Journal article
Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces
The Plant cell, Vol.22(6), pp.1686-1701
2010
Handle:
https://hdl.handle.net/2376/114027
PMCID: PMC2910976
PMID: 20581307
Abstract
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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Details
- Title
- Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces
- Creators
- Frédéric Choulet - Génétique Diversité et Ecophysiologie des CéréalesThomas Wicker - Institute of Plant BiologyCamille Rustenholz - Génétique Diversité et Ecophysiologie des CéréalesEtienne Paux - Génétique Diversité et Ecophysiologie des CéréalesJerome Salse - Génétique Diversité et Ecophysiologie des CéréalesPhilippe Leroy - Génétique Diversité et Ecophysiologie des CéréalesStéphane Schlub - Etude du Polymorphisme des Génomes VégétauxMarie-Christine Le Paslier - Etude du Polymorphisme des Génomes VégétauxGhislaine Magdelenat - Genoscope - Centre national de séquençage [Evry]Catherine Gonthier - Genoscope - Centre national de séquençage [Evry]Arnaud Couloux - Genoscope - Centre national de séquençage [Evry]Hikmet Budak - Engineering and Natural Sciences, Biological Science and Bioengineering ProgramJames Breen - Centre for Comparative GenomicsMichael Pumphrey - Department of Plant Pathology, Wheat Genetic and Genomic Resources CenterSixin Liu - Department of Agronomy and Plant GeneticsXiuying Kong - National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture Institute of Crop ScienceJizeng Jia - National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture Institute of Crop ScienceMarta Gut - Centre National de GénotypageDominique Brunel - Etude du Polymorphisme des Génomes VégétauxJames Anderson - Department of Agronomy and Plant GeneticsBikram Gill - Department of Plant Pathology, Wheat Genetic and Genomic Resources CenterRudi Appels - Centre for Comparative GenomicsBeat Keller - Institute of Plant BiologyCatherine Feuillet - Génétique Diversité et Ecophysiologie des Céréales
- Publication Details
- The Plant cell, Vol.22(6), pp.1686-1701
- Academic Unit
- Crop and Soil Sciences, Department of
- Publisher
- American Society of Plant Biologists (ASPB)
- Identifiers
- 99900547654201842
- Language
- English
- Resource Type
- Journal article