooideae (Poaceae) based on nuclear rDNA (ITS) sequences. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 90, 389–398.

    Huang, J., Vendramin, S., Shi, L., & McGinnis, K.M. (2017a) Construction and Optimization of a Large Gene Coexpression Network in Maize Using RNA-Seq Data. Plant physiology, 175, 568–583.

    Huang, Y.Y., Cho, S.T., Haryono, M., & Kuo, C.H. (2017b) Complete chloroplast genome sequence of common bermudagrass (Cynodon dactylon (L.) Pers.) and comparative analysis within the family Poaceae. PLoS ONE, 12, 1–16.

    Huber, K.T., Oxelman, B., Lott, M., & Moulton, V. (2006) Reconstructing the Evolutionary History of Polyploids from Multilabeled Trees. Molecular Biology and Evolution, 23, 1784–1791.

    Huelsenbeck, J.P. & Rannala, B. (2004) Frequentist Properties of Bayesian Posterior Probabilities of Phylogenetic Trees Under Simple and Complex Substitution Models. Systematic Biology, 53, 904–913.

    Huelsenbeck, J.P., Ronquist, F., Nielsen, R., & Bollback, J.P. (2001) Bayesian Inference of Phylogeney and Its Impact on Evolutionary Biology. Science, 294, 2310–2314.

    Huson, D.H. & Scornavacca, C. (2012) Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks. Systematic Biology, 61, 1061–1067.

    IBI (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature, 463, 763–768.

    Idziak, D., Hazuka, I., Poliwczak, B., Wiszynska, A., Wolny, E., & Hasterok, R. (2014) Insight into the Karyotype Evolution of Brachypodium Species Using Comparative Chromosome Barcoding. PLoS ONE, 9, e93503.

    Illumina Inc (2017) An Introduction to Next-Generation Sequencing Technology. 1–6. https://www.illumina.com/content/dam/illumina-marketing/documents/products/illumina_sequencing_introduction.pdf.

    Inda, L.A., Sanmart, I., Buerki, S., & Catalán, P. (2014) Mediterranean origin and Miocene – Holocene Old World diversification of meadow fescues and ryegrasses (Festuca subgenus Schedonorus and Lolium). Journal of Biogeography, 41, 600–614.

    Jacobs, S.W.L. & Everett, J. (2000) Grasses: Systematics and Evolution. Csiro Publishing, 416 pp.

    Janiak, A., Kwa, M., & Szarejko, I. (2015) Gene expression regulation in roots under drought. Journal of Experimental Botany, 67, 1003–1014.

    Jansen, R.K. & Ruhlman, T.A. (2012) Plastid genomes of seed plants. Genomics of chloroplast and mitochondria (ed. by R. Bock and V. Knoop), pp. 103–126. Springer, Jenkins, D.G., Carey, M., Czerniewska, J., et al. (2010) A meta-analysis of isolation by distance: relic or reference standard for landscape genetics? Ecography, 33, 315–320.

    Jiao, W.B. & Schneeberger, K. (2017) The impact of third generation genomic technologies on plant genome assembly. Current Opinion in Plant Biology, 36, 64–70.

    Jiao, Y., Leebens-Mack, J., Ayyampalayam, S., et al. (2012) A genome triplication associated with early diversification of the core eudicots. Genome Biology, 13, 1–14.

    Jiao, Y., Wickett, N.J., Ayyampalayam, S., Chanderbali, S., Landherr, L., Ralph, P.E., Tomsho, L.P., Hu, Y., Liang, H., Soltis, P.S., Soltis, D.E., Clifton, S.W., Schlarbaum, S.E., Schuster, S.C., Ma, H., Leebens-Mack, J., & DePamphilis, C.W. (2011) Ancestral polyploidy in seed plants and angiosperms. Nature, 473, 97–100.

    Johnston, J.S., Bennett, M.D., Rayburn, A.L., Galbraith, D.W., & Price, H.J. (1999) Reference standards for determination of DNA content of plant nuclei. American Journal of Botany, 86, 609–613.

    Jones, G., Sagitov, S., & Oxelman, B. (2013) Statistical Inference of Allopolyploid Species Networks in the Presence of Incomplete Lineage Sorting. Systematic Biology, 62, 467–478.

    Joshi, R., Wani, S.H., Singh, B., Bohra, A., Dar, Z.A., Lone, A.A., Pareek, A., & Singla-Pareek, S.L. (2016) Transcription Factors and Plants Response to Drought Stress: Current Understanding and Future Directions. Frontiers in plant science, 7, 1–15.

    Judd, W.S., Campbell, C.S., Kellogg, E.A., Stevens, P.F., & Donoghue, M.J. (2008) Plant Systematics. A Phylogenetic Approach. Sinauer Associates, Sunderland, Massachusetts, USA.

    Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K.F., von Haeseler, A., & Jermiin, L.S. (2017) ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods, 14, 587–589.

    Kamata, N., Okada, H., Komeda, Y., & Takahashi, T. (2013) Mutations in epidermis-specific HD-ZIP IV genes affect floral organ identity in Arabidopsis thaliana. The Plant Journal, 75, 430–440.

    Kamneva, O.K., Syring, J., Liston, A., & Rosenberg, N.A. (2017) Evaluating allopolyploid origins in strawberries (Fragaria) using haplotypes generated from target capture sequencing. BMC Evolutionary Biology, 17, 1–19.

    Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y., & Morishima, K. (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic acids research, 45, D353–D361.

    Kanehisa, M. & Goto, S. (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic acids research, 28, 27–30.

    Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., & Tanabe, M. (2016) KEGG as a reference resource for gene and protein annotation. Nucleic acids research, 44, D457–D462.

    Kannan, L. & Wheeler, W.C. (2012) Maximum Parsimony on Phylogenetic networks. Algorithms for Molecular Biology, 7, 1–10.

    Katoh, K. & Standley, D.M. (2013) MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution, 30, 772–780.

    Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Meintjes, P., & Drummond, A. (2012) Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28, 1647–1649.

    Kellogg, E.A. (2001) Update on Evolution Evolutionary History of the Grasses. Plant Physiology, 125, 1198–1205.

    Kellogg, E.A. (2015a) The Families and Genera of Vascular Plants. Vol. XIII. Flowering Plants. Monocots. Poaceae. Springer, New York.

    Kellogg, E.A. (2015b) Brachypodium distachyon as a Genetic Model System. Annual reviews of genetics, 49, 1–20.

    Khan, M.A. & Stace, C.A. (1999) Breeding relationships in the genus Brachypodium (Poaceae: Pooideae). Nordic Journal of Botany, 19, 257–269.

    Kidd, K.K. & Sgaramella-Zonta, L.A. (1971) Phylogenetic Analysis: Concepts and Methods. American Journal of Human Genetics, 23, 235–252.

    Kim, C., Guo, H., Kong, W., Chandnani, R., Shuang, L., & Paterson, A.H. (2016) Plant Science Application of genotyping by sequencing technology to a variety of crop breeding programs. Plant Science, 242, 14–22.

    Kim, D., Langmead, B., & Salzberg, S.L. (2015) HISAT: a fast spliced aligner with low memory requirements. Nature Methods, 12, 357–360.

    Krijgsman, W. (2002) The Mediterranean: Mare Nostrum of Earth sciences. Earth and Planetary Science Letters, 205, 1–12.

    Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S.J., & Marra, M.A. (2009) Circos: An information aesthetic for comparative genomics. Genome Research, 19, 1639–1645.

    Kumar, S., Stecher, G., & Tamura, K. (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870-1874.

    Langfelder, P. & Horvath, S. (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics, 9, 1–13.

    Langfelder, P. & Horvath, S. (2010) Available at: https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/ModulePreservation/Tutorials/glossaryTable.pdf.

    Leary, N.A.O., Wright, M.W., Brister, J.R., et al. (2016) Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Research, 44, 733–745.

    Leigh, J.W. & Bryant, D. (2015) POPART: full-feature software for haplotype network construction. Molecular in Ecology and Evolution, 6, 1110–1116.

    Leitch, I.J. & Bennett, M.D. (2004) Genome downsizing in polyploid plants. Biological Journal of the Linnean Society, 82, 521–536.

    Leonelli, S. & Ankeny, R.A. (2013) What makes a model organism? Endeavour, 37, 209–212.

    Levin, D.A. (2013) The timetable for allopolyploidy in flowering plants. Annals of Botany, 112, 1201–1208.

    Li, H. & Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754–1760.

    Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., & Durbin, R. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078–2079.

    Li, M., Copeland, A., & Han, J. (2011a) DUK – A Fast and Efficient Kmer Matching Tool. Lawrence Berkeley National Laboratory. LBNL Paper LBNL-4516E-Poster p, https://www.osti.gov/servlets/purl/1016000.

    Li, M., Copeland, A., & Han, J. (2011b) DUK - A Fast and Efficient Kmer Based Sequence Matching Tool. http://duk.sourceforge.net/.

    Li, S., Pearl, D.K., & Doss, H. (2000) Phylogenetic Tree Construction Using Markov Chain Monte Carlo. Journal of the American Statistical Association, 95, 493–508.

    Li, W. & Cui, X. (2014) A Special Issue on Plant Stress Biology: From Model Species to Crops. Molecular Plant, 7, 755–757.

    Li, Y., Zuo, S., Zhang, Z., Li, Z., Han, J., Chu, Z., Hasterok, R., & Wang, K. (2018) Centromeric DNA characterization in the model grass Brachypodium distachyon provides insights on the evolution of the genus. The Plant Journal, 93, 1088–1101.

    Liang, H. & Hilu, K.W. (1996) Application of the matK gene sequences to grass systematics. Canadian Journal of Botany, 74, 125–134.

    Librado, P. & Rozas, J. (2009) DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451–1452.

    Linder, H.P. & Barker, N.P. (2014) Does polyploidy facilitate long-distance dispersal? Annals of Botany, 113, 1175–1183.

    Lipscomb, D. (1998) Basics of Cladistic Analysis. http://taxonomy.zoology.gla.ac.uk/teaching/Cladistics.pdf.

    Liu, C., Shi, L., Zhu, Y., Chen, H., Zhang, J., Lin, X., & Guan, X. (2012a) CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. BMC genomics, 13, 715.

    Liu, L., Li, Y., Li, S., Hu, N., He, Y., Pong, R., Lin, D., Lu, L., & Law, M. (2012b) Comparison of next-generation sequencing systems. Journal of Biomedicine and Biotechnology, 2012, 1–11.

    Liu, Y., Schröder, J., & Schmidt, B. (2013) Musket: A multistage k-mer spectrum-based error corrector for Illumina sequence data. Bioinformatics, 29, 308–315.

    Lohman, B.K., Weber, J.N., & Bolnick, D.I. (2016) Evaluation of TagSeq, a reliable low-cost alternative for RNAseq. Molecular Ecology Resources, 16, 1315–1321.

    Lohse, M., Drechsel, O., Kahlau, S., & Bock, R. (2013) OrganellarGenomeDRAW--a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic acids research, 41, 575–581.

    López-Alvarez, D., López-Herranz, M.L., Betekhtin, A., & Catalán, P. (2012) A DNA Barcoding Method to Discriminate between the Model Plant Brachypodium distachyon and Its Close Relatives B. stacei and B. hybridum (Poaceae). PLoS ONE, 7, e51058.

    López-Alvarez, D., Manzaneda, A.J., Rey, P.J., Giraldo, P., Benavente, E., Allainguillaume, J., Mur, L., Caicedo, A.L., Hazen, S.P., Breiman, A., Ezrati, S., & Catalan, P. (2015) Environmental niche variation and evolutionary diversification of the Brachypodium distachyon grass complex species in their native circum-Mediterranean range. American Journal of Botany, 102, 1073–1088.

    López-Álvarez, D., Zubair, H., Beckmann, M., Draper, J., & Catalán, P. (2017) Diversity and association of phenotypic and metabolomic traits in the close model grasses Brachypodium distachyon, B. stacei and B. hybridum. Annals of Botany, 119, 545–561.

    Lowry, D.B., Modliszewski, J.L., Wright, K.M., Wu, C.A., & Willis, J.H. (2008) The strength and genetic basis of reproductive isolating barriers in flowering plants. Philosophical transactions of the Royal Society, 363, 3009–3021.

    Luo, M.C., Deal, K.R., Akhunov, E.D., et al. (2009) Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae. Proceedings of the National Academy of Sciences, 106, 15780–15785.

    Lyons, C.W.P. & Scholthof, K.-B.G. (2016) Brachypodium as an Arabidopsis for the grasses: Are we there yet? Genetics and genomics of Brachypodium. Plant Genetics and Genomics: Crops Models (ed. by J.P. Vogel), pp. 327–342. Springer, Switzerland.

    Ma, P.F., Zhang, Y.X., Zeng, C.X., Guo, Z.H., & Li, D.Z. (2014) Chloroplast phylogenomic analyses resolve deep-level relationships of an intractable bamboo tribe Arundinarieae (Poaceae). Systematic Biology, 63, 933–950.

    Ma, X.F. & Gustafson, J.P. (2005) Genome evolution of allopolyploids: a process of cytological and genetic diploidization. Cytogenetic and Genome Research, 109, 236–249.

    Madlung, A. (2013) Polyploidy and its effect on evolutionary success: old questions revisited with new tools. Heredity, 110, 99–104.

    Mairal, M., Pokorny, L., Aldasoro, J.J., Alarcón, M.L., & Sanmartín, I. (2015) Ancient vicariance and climate-driven extinction explain continental-wide disjunctions in Africa: the case of the Rand Flora genus Canarina (Campanulaceae). Molecular ecology, 24, 1335–1354.

    Manzaneda, A.J., Rey, P.J., Anderson, J.T., Raskin, E., Weiss-Lehman, C., & Mitchell-Olds, T. (2015) Natural variation, differentiation, and genetic trade-offs of ecophysiological traits in response to water limitation in Brachypodium distachyon and its descendent allotetraploid B. hybridum (Poaceae ). Evolution, 69, 2689–2704.

    Manzaneda, A.J., Rey, P.J., Bastida, J.M., Weiss-Lehman, C., Raskin, E., & Mitchell-Olds, T. (2012) Environmental aridity is associated with cytotype segregation and polyploidy occurrence in Brachypodium distachyon (Poaceae). New Phytologist, 193, 797–805.

    Mao, H., Wang, H., Liu, S., Li, Z., Yang, X., Yan, J., Li, J., Tran, L.P., & Qin, F. (2015) A transposable element in a NAC gene is associated with drought tolerance in maize seedlings. Nature Communications, 6, 1–13.

    Mao, L., Hemert, J.L. Van, Dash, S., & Dickerson, J.A. (2009) Arabidopsis gene co-expression network and its functional modules. BMC Bioinformatics, 10, 1–24.

    Marcussen, T., Heier, L., Brysting, A.K., Oxelman, B., & Jakobsen, K.S. (2015) From Gene Trees to a Dated Allopolyploid Network: Insights from the Angiosperm Genus Viola (Violaceae). Systematic Biology, 64, 84–101.

    Marcussen, T., Sandve, S.R., Heier, L., Spannagl, M., Pfeifer, M., Jakobsen, K.S., Wulff, B.B.H., Steuernagel, B., Mayer, K.F.X., & Olsen, O.A. (2014) Ancient hybridizations among the ancestral genomes of bread wheat. Science, 345, .

    Mardis, E.R. (2013) Next-Generation Sequencing Platforms. Annual Review of Analytical Chemistry, 6, 287–303.

    Marques, I., Shiposha, V., López-Alvarez, D., Manzaneda, A.J., Hernandez, P., Olonova, M., & Catalán, P. (2017) Environmental isolation explains Iberian genetic diversity in the highly homozygous model grass Brachypodium distachyon. BMC Evolutionary Biology, 17, 1–14.

    Martin, D.P., Murrell, B., Golden, M., Khoosal, A., & Muhire, B. (2015) RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evolution, 1, 1–5.

    Martínez, L.M., Fernández-ocaña, A., Rey, P.J., Salido, T., Amil-ruiz, F., & Manzaneda, A.J. (2018) Variation in functional responses to water stress and differentiation between natural allopolyploid populations in the Brachypodium distachyon species complex. Annals of Botany, 00, 1–14.

    Masalia, R.R., Bewick, A.J., & Burke, J.M. (2017) Connectivity in gene coexpression networks negatively correlates with rates of molecular evolution in flowering plants. PLoS ONE, 12, e0182289.

    Mascher, M., Gundlach, H., Himmelbach, A., et al. (2017) A chromosome conformation capture ordered sequence of the barley genome. Nature, 544, 427–433.

    Mathews, S. & Sharrock, R.A. (1996) The phytochrome gene family in grasses (Poaceae): A phylogeny and evidence that grasses have a subset of the loci found in dicot angiosperms. Molecular Biology and Evolution, 13, 1141–1150.

    Mathews, S., Tsai, R.C., & Kellogg, E.A. (2000) Phylogenetic structure in the grass family (Poaceae): Evidence from the nuclear gene phytochrome B. American Journal of Botany, 87, 96–107.

    Matsuoka, Y., Takumi, S., & Nasuda, S. (2014) Genetic Mechanisms of Allopolyploid Speciation Through Hybrid Genome Doubling. Novel Insights from Wheat (Triticum and Aegilops) Studies. International Review of Cell and Molecular Biology (ed. by K.W. Jeon), pp. 199–258. Academic Press.

    Matsuoka, Y., Yamazaki, Y., Ogihara, Y., & Tsunewaki, K. (2002) Whole Chloroplast Genome Comparison of Rice, Maize, and Wheat: Implications for Chloroplast Gene Diversification and Phylogeny of Cereals. Molecular Biology and Evolution, 19, 2084–2091.

    Matthee, C.A. & Davis, S.K. (2001) Molecular Insights into the Evolution of the Family Bovidae: A Nuclear DNA Perspective. Molecular Biology and Evolution, 18, 1220–1230.

    Mattioli, R., Costantino, P., & Trovato, M. (2009) Proline accumulation in plants. Not only stress. Plant Signaling and Behavior, 4, 1016–1018.

    Mau, B., Newton, M.A., & Larget, B. (1999) Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods. Biometrics, 55, 1–12.

    Mayrose, I., Zhan, S.H., Rothfels, C.J., Magnuson-Ford, K., Barker, M.S., Rieseberg, L.H., & Otto, S.P. (2011) Recently formed polyploid plants diversify at lower rates. Science, 333, 1257.

    Medgyesy, P., Fejes, E., & Maliga, P. (1985) Interspecific chloroplast recombination in a Nicotiana somatic hybrid. Proceedings of the National Academy of Sciences of the United States of America, 82, 6960–6964.

    Meijer, P.T. & Krijgsman, W. (2005) A quantitative analysis of the desiccation and re-filling of the Mediterranean during the Messinian Salinity Crisis. Earth and Planetary Science Letters, 240, 510–520.

    Meimberg, H., Rice, K.J., Milan, N.F., Njoku, C.C., & McKay, J.K. (2009) Multiple origins promote the ecological amplitude of allopolyploid Aegilops (Poaceae). American Journal of Botany, 96, 1262–1273.

    Metzker, M.L. (2010) Sequencing technologies - the next generation. Nature Reviews Genetics, 11, 31–46.

    Meulenkamp, J.E. & Sissingh, W. (2003) Tertiary palaeogeography and tectonostratigraphic evolution of the Northern and Southern Peri-Tethys platforms and the intermediate domains of the African-Eurasian convergent plate boundary zone. Palaeogeography, Palaeoclimatology, Palaeoecology, 196, 209–228.

    Meyer, E., Aglyamova, G. V., & Matz, M. V. (2011) Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure. Molecular Ecology, 20, 3599–3616.

    Meyer, S. & Haeseler, A. Von (2003) Identifying Site-Specific Substitution Rates. Molecular Biology and Evolution, 20, 182–189.

    Mi, H., Muruganujan, A., & Thomas, P.D. (2013) PANTHER in 2013: modeling the evolution of gene function, and other gene attribute, in the context of phylogenetic trees. Nucleic Acids Research, 41, D377–D386.

    Miao, Z., Han, Z., Zhang, T., Chen, S., & Ma, C. (2017) A systems approach to a spatio- temporal understanding of the drought stress response in maize. Scientific Reports, 7, 1–14.

    Middleton, C.P., Senerchia, N., Stein, N., Akhunov, E.D., Keller, B., Wicker, T., & Kilian, B. (2014) Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the triticeae tribe. PLoS ONE, 9, e85761.

    Minaya, M., Díaz-Pérez, A., Mason-Gamer, R., Pimentel, M., & Catalán, P. (2015) Evolution of the beta-amylase gene in the temperate grasses: Non-purifying selection, recombination, semiparalogy, homeology and phylogenetic signal. Molecular Phylogenetics and Evolution, 91, 68–85.

    Minaya, M., Hackel, J., Namaganda, M., Brochmann, C., Vorontsova, M.S., Besnard, G., & Catalán, P. (2017) Contrasting dispersal histories of broad- and fine-leaved temperate Loliinae grasses: range expansion, founder events, and the roles of distance and barriers. Journal of Biogeography, 1–14.

    Minh, B.Q., Nguyen, M.A.T., & von Haeseler, A. (2013) Ultrafast Approximation for Phylogenetic Bootstrap. Molecular Biology and Evolution, 30, 1188–1195.

    Mochida, K., Uehara-Yamaguchi, Y., Yoshida, T., Sakurai, T., & Shinozaki, K. (2011) Global Landscape of a Co-Expressed Gene Network in Barley and its Application to Gene Discovery in Triticeae Crops. Plants and Cell Physiology, 52, 785–803.

    Morris, L.M. & Duvall, M.R. (2010) The chloroplast genome of Anomochloa marantoidea (Anomochlooideae; Poaceae) comprises a mixture of grass-like and unique features. American Journal of Botany, 97, 620–627.

    Mun, B.-G., Lee, S.-U., Park, E.-J., Kim, H.-H., Hussain, A., Muhammad Imran, Q., Lee, I.-J., & Yun, B.-W. (2017) Analysis of transcription factors among differentially expressed genes induced by drought stress in Populus davidiana. 3 Biotech, 7, 1–12.

    Mur, L.A.J., Allainguillaume, J., Catalán, P., Hasterok, R., Jenkins, G., Lesniewska, K., Thomas, I., & Vogel, J. (2011) Exploiting the Brachypodium tool box in cereal and grass research. New Phytologist, 191, 334–347.

    Murat, F., Xu, J., Tannier, E., Abrouk, M., Guilhot, N., Pont, C., & Messing, J. (2010) Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Research, 20, 1545–1557.

    Nadalin, F., Vezzi, F., & Policriti, A. (2012) GapFiller: a de novo assembly approach to fill the gap within paired reads. BMC Bioinformatics, 13, S8.

    Nadot, S., Bajon, R., & Lejeune, B. (1994) The Chloroplast Gene Rps4 as a Tool for the Study of Poaceae Phylogeny. Plant Systematics and Evolution, 191, 27–38.

    Nakashima, K., Ito, Y., & Yamaguchi-Shinozaki, K. (2009) Transcriptional Regulatory Networks in Response to Abiotic Stresses in Arabidopsis and Grasses. Plant Physiology, 149, 88–95.

    Nakashima, K., Yamaguchi-Shinozaki, K., & Shinozaki, K. (2014) The transcriptional regulatory network in the drought response and its crosstalk in abiotic stress responses including drought, cold, and heat. Frontiers in plant science, 5, 1–7.

    Nakato, R. & Gotoh, O. (2010) Cgaln: fast and space-efficient whole-genome alignment. BMC Bioinformatics, 11, 1-14.

    Nguyen, L.-T., Schmidt, H.A., von Haeseler, A., & Minh, B.Q. (2014) IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies. Molecular Biology and Evolution, 32, 268–274.

    Nguyen, N.T.T., Contreras-Moreira, B., Castro-Mondragon, J.A., Santana-Garcia, W., Ossio, R., Robles-Espinoza, C.D., Bahin, M., Collombet, S., Vincens, P., Thieffry, D., Helden, J. Van, Medina-Rivera, A., & Thomas-Chollier, M. (2018) RSAT 2018: regulatory sequence analysis tools 20th anniversary. Nucleic Acids Research, 1, 1–6.

    Nieto-Feliner, G. & Rosselló, J.A. (2007) Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Molecular Phylogenetics and Evolution, 44, 911–919.

    Van Nieuwerburgh, F., Thompson, R.C., Ledesma, J., Deforce, D., Gaasterland, T., Ordoukhanian, P., & Head, S.R. (2012) Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination. Nucleic Acids Research, 40, e24.

    Niu, X., Guan, Y., Chen, S., & Li, H. (2017) Genome-wide analysis of basic helix-loop- helix (bHLH) transcription factors in Brachypodium distachyon. BMC Genomics, 18, 1–20.

    Nock, C.J., Waters, D.L.E., Edwards, M.A., Bowen, S.G., Rice, N., Cordeiro, G.M., & Henry, R.J. (2011) Chloroplast genome sequences from total DNA for plant identification. Plant Biotechnology Journal, 9, 328–333.

    Noirot, M., Charrier, A., Stoffelen, P., & Anthony, F. (2015) Reproductive isolation, gene flow and speciation in the former Coffea subgenus: a review. Trees. Structure and function, 1–12.

    Novikova, P.Y., Hohmann, N., Nizhynska, V., et al. (2016) Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nature Genetics, 48, 1077–1082.

    O’Mara, F.P. (2012) The role of grasslands in food security and climate change. Annals of Botany, 110, 1263–1270.

    Osborne, C.P. & Beerling, D.J. (2006) Nature’s green revolution: the remarkable evolutionary rise of C4 plants. Philosophical Transactions of the Royal Society B: Biological Sciences, 361, 173–194.

    Otto, F. (1992) Preparation and Staining of Cells for High-Resolution DNA Analysis. Flow Cytometry and Cell Sorting (ed. by A. Radbruch), pp. 65–68. Springer Laboratory, Berlin, Heidelberg.

    Otto, S.P. (2007) The Evolutionary Consequences of Polyploidy. Cell, 131, 452–462.

    Otto, S.P. & Whitton, J. (2000) Polyploid incidence and evolution. Annual Review of Genetics, 401–37.

    Ouyang, S., Zhu, W., Hamilton, J., Lin, H., Campbell, M., Childs, K., Thibaud-Nissen, F., Malek, R.L., Lee, Y., Zheng, L., Orvis, J., Haas, B., Wortman, J., & Buell, R.C. (2007) The TIGR Rice Genome Annotation Resource: Improvements and new features. Nucleic Acids Research, 35, 883–887.

    Palisot de Beauvois, A.-M.-F.-J. (1812) Essai d’une nouvelle agrostographie. Paris.

    Panchy, N., Lehti-shiu, M., & Shiu, S. (2016) Evolution of Gene Duplication in Plants. Plant physiology, 171, 2294–2316.

    Paradis, E., Claude, J., & Strimmer, K. (2004) APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics, 20, 289–290.

    Patel, D.A., Zander, M., Dalton-Morgan, J., & Batley, J. (2015) Advances in Plant Genotyping: Where the Future Will Take Us. Plant Genotyping. Methods and Protocols (ed. by J. Batley), pp. 1–11. Springer Science+Business Media, New York.

    Paterson, A.H., Bowers, J.E., & Chapman, B.A. (2004) Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proceedings of the National Academy of Sciences, 101, 9903–9908.

    Van de Peer, Y., Maere, S., & Meyer, A. (2009) The evolutionary significance of ancient genome duplications. Nature Reviews Genetics, 10, 725–732.

    Peng, X., Zhao, Y., Cao, J., Zhang, W., Jiang, H., Li, X., Ma, Q., & Zhu, S. (2012) CCCH-Type Zinc Finger Family in Maize: Genome-Wide Identification, Classification and Expression Profiling under Abscisic Acid and Drought Treatments. PLoS ONE, 7, e40120.

    Perea, C., Fernando, J., Hoz, D. La, Cruz, D.F., Lobaton, J.D., Izquierdo, P., Quintero, J.C., Raatz, B., & Duitama, J. (2016) Bioinformatic analysis of genotype by sequencing (GBS) data with NGSEP. BMC genomics, 17, suppl. 5.

    Pereira, A. (2016) Plant Abiotic Stress Challenges from the Changing Environment. Frontiers in plant science, 7, 1–3.

    Peterson, D.G., Tomkins, J.P., Frisch, D.A., Wing, R.A., & Paterson, A.H. (2000) Construction of plant bacterial artificial chromosome (BAC) libraries: An illustrated guide. Journal of Agricultural Genomics, 5, 1–100.

    Philippe, H., Brinkmann, H., Lavrov, D. V., Littlewood, D.T.J., Manuel, M., Wörheide, G., & Baurain, D. (2011) Resolving difficult phylogenetic questions: Why more sequences are not enough. PLoS Biology, 9, e1000602.

    Pimentel, H., Bray, N.L., Puente, S., Melsted, P., & Pachter, L. (2017a) Differential analysis of RNA-seq incorporating quantification uncertainty. Nature Methods, 14, 687–690.

    Pimentel, M., Escudero, M., Sahuquillo, E., Minaya, M.Á., & Catalán, P. (2017b) Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene? PeerJ, 5, e3815.

    Pokorny, L., Oliván, G., & Shaw, A.J. (2011) Phylogeographic Patterns in Two Southern Hemisphere Species of Calyptrochaeta (Daltoniaceae, Bryophyta). Systematic Botany, 36, 542–553.

    Pootakham, W., Jomchai, N., Ruang-areerate, P., Shearman, J.R., Sonthirod, C., Sangsrakru, D., Tragoonrung, S., & Tangphatsornruang, S. (2015) Genomics Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS). Genomics, 105, 288–295.

    Porras-Huratdo, L., Ruiz, Y., Santos, C., Phillips, C., Carracedo, Á., & Lareu, M. V (2013) An overview of STRUCTURE: applications, parameter settings, and supporting software. Frontiers in Genetics, 4, 1–13.

    Posada, D. & Crandall, K.A. (1998) MODELTEST: Testing the model of DNA substitution. Bioinformatics, 14, 817–818.

    Prasad, V., Strömberg, C.A.E., Alimohammadian, H., & Sahni, A. (2005) Dinosaur Coproliites and the Early Evolution of Grasses and Grazers. Science, 310, 1177–1180.

    Pritchard, J.K., Stephens, M., & Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945–959.

    Rambaut, A., Suchard, M.A., Xie, D., & Drummond, A.J. (2014) Tracer. .

    Ramsey, J. & Schemske, D.W. (1998) Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annual Review of Ecology and Systematics, 29, 467–501.

    Rannala, B. & Yang, Z. (1996) Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. Journal of Molecular Evolution, 43, 304–311.

    Ranocha, P., Denance, N., Vanholme, R., Freydier, A., Martinez, Y., Hoffmann, L., Köhler, L., Pouzet, C., Renou, J.-P., Sundberg, B., Boernjan, W., & Goffner, D. (2010) Walls are thin 1 (WAT1), an Arabidopsis homolog of Medicago truncatula NODULIN21, is a tonoplast-localized protein required for secondary wall formation in fibers. The Plant Journal, 63, 469–483.

    Ream, T.S., Woods, D.P., Schwartz, C.J., Sanabria, C.P., Mahoy, J.A., Walters, E.M., Kaeppler, H.F., & Amasino, R.M. (2014) Interaction of photoperiod and vernalization determines flowering time of Brachypodium distachyon. Plant physiology, 164, 694–709.

    Ree, R.H., Moore, B.R., Webb, C.O., & Donoghue, M.J. (2005) A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution, 59, 2299–2311.

    Ree, R.H. & Smith, S.A. (2008) Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology, 57, 4–14.

    Reuter, J.A., Spacek, D. V., & Snyder, M.P. (2015) High-Throughput Sequencing Technologies. Molecular Cell, 58, 586–597.

    Rey, P.J., Manzaneda, A.J., & Alcántara, J.M. (2017) The interplay between aridity and competition determines colonization ability, exclusion and ecological segregation in the heteroploid Brachypodium distachyon species complex. New Phytologist, 215, 85–96.

    Rieux, A. & Balloux, F. (2016) Inferences from tip-calibrated phylogenies: a review and a practical guide. Molecular Ecology, 25, 1911–1924.

    Ritchie, S.C., Watts, S., Fearnley, L.G., Holt, K.E., Abraham, G., & Inouye, M. (2016) A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets. Cell Systems, 3, 71–82.

    Robertson, I.H. (1981) Chromosome numbers in Brachypodium Beauv. (Gramineae). Genetica, 56, 55–60.

    Romay, M.C., Millard, M.J., Glaubitz, J.C., Peiffer, J.A., Swarts, K.L., Casstevens, T.M., Elshire, R.J., Acharya, C.B., Mitchell, S.E., Flint-garcia, S.A., Mcmullen, M.D., Holland, J.B., Buckler, E.S., & Gardner, C.A. (2013) Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biology, 14, R55.

    Ronaghi, M., Uhlén, M., & Nyrén, P. (1998) A sequencing method based on real-time pyrophosphate. Science, 281, 363–365.

    Ronen, R., Boucher, C., Chitsaz, H., & Pevzner, P. (2012) SEQuel: Improving the accuracy of genome assemblies. Bioinformatics, 28, 188–196.

    Ronquist, F., Huelsenbeck, J., & Teslenko, M. (2011) MrBayes Version 3.2 Manual: Tutorials and Model Summaries. 1–103.

    Ronquist, F. & Huelsenbeck, J.P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572–1574.

    Rubio, V., Bustos, R., Irigoyen, M.L., Cardona-López, X., Rojas-Triana, M., & Paz-Ares, J. (2009) Plant hormones and nutrient signaling. Plant Molecular Biology, 69, 361–373.

    Rutschmann, F. (2006) Molecular dating of phylogenetic trees: A brief review of current methods that estimate divergence times. Diversity and Distributions, 12, 35–48.

    Rzhetsky, A. & Nei, M. (1992) A Simple Method for Estimating and Testing Minimum-Evolution Trees. Molecular biology and evolution, 9, 945–967.

    Saarela, J.M., Bull, R.D., Paradis, M.J., Ebata, S.N., Peterson, P.M., Soreng, R.J., & Paszko, B. (2017) Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1). PhytoKeys, 87, 1–139.

    Saarela, J.M., Burke, S. V., Wysocki, W.P., Barrett, M.D., Clark, L.G., Craine, J.M., Peterson, P.M., Soreng, R.J., Vorontsova, M.S., & Duvall, M.R. (2018) A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions. PeerJ, 6, e4299.

    Saarela, J.M., Wysocki, W.P., Barrett, C.F., Soreng, R.J., Davis, J.I., Clark, L.G., Kelchner, S.A., Pires, J.C., Edger, P.P., Mayfield, D.R., & Duvall, M.R. (2015) Plastid phylogenomics of the cool-season grass subfamily: Clarification of relationships among early-diverging tribes. AoB PLANTS, 7, 1–27.

    Saitou, N. & Nei, M. (1987) The Neighbor-joining Method: A New Method for Reconstructing Phylogenetic Trees. Molecular biology and evolution, 4, 406–425.

    Salse, J., Bolot, S., Throude, M., Jouffe, V., Piegu, B., Masood-Quraishi, U., Calcagno, T., Cooke, R., Delseny, M., & Feuillet, C. (2008) Identification and Characterization of Shared Duplications between Rice and Wheat Provide New Insight into Grass Genome Evolution. The Plant Cell, 20, 11–24.

    Sánchez-Ken, J.G. & Clark, L.G. (2010) Phylogeny and a new tribal classification of the Panicoideae S.L. (Poaceae) based on plastid and nuclear sequence data and structural data. American Journal of Botany, 97, 1732–1748.

    Sancho, R., Cantalapiedra, C.P., López-Alvarez, D., Gordon, S.P., Vogel, J.P., Catalán, P., & Contreras-Moreira, B. (2018) Comparative plastome genomics and phylogenomics of Brachypodium: Flowering time signatures, introgression and recombination in recently diverged ecotypes. New Phytologist, 218, 1631–1644.

    Sanger, F., Nicklen, S., & Coulson, A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences, 74, 5463–5467.

    Sanmartín, I. (2012) Historical Biogeography: Evolution in Time and Space. Evolution: Education and Outreach, 5, 555–568.

    Sanmartin, I., Enghoff, H., & Ronquist, F. (2001) Patterns of animal dispersal, vicariance and diversification in the Holarctic. Biological Journal of the Linnean Society, 73, 345–390.

    Sasaki, T. & Antonio, B.A. (2004) Rice genome as a model system for cereals. Cereal Genomics (ed. by P.K. Gupta and R.K. Varshney), pp. 535–557. Kluwer Academic Publishers, Netherlands.

    Saski, C., Lee, S.-B., Siri, F., Chittibabu, G., Jansen, R.K., Luo, H., Tomkins, J., Rognli, O.A., Daniell, H., & Clarke, J.L. (2007) Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes. Theoretical and Applied Genetics, 115, 571–590.

    Scheben, A., Batley, J., & Edwards, D. (2017) Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application. Plant Biotechnology Journal, 15, 149–161.

    Schippmann, U. (1990) Brachypodium boissieri. An endemic grass species of southern Spain. Lagascalia, 15, 179–188.

    Schippmann, U. (1991) Revision der europäischen Arten der Gattung Brachypodium Palisot de Beauvois (Poaceae). Boissiera, 45, 249 pp.

    Schneider, J., Winterfeld, G., Hoffmann, M.H., & Röser, M. (2011) Duthieeae, a new tribe of grasses (Poaceae) identified among the early diverging lineages of subfamily Pooideae: molecular phylogenetics, morphological delineation, cytogenetics, and biogeography. Systematics and Biodiversity, 9, 27–44.

    Scholthof, K.-B.G., Irigoyen, S., Catalán, P., & Mandadi, K.K. (2018) Brachypodium: A monocot grass model system for plant biology. Plant Cell. [in press].

    Schuh, R.T. (2000) Biological Systematics. Principles and applications. Cornell University Press, United States of America, 328 pp.

    Schuster, S.C. (2008) Next-generation sequencing transforms today’s biology. Nature Methods, 5, 16–18.

    Schwartz, C.J., Doyle, M.R., Manzaneda, A.J., Rey, P.J., Mitchell-Olds, T., & Amasino, R.M. (2010) Natural variation of flowering time and vernalization responsiveness in Brachypodium distachyon. Bioenergy Research, 3, 38–46.

    Sebastian, A. & Contreras-Moreira, B. (2014) footprintDB: a database of transcription factors with annotated cis elements and binding interfaces. Bioinformatics, 30, 258–265.

    Serin, E.A.R., Nijveen, H., Hilhorst, H.W.M., & Ligterink, W. (2016) Learning from Co-expression Networks: Possibilities and Challenges. Frontiers in Genetics, 7, 1–18.

    Shendure, J. & Ji, H. (2008) Next-generation DNA sequencing. Nature Biotechnology, 26, 1135–1145.

    Shi, Y. (1991) Molecular studies of the evolutionary relationships of Brachypodium (Poaceae). Ph.D thesis, University of Leicester.

    Shi, Y., Draper, J., & Stace, C. (1993) Ribosomal DNA variation and its phylogenetic implication in the genus Brachypodium (Poaceae). Plant Systematics and Evolution, 188, 125–138.

    Shinozaki, K. & Yamaguchi-Shinozaki, K. (2007) Gene networks involved in drought stress response and tolerance. Journal of Experimental Botany, 58, 221–227.

    Shiposha, V., Catalán, P., Olonova, M., & Marques, I. (2016) Genetic structure and diversity of the selfing model grass Brachypodium stacei (Poaceae) in Western Mediterranean: out of the Iberian Peninsula and into the islands. PeerJ, 4, e2407.

    Sievers, F., Wilm, A., Dineen, D., Gibson, T.J., Karplus, K., Li, W., Lopez, R., Mcwilliam, H., Remmert, M., Söding, J., Thompson, J.D., & Higgins, D.G. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systematics Biology, 7, 1–6.

    Silvertown, J., Servaes, C., Biss, P., & Macleod, D. (2005) Reinforcement of reproductive isolation between adjacent populations in the Park Grass Experiment. Heredity, 95, 198–205.

    Sneath, P.H.A. & Sokal, R.R. (1973) Numerical Taxonomy. The principles and practice of numerical classification. W. H. Freeman and Company, San Francisco, 588 pp.

    Sokal, R. & Michener, C. (1958) A statistical method for evaluating systematic relationships. The University of Kansas Science Bulletin, 38, 1409–1438.

    Soltis, D.E., Segovia-Salcedo, M.C., Jordon-Thaden, I., Majure, L., Miles, N.M., Mavrodiev, E. V., Mei, W., Cortez, M.B., Soltis, P.S., & Gitzendanner, M.A. (2014a) Are polyploids really evolutionary dead-ends (again)? A critical reappraisal of Mayrose et al. New Phytologist, 202, 1105–1117.

    Soltis, D.E., Visger, C.J., Blaine Marchant, D., & Soltis, P.S. (2016) Polyploidy: Pitfalls and paths to a paradigm. American Journal of Botany, 103, 1146–1166.

    Soltis, D.E., Visger, C.J., & Soltis, P.S. (2014b) The polyploidy revolution then...and now: Stebbins revisited. American Journal of Botany, 101, 1057–1078.

    Soltis, P.S. & Soltis, D.E. (2016) Ancient WGD events as drivers of key innovations in angiosperms. Current Opinion in Plant Biology, 30, 159–165.

    Soreng, R., Davidse, G., Peterson, P., Zuloaga, F., Judziewicz, E., Filgueiras, T., Morrone, O., & Romaschenko, K. (2014) Available at: http://www.tropicos.org/docs/meso/WWP A WORLDWIDE CLASSIFICATION OF POACEAE TROPICOS version JUN 30 2017.htm.

    Soreng, R.J. & Davis, J.I. (1998) Phylogenetics and Character Evolution in the Grass Family (Poaceae): Simultaneous Analysis of Morphological and Chloroplast DNA Restriction Site Character Sets. The Botanical Review, 64, 1–85.

    Soreng, R.J., Peterson, P.M., Romaschenko, K., Davidse, G., Teisher, J.K., Clark, L.G., Barberá, P., Gillespie, L.J., & Zuloaga, F.O. (2017) A worldwide phylogenetic classification of the Poaceae (Gramineae) II: An update and a comparison of two 2015 classifications. Journal of Systematics and Evolution, 55, 259–290.

    Soreng, R.J., Peterson, P.M., Romaschenko, K., Davidse, G., Zuloaga, F.O., Judziewicz, E.J., Filgueiras, T.S., Davis, J.I., & Morrone, O. (2015) A worldwide phylogenetic classification of the Poaceae (Gramineae). Journal of Systematics and Evolution, 53, 117–137.

    Stamatakis, A. (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688–2690.

    Stamatakis, A. (2014) RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30, 1312–1313.

    Stebbins, G.L. (1949) The evolutionary significance of natural and artificial polyploids in the family Gramineae. Hereditas, 35, 461–458.

    Stebbins, G.L. (1985) Polyploidy, hybridization and the invasion of new habitats. Annals of the Missouri Botanical Garden, 72, 824–832.

    Steinwand, M.A., Young, H.A., Bragg, J.N., Tobias, C.M., & Vogel, J.P. (2013) Brachypodium sylvaticum, a Model for Perennial Grasses: Transformation and Inbred Line Development. PLoS ONE, 8, e75180.

    Stetter, M.G. & Schmid, K.J. (2017) Molecular Phylogenetics and Evolution Analysis of phylogenetic relationships and genome size evolution of the Amaranthus genus using GBS indicates the ancestors of an ancient crop. Molecular Phylogenetics and Evolution, 109, 80–92.

    Strien, M.J. Van, Holderegger, R., & Heck, H.J. Van (2014) Isolation-by-distance in landscapes: considerations for landscape genetics. Heredity, 114, 27–37.

    Strömberg, C.A.E. (2005) Decoupled taxonomic radiation and ecological expansion of open-habitat grasses in the Cenozoic of North America. Proceedings of the National Academy of Sciences, 102, 11980–11984.

    Strömberg, C.A.E. (2011) Evolution of Grasses and Grassland Ecosystems. Annual Review of Earth and Planetary Sciences, 39, 517–544.

    Stuart, J.M., Segal, E., Koller, D., & Kim, S.K. (2003) A Gene Coexpression Network for Global Discovery of Conserved Genetic Modules. Science, 302, 249–255.

    Suda, J., Kyncl, T., & Jarolímová, V. (2005) Genome size variation in Macaronesian angiosperms: forty percent of the Canarian endemic flora completed. Plant Systematics and Evolution, 252, 215–238.

    Swofford, D.L. (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods). Version 4b10. Sinauer Associates, Sunderland, Massachusetts, USA.

    Takahashi, F., Suzuki, T., Osakabe, Y., Betsuyaku, S., Kondo, Y., Dohmae, N., Fukuda, H., Yamaguchi-Shinozaki, K., & Shinozaki, K. (2018) A small peptide modulates stomatal control via abscisic acid in long-distance signalling. Nature, 556, 235–238.

    Talavera, S. (1978) Aportacion al estudio cariologico de las gramineas españolas. Lagascalia, 7, 133–142.

    Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731–2739.

    Tandonnet, S. & Torres, T.T. (2017) Traditional versus 3′ RNA-seq in a non-model species. Genomics Data, 11, 9–16.

    Tang, H., Bowers, J.E., Wang, X., Ming, R., Alam, M., & Paterson, A.H. (2008) Synteny and Collinearity in Plant Genomes. Science, 320, 486–489.

    Teixeira Torres, T., Metta, M., Ottenwälder, B., & Schlötterer, C. (2008) Gene expression profiling by massively parallel sequencing. Genome Research, 18, 172–177.

    The Gene Ontology Consortium (2000) Gene Ontology: tool for the unification of biology. Nature Communications, 25, 25–29.

    The Gene Ontology Consortium (2017) Expansion of the Gene Ontology knowledgebase and resources. Nucleic acids research, 45, D331–D338.

    The UniProt Consortium (2017) UniProt: the universal protein knowledgebase. Nucleic Acids Research, 45, D158–D169.

    Thomas, G.W.C., Ather, S.H., & Hahn, M.W. (2017) Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events. Systematic Biology, 0, 1–12.

    Thomas, P.D., Campbell, M.J., Kejariwal, A., Mi, H., Karlak, B., Daverman, R., Diemer, K., Muruganujan, A., & Narechania, A. (2003) PANTHER: A Library of Protein Families and Subfamilies Indexed by Function. Genome Research, 13, 2129–2141.

    Thorvaldsdóttir, H., Robinson, J.T., & Mesirov, J.P. (2013) Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration. Briefings in Bioinformatics, 14, 178–192.

    Thudi, M., Li, Y., Jackson, S.A., May, G.D., & Varshney, R.K. (2012) Current state-of-art of sequencing technologies for plant genomics research. Briefings in Functional Genomics, 11, 3–11.

    Tyler, L., Lee, S.J., Young, N.D., Deiulio, G.A., Benavente, E., Reagon, M., Sysopha, J., Baldini, R.M., Troìa, A., Hazen, S.P., & Caicedo, A.L. (2016) Population structure in the model grass Brachypodium distachyon is highly correlated with flowering differences across broad geographic areas. Plant Genome, 9, 1–55.

    Uozu, S., Ikehashi, H., Ohmido, N., Ohtsubo, H., Ohtsubo, E., & Fukui, K. (1997) Repetitive sequences: cause for variation in genome size and chromosome morphology in the genus Oryza. Plant Molecular Biology, 35, 791–799.

    Vanderlaan, T.A., Ebach, Malte, C., Williams, D.M., & Wilkins, J.S. (2013) Defining and redefining monophyly: Haeckel, Hennig, Ashlock, Nelson and the proliferation of definitions. Austraian Systematics Botany, 26, 347–355.

    Vaughan, D.A. (1994) The wild relatives of rice. A genetic resources handbook. IRRI, Manila, 137 pp.

    Vicentini, A., Barber, J.C., Aliscioni, S.S., Giussani, L.M., & Kellogg, E.A. (2008) The age of the grasses and clusters of origins of C4 photosynthesis. Global Change Biology, 14, 2963–2977.

    Vinuesa, P., Ochoa-Sánchez, L.E., & Contreras-Moreira, B. (2018) GET _ PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies , used for a critical geno-taxonomic revision of the genus Stenotrophomonas. Frontiers in Microbiology, 9, 1-22.

    Vogel, J. & Bragg, J. (2009) Brachypodium distachyon, a New Model for the Triticeae. Genetics and Genomics of the Triticeae. Plant Genetics and Genomics: Crops and Models 7 (ed. by C. Feuillet and G.J. Muehlbauer), pp. 427–449. Springer.

    Vogel, J. & Hill, T. (2008) High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd21-3. Plant Cell Reports, 27, 471–478.

    Vogel, J.P. (2016) The Rise of Brachypodium as a Model System. Genetics and genomics of Brachypodium. Plant Genetics and Genomics: Crops Models (ed. by J.P. Vogel), pp. 1–8. Springer.

    Vogel, J.P., Garvin, D.F., Leong, O.M., & Hayden, D.M. (2006) Agrobacterium-mediated transformation and inbred line development in the model grass Brachypodium distachyon. Plant Cell, Tissue and Organ Culture, 84, 199–211.

    Vogel, J.P., Garvin, D.F., Mockler, T.C., et al. (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature, 463, 763–768.

    Vogel, J.P., Tuna, M., Budak, H., Huo, N., Gu, Y.Q., & Steinwand, M.A. (2009) Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon. BMC plant biology, 9, 88.

    von Bothmer, R., Jacobsen, N., Baden, C., Bagger Jørgensen, R., & Linde-Laursen, I. (1995) An ecogeographical study of the genus Hordeum. IPGRI, Rome.

    Wang, R.-J., Cheng, C.-L., Chang, C.-C., Wu, C.-L., Su, T.-M., & Chaw, S.-M. (2008) Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. BMC evolutionary biology, 8, 36.

    Wang, Y. & Ma, H. (2015) Step-wise and lineage-specific diversification of plant RNA polymerase genes and origin of the largest plant-specific subunits. New Phytologist, 207, 1198–1212.

    Wang, Z., Gerstein, M., & Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics, 10, 57–63.

    Washburn, J.D., Schnable, J.C., Conant, G.C., Brutnell, T.P., Shao, Y., Zhang, Y., Ludwig, M., Davidse, G., & Pires, J.C. (2017) Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses. Scientific Reports, 7, 13528.

    Waters, D.L.E., Nock, C.J., Ishikawa, R., Rice, N., & Henry, R.J. (2012) Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice. Ecology and Evolution, 2, 211–217.

    Wickham, H. (2009) ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag, New York.

    Wisecaver, J.H., Borowsky, A.T., Tzin, V., Jander, G., Kliebenstein, D.J., & Rokas, A. (2017) A Global Co-expression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants. Plant Cell, 25, 944–959.

    Wolfe, C.J., Kohane, I.S., & Butte, A.J. (2005) Systematic survery reveals general applicability of “guilt-by-association” within gene coexpression networks. BMC Bioinformatics, 6, 1–10.

    Wolny, E. & Hasterok, R. (2009) Comparative cytogenetic analysis of the genomes of the model grass Brachypodium distachyon and its close relatives. Annals of Botany, 104, 873–881.

    Wolny, E., Lesniewska, K., Hasterok, R., & Langdon, T. (2011) Compact genomes and complex evolution in the genus Brachypodium. Chromosoma, 120, 199–212.

    Woods, D.P., Mckeown, M.A., Dong, Y., Preston, J.C., & Amasino, R.M. (2016) Evolution of VRN2/GhD7- Like Genes in Vernalization-Mediated Repression of Grass. Plant Physiology, 170, 1–12.

    Woods, D.P., Ream, T.S., & Amasino, R.M. (2014) Memory of the vernalized state in plants including the model grass Brachypodium distachyon. Frontiers in plant science, 5, 99.

    Wright, S. (1943) Isolation by distance. Genetics, 28, 114–138.

    Wu, Z.Q. & Ge, S. (2012) The phylogeny of the BEP clade in grasses revisited: Evidence from the whole-genome sequences of chloroplasts. Molecular Phylogenetics and Evolution, 62, 573–578.

    Wysocki, W.P., Clark, L.G., Attigala, L., Ruiz-Sanchez, E., & Duvall, M.R. (2015) Evolution of the bamboos (Bambusoideae; Poaceae): a full plastome phylogenomic analysis. BMC evolutionary biology, 15, 50.

    Xiang, Q.P., Wei, R., Shao, Y.Z., Yang, Z.Y., Wang, X.Q., & Zhang, X.C. (2015) Phylogenetic relationships, possible ancient hybridization, and biogeographic history of Abies (Pinaceae) based on data from nuclear, plastid, and mitochondrial genomes. Molecular Phylogenetics and Evolution, 82, 1–14.

    Yang, Y. & Smith, S.A. (2014) Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics. Molecular Biology and Evolution, 31, 3081–3092.

    Yu, H., Jiao, B., & Liang, C. (2017) High-quality rice RNA-seq-based co-expression network for predicting gene function and regulation. bioRxiv, https://www.biorxiv.org/content/early/2017/05/15/138040.

    Yuan, H. & Liu, D. (2008) Signaling components involved in plant responses to phosphate starvation. Journal of Integrative Plant Biology, 50, 849–859.

    Zerbino, D.R. (2010) Using the Columbus extension to Velvet. http://gensoft.pasteur.fr/docs/velvet/1.1.02/Columbus_manual.pdf.

    Zerbino, D.R. & Birney, E. (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18, 821–829.

    Zhang, B. & Horvath, S. (2005) A General Framework for Weighted Gene Co-expression Network Analysis. Statistical Applications in Genetics and Molecular Biology, 4, Article 17.

    Zhang, W. (2000) Phylogeny of the grass family (Poaceae) from rpl16 intron sequence data. Molecular Phylogenetics and Evolution, 15, 135–146.

    Zhao, Q., Feng, Q., Lu, H., et al. (2018) Pan-genome analysis highlihgts the extent of genomic variation in cultivated and wild rice. Nature Genetics, 50, 278–284.

    Zhou, L., Wang, S.-B., Jian, J., Geng, Q.-C., Wen, J., Song, Q., Wu, Z., Li, G.-J., Liu, Y.-Q., Dunwell, J.M., Zhang, J., Feng, J.-Y., Niu, Y., Zhang, L., Ren, W.-L., & Zhang, Y.-M. (2015) Identification of domestication-related loci associated with flowering time and seed size in soybean with the RAD-seq genotyping method. Scientific Reports, 5, 1–8.

    Zhou, S., Yan, B., Li, F., Zhang, J., Zhang, J., Ma, H., Liu, W., Lu, Y., Yang, X., Li, X., Liu, X., & Li, L. (2017) RNA-Seq Analysis Provides the First Insights into the Phylogenetic Relationship and Interspecific Variation between Agropyron cristatum and Wheat. Frontiers in Plant Science, 8, 1–13.