Impact of transposition on the generation of genetic variability in prunus crop species
- Autores: Fabio Barteri
- Directores de la Tesis: Josep Maria Casacuberta i Suñer (dir. tes.)
- Lectura: En la Universitat Autònoma de Barcelona ( España ) en 2019
- Idioma: español
- Tribunal Calificador de la Tesis: Pere Puigdomènech i Rosell (presid.), Olivier Panaud (secret.), Juan José López Moya Gómez (voc.)
- Programa de doctorado: Programa de Doctorado en Biología y Biotecnología Vegetal por la Universidad Autónoma de Barcelona
- Materias:
- Enlaces
- Tesis en acceso abierto en: TESEO
- Resumen
Transposable Elements (TEs) are mobile genetic units that are capable to change their position in the genome and to spread autonomously. In eukaryotes, TEs make up a considerable part of the genomic DNA and their spread has been linked to the growth of the genome size and the increase of genetic variability during evolution. However, the extent of their impact on genome structure, function and disease remains a matter of open investigation. Despite the rise of genomics and large-scale bioinformatics allowed to unravel several aspects of these mobile elements, the increasing amount of complex genomics data calls for efforts in developing and testing more efficient software implementations.
In this optics, the PhD thesis submitted through this application unfolds on a double track. On one side, the dissertation discusses the impact of TEs in the generation of genetic variability in the major crops peach (Prunus persica) and almond (Prunus dulcis). On the other side, a technical assessment of the performance of software dedicated to the detection and characterisation of TEs from NGS data.
The dissertation is divided into three chapters. The first chapter discusses the results of the benchmarking of several software packages designed to detect structural polymorphisms from DNA-seq data.
The second chapter reports the results from the annotation of TEs in peach and almond. After a global annotation of the TEs content in both genomes, we have refined the annotation of the LTR- retrotransposons (LTR-RTs), a subclass of retrotransposons that are usually active in plant genomes. Each of the resulting elements, identified on the reference genomes, has been then associated with two variables: their inferred insertion time, and their conservation within a population of 16 peach and 19 almond cultivated varieties, made available as Whole-Genome re-Sequencing (WGS) samples. The combination of these two variables indicates that peach precursor underwent a serious population shrinkage before its separation from sister species almond and that a burst of new insertions affected the peach genome after the separation of these two species. The LTR-RTs dynamics is hereby different in peach and almond, represents a major genetic difference between two very close species and it is a potential source of genetic differentiation between these two species.
This result is further investigated in Chapter 3, where we perform a transcriptional quantitation of LTR-RTs elements in Peach. Starting from publicly available RNA-seq data of a Xanthomonas arboricola infection time-course experiment in two peach varieties (JH Hale and Redkist), we have tried the package TEtranscripts, that is specifically dedicated to the assessment of the transcriptional level of TEs. Results confirm the high transcriptional activity of 11 LTR-RTs families. Also, the potential impact of transposition on gene regulation is indicated by the proximity to a LTR-RTs insertion of a considerable proportion of the genes that are differentially expressed during the course of the infection.
Globally, this thesis work represents both an effort in the technical improvement of the computational protocols to study transposition and a biological assessment of the impact of TEs in the genetic differentiation of two important crop species.
