Premium
Transpositional landscape of the rice genome revealed by paired‐end mapping of high‐throughput re‐sequencing data
Author(s) -
Sabot François,
Picault Nathalie,
ElBaidouri Moaine,
Llauro Christel,
Chaparro Cristian,
Piegu Benoit,
Roulin Anne,
Guiderdoni Emmanuel,
Delabastide Mélissa,
McCombie Richard,
Panaud Olivier
Publication year - 2011
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/j.1365-313x.2011.04492.x
Subject(s) - transposable element , genome , biology , computational biology , dna sequencing , reference genome , genetics , mobile genetic elements , genomics , whole genome sequencing , gene
Summary 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.