Transpositional landscape of the rice genome revealed by paired-end mapping of high-throughput re-sequencing data

Sabot François, Picault Nathalie, El-Baidouri Moaine, Llauro Christel, Chaparro Christian, Piegu Benoît, Roulin Anne, Guiderdoni Emmanuel, Delabastide Mélissa, McCombie Richard, Panaud Olivier. 2011. Transpositional landscape of the rice genome revealed by paired-end mapping of high-throughput re-sequencing data. Plant Journal, 66 (2) : 241-246.

Quartile : Outlier, Sujet : PLANT SCIENCES

Résumé : 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.

Mots-clés Agrovoc : Oryza sativa

Classification Agris : F30 - Génétique et amélioration des plantes

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

Auteurs et affiliations

• Sabot François, CNRS (FRA)
• Picault Nathalie, CNRS (FRA)
• El-Baidouri Moaine, CNRS (FRA)
• Llauro Christel, CNRS (FRA)
• Chaparro Christian, CNRS (FRA)
• Piegu Benoît, CNRS (FRA)
• Roulin Anne, CNRS (FRA)
• Guiderdoni Emmanuel, CIRAD-BIOS-UMR AGAP (FRA)
• Delabastide Mélissa, Cold Spring Harbor (USA)
• McCombie Richard, Cold Spring Harbor (USA)
• Panaud Olivier, CNRS (FRA)

Source : Cirad - Agritrop (https://agritrop.cirad.fr/559672/)

Métriques

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