State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China.
USDA-ARS West Regional Research Center, Albany, CA 94710, USA; Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA.
J Genet Genomics. 2017 Jan 20;44(1):51-61. doi: 10.1016/j.jgg.2016.09.005. Epub 2016 Oct 5.
Bread wheat (Triticum aestivum, AABBDD) is an allohexaploid species derived from two rounds of interspecific hybridizations. A high-quality genome sequence assembly of diploid Aegilops tauschii, the donor of the wheat D genome, will provide a useful platform to study polyploid wheat evolution. A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path (MTP) of 3176 BAC clones from the short arm of Ae. tauschii chromosome 3 (At3DS). The final assembly of 135 super-scaffolds with an N50 of 4.2 Mb was used to build a 247-Mb pseudomolecule with a total of 2222 predicted protein-coding genes. Compared with the orthologous regions of rice, Brachypodium, and sorghum, At3DS contains 38.67% more genes. In comparison to At3DS, the short arm sequence of wheat chromosome 3B (Ta3BS) is 95-Mb large in size, which is primarily due to the expansion of the non-centromeric region, suggesting that transposable element (TE) bursts in Ta3B likely occurred there. Also, the size increase is accompanied by a proportional increase in gene number in Ta3BS. We found that in the sequence of short arm of wheat chromosome 3D (Ta3DS), there was only less than 0.27% gene loss compared to At3DS. Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome.
面包小麦（Triticum aestivum，AABBDD）是一种异源六倍体物种，由两轮种间杂交产生。二倍体节节麦（Aegilops tauschii）基因组序列的高质量组装，为研究多倍体小麦进化提供了一个有用的平台，节节麦是小麦 D 基因组的供体。我们采用 BAC 池和新一代测序技术相结合的方法，对来自节节麦 3 号染色体短臂的 3176 个 BAC 克隆的最小平铺路径（MTP）进行测序。最终组装得到 135 个超级支架，N50 为 4.2 Mb，用于构建一个 247 Mb 的假染色体，共包含 2222 个预测的蛋白编码基因。与水稻、短柄草和高粱的同源区域相比，At3DS 含有 38.67%更多的基因。与 At3DS 相比，小麦 3B 号染色体（Ta3BS）的短臂序列大小为 95 Mb，主要是由于非着丝粒区域的扩展，表明 Ta3B 中的转座元件（TE）爆发可能发生在那里。此外，大小的增加伴随着 Ta3BS 中基因数量的比例增加。我们发现，与 At3DS 相比，小麦 3D 号染色体短臂（Ta3DS）的序列中基因丢失不到 0.27%。我们的研究揭示了草类基因组的趋异进化，并为多倍体小麦基因组序列变化提供了新的见解。
