Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces
Choulet, Frederic and Wicker, Thomas and Rustenholz, Camille and Paux, Etienne and Salse, Jerome and Leroy, Philippe and Schlub, Stephane and Le Paslier, Marie-Christine and Magdelenat, Ghislaine and Gonthier, Catherine and Couloux, Arnaud and Budak, Hikmet and Breen, James and Pumphrey, Michael and Liu, Sixin and Kong, Xiuying and Jia, Jizeng and Gut, Marta and Brunel, Dominique and Anderson, James A. and Gill, Bikram S. and Appels, Rudi and Keller, Beat and Feuillet, Catherine (2010) Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell , 22 (6). pp. 1686-1701. ISSN 1040-4651
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Official URL: http://dx.doi.org/10.1105/tpc.110.074187
To improve our understanding of the organization and evolution of the wheat (Triticum aestivum) genome, we sequenced and annotated 13-Mb contigs (18.2 Mb) originating from different regions of its largest chromosome, 3B (1 Gb), and produced a 2x chromosome survey by shotgun Illumina/Solexa sequencing. All regions carried genes irrespective of their chromosomal location. However, gene distribution was not random, with 75% of them clustered into small islands containing three genes on average. A twofold increase of gene density was observed toward the telomeres likely due to high tandem and interchromosomal duplication events. A total of 3222 transposable elements were identified, including 800 new families. Most of them are complete but showed a highly nested structure spread over distances as large as 200 kb. A succession of amplification waves involving different transposable element families led to contrasted sequence compositions between the proximal and distal regions. Finally, with an estimate of 50,000 genes per diploid genome, our data suggest that wheat may have a higher gene number than other cereals. Indeed, comparisons with rice (Oryza sativa) and Brachypodium revealed that a high number of additional noncollinear genes are interspersed within a highly conserved ancestral grass gene backbone, supporting the idea of an accelerated evolution in the Triticeae lineages.
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