Transpositional landscape of rice genome revealed by Paired-End Mapping of high-throughput resequencing data

Sabot, F., Picault, N., Elbaidouri, M., Llauro, C., Chaparro, C., Piegu, B., Roulin, A., Guiderdoni, E., Delabastide, M., McCombie, W. R., Panaud, O. (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

URL: http://www.ncbi.nlm.nih.gov/pubmed/21219509
DOI: 10.1111/j.1365-313X.2011.04492.x

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.

Item Type: Paper
Uncontrolled Keywords: rice transposable elements next-generation sequencing genomics mutant line paired-end mapping transposable elements epigenetic regulation retrotransposon evolution identification mutations update family genes
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
Investigative techniques and equipment
Investigative techniques and equipment > assays
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression > transposable elements
Investigative techniques and equipment > whole exome sequencing
Investigative techniques and equipment > assays > whole exome sequencing
CSHL Authors:
Communities: CSHL labs > McCombie lab
CSHL Cancer Center Shared Resources > DNA Sequencing Service
Depositing User: Matt Covey
Date Deposited: 07 Feb 2013 16:47
Last Modified: 26 Dec 2014 19:44
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27116

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