title: Transpositional landscape of the rice genome revealed by paired-end mapping of high-throughput re-sequencing data.
abstract: Transposable elements (TEs) are mobile entities that densely populate most eukaryotic genomes and contribute to both their structural and functional dynamics. However, most TE-related sequences in both plant and animal genomes correspond to inactive, degenerated elements, due to the combined effect of silencing pathways and elimination through deletions. One of the major difficulties in fully characterizing the molecular basis of genetic diversity of a given species lies in establishing its genome-wide transpositional activity. Here, we provide an extensive survey of the transpositional landscape of a plant genome using a deep sequencing strategy. This was achieved through paired-end mapping of a fourfold coverage of the genome of rice mutant line derived from an in vitro callus culture using Illumina technology. Our study shows that at least 13 TE families are active in this genotype, causing 34 new insertions. This next-generation sequencing-based strategy provides new opportunities to quantify the impact of TEs on the genome dynamics of the species.
authors.affiliation: Laboratoire Génome et Développement des Plantes, UMR CNRS/IRD/UPVD, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, F-66860 Perpignan Cedex, France.
authors.forename: François
authors.initials: F
authors.lastname: Sabot
authors.forename: Nathalie
authors.initials: N
authors.lastname: Picault
authors.forename: Moaine
authors.initials: M
authors.lastname: El-Baidouri
authors.forename: Christel
authors.initials: C
authors.lastname: Llauro
authors.forename: Cristian
authors.initials: C
authors.lastname: Chaparro
authors.forename: Benoit
authors.initials: B
authors.lastname: Piegu
authors.forename: Anne
authors.initials: A
authors.lastname: Roulin
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Guiderdoni
authors.forename: Mélissa
authors.initials: M
authors.lastname: Delabastide
authors.forename: Richard
authors.initials: R
authors.lastname: McCombie
authors.forename: Olivier
authors.initials: O
authors.lastname: Panaud
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D004251:DNA Transposable Elements; D018744:DNA, Plant / Q000235:genetics; D014644:Genetic Variation; D018745:Genome, Plant; D016254:Mutagenesis, Insertional; D012275:Oryza / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D004251:DNA Transposable Elements; D018744:DNA, Plant