Transposable elements in plant genomes

Transposable elements (TEs) are genomic units able to move within and among the genomes of virtually all organisms. They are the main contributors to genomic diversity and genome size variation, with the exception of polyploidy events. An important issue in genome sequence analyses is to rapidly identify and to reliably annotate TEs. There are major obstacles and challenges in the analysis of these elements, including their repetitive nature, structural polymorphism, species specificity, and, conversely, their conservation across genera and families, as well as their high divergence rate, even across close relative species. They are able to move in the genomes, generate mutations, and obviously amplify the number of their copies. Usually they are classified according to their coding regions involved in the replication of the element. TEs moving via an RNA molecule called retrotransposons fall into Class I, while elements moving via a DNA molecule, called transposons, are classified into Class II. They represent the vast majority of TEs found in plant genomes due to their mobility mechanisms. Retrotransposons can be further subclassified into four orders according to their structural features and the element’s life cycle: Long Terminal Repeat retrotransposon (LTR-RT), non-LTR retrotransposons, PLEs, and DIRS.

LTR-RT is the most common order, and they can contribute up to 80% of the plant genome size, as in wheat, barley, or the rubber tree. The LTR-RT order is composed of two superfamilies in plants: Copia and Gypsy, based on the internal organization of the coding domain. Each Copia and Gypsy superfamily is further sub-classified into lineages and families through phylogenetic analysis based on coding region similarities (often of the enzymatic domain known as reverse transcriptase). For plant genomes, Ale (also known as Retrofit), Alesia, Angela, Bianca, Bryco, Lyco, Gymco, Ikeros (also known as Tork sto-4), Ivana (or Oryco), Osser, SIRE, Tar (also known as Tork), and Tork lineages belong to the Copia superfamily, while Athila, Clamyvir, Galadriel, Selgy, Tcn1, Reina, Tekay (or Del), CRM (also named Centromeric Retrotransposon), Phygy, and TAT are grouped into the Gypsy superfamily. Phylogenetic studies have divided Gypsy into different groups according to the presence of a chromodomain. The Galadriel, Reina, Tekay (Del), and CRM lineages were grouped into the Chromovirus branch. Several methods were developed to identify and annotate transposable elements in sequenced genomes. These are classified into four categories: de novo, structure-based, comparative genomics, and homology-based. These approaches offer different specificities and sensibilities and all suffer from a relatively high rate of false positive detections.

Our objectives are to study transposable elements in the genomes of plants and more specifically in the genomes of coffee trees. Our studies focus on the impact of transposable elements on the genomes evolution and species adaptation as well as and their direct contribution to the genome size variations. To achieve these objectives, new bioinformatic tools for the detection and annotation of retrotransposons at LTR are under development.