Contrasted patterns of organization and evolution of the wheat gene and transposable element spaces revealed by megabase level genome sequencing. PlantReSeq

To improve our understanding of the composition and evolution of the large (17 Gb) and complex hexaploid wheat genome and prepare for its future sequencing, we sequenced and annotated 13 Mb-sized contigs (18.2 Mb in total) originating from different regions of the largest wheat chromosome, 3B (1 Gb), and produced a 2x chromosome survey by shotgun Solexa sequencing. Analysis of this unique data set provided novel insights into the gene and Transposable Element (TE) distribution and illustrated the potential of a high quality annotated genome for unlimited marker development to support molecular breeding. All BAC contigs carried genes irrespective of their chromosomal location. However, gene distribution was not random with 75% of the genes clustered into small islands containing 3 genes on average and a maximum of 800 kb of gene-less region. Analyses indicated a 2-fold increase of gene density towards the telomeres likely due to high tandem and interchromosomal duplication activities. Most of the TEs were found complete but highly nested and spread over distances as large as 200 kb. Furthermore, a succession of amplification waves involving different TE families led to contrasted sequence compositions between the proximal and distal regions of the chromosome. With an estimate of 50,000 genes per diploid genome, wheat may carry a higher gene number than other cereals. Comparisons with rice and Brachypodium distachyon revealed that these additional non collinear genes are interspersed within a very conserved ancestral grass gene backbone supporting the idea of an accelerated evolution in the Triticeae lineages.

为加深对大型（17 Gb）且结构复杂的六倍体小麦基因组的组成与演化机制的理解，并为其后续测序工作做好筹备，我们对源自小麦最大染色体3B（总长1 Gb）不同区域的13 Mb级重叠群（总长度18.2 Mb）开展了测序与注释，并通过鸟枪法Solexa测序完成了2倍染色体覆盖度的调查测序。对这一独特数据集的分析，为基因与转座因子（Transposable Element, TE）的分布模式提供了全新认知，同时证实了高质量注释基因组可用于开发无限量分子标记以支撑分子育种的应用潜力。
所有细菌人工染色体（Bacterial Artificial Chromosome, BAC）重叠群均携带基因，与其所在染色体位置无关。但基因的分布并非随机：75%的基因聚集于小型基因岛中，平均每个基因岛包含3个基因，且存在最长达800 kb的无基因间隔区域。分析结果显示，向染色体端粒方向的基因密度提升了一倍，这一现象可能源于高水平的串联复制与染色体间复制活动。
绝大多数转座因子保持完整结构，但呈现高度嵌套状态，且分布跨度可达200 kb。此外，涉及不同转座因子家族的多轮扩增浪潮，导致染色体近端与远端区域的序列组成存在显著差异。
据估算，二倍体小麦基因组约含50 000个基因，其基因数量或高于其他谷类作物。与水稻及二穗短柄草（Brachypodium distachyon）的比较分析显示，这些额外的非共线性基因散布于高度保守的禾本科祖先基因骨架中，这一结果支持了小麦族（Triticeae）类群演化速率加快的观点。