Sabot, F., Picault, N., Elbaidouri, M., Llauro, C., Chaparro, C., Piegu, B., Roulin, A., Guiderdoni, E., Delabastide, M., McCombie, W. R., Panaud, O. (January 2011) Transpositional landscape of rice genome revealed by Paired-End Mapping of high-throughput resequencing data. Plant Journal, 66 (2). pp. 241-246. ISSN 0960-7412
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 found in both plant and animal genomes correspond to inactive, degenerated elements, due to the combined effect of silencing pathways and elimination through deletions. Therefore, one of the major difficulties in fully characterizing the molecular basis of genetic diversity of a given species is to establish its genome-wide transpositional activity. In this report, 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 (PEM) of a 4x coverage of the genome of rice mutant line derived from in vitro callus culture using the Illumina technology. Our study reveals that at least 13 TE families are active in this genotype, causing 34 new insertions. This NGS-based strategy provides new opportunities to quantify the impact of TEs on the genome dynamics of the species.
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