Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces
Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces
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DOI：
10.1105/tpc.110.074187
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发表时间：
2010-06-01
期刊：
影响因子：
11.6
通讯作者：
Feuillet, Catherine
中科院分区：
文献类型：
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作者：
Choulet, Frederic;Wicker, Thomas;Feuillet, Catherine
为了加深对小麦 (Triticum aestivum) 基因组的组织和进化的理解，我们对源自其最大染色体 3B (1 Gb) 不同区域的 13 Mb 重叠群 (18.2 Mb) 进行了测序和注释，并通过霰弹枪 Illumina/Solexa 测序进行了 2x 染色体调查。所有区域都携带基因，无论其染色体位置如何。然而，基因分布并不是随机的，75%的基因聚集成平均含有3个基因的小岛。观察到端粒基因密度增加了一倍，这可能是由于高串联和染色体间重复事件所致。共鉴定出3222个转座因子，其中包括800个新家族。其中大多数都是完整的，但显示出高度嵌套的结构，分布距离长达 200 kb。涉及不同转座元件家族的一系列放大波导致近端和远端区域之间形成对比的序列组成。最后，根据每个二倍体基因组估计 50,000 个基因，我们的数据表明小麦可能比其他谷物具有更高的基因数量。事实上，与水稻（Oryza sativa）和短柄草的比较表明，高度保守的祖先草基因主干中散布着大量额外的非共线基因，支持了小麦科谱系加速进化的想法。
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.