Page Justin T, Huynh Mark D, Liechty Zach S, Grupp Kara, Stelly David, Hulse Amanda M, Ashrafi Hamid, Van Deynze Allen, Wendel Jonathan F, Udall Joshua A
Biology Department, Brigham Young University, Provo, Utah 84602.
G3 (Bethesda). 2013 Oct 3;3(10):1809-18. doi: 10.1534/g3.113.007229.
Understanding the composition, evolution, and function of the Gossypium hirsutum (cotton) genome is complicated by the joint presence of two genomes in its nucleus (AT and DT genomes). These two genomes were derived from progenitor A-genome and D-genome diploids involved in ancestral allopolyploidization. To better understand the allopolyploid genome, we re-sequenced the genomes of extant diploid relatives that contain the A1 (Gossypium herbaceum), A2 (Gossypium arboreum), or D5 (Gossypium raimondii) genomes. We conducted a comparative analysis using deep re-sequencing of multiple accessions of each diploid species and identified 24 million SNPs between the A-diploid and D-diploid genomes. These analyses facilitated the construction of a robust index of conserved SNPs between the A-genomes and D-genomes at all detected polymorphic loci. This index is widely applicable for read mapping efforts of other diploid and allopolyploid Gossypium accessions. Further analysis also revealed locations of putative duplications and deletions in the A-genome relative to the D-genome reference sequence. The approximately 25,400 deleted regions included more than 50% deletion of 978 genes, including many involved with starch synthesis. In the polyploid genome, we also detected 1,472 conversion events between homoeologous chromosomes, including events that overlapped 113 genes. Continued characterization of the Gossypium genomes will further enhance our ability to manipulate fiber and agronomic production of cotton.
陆地棉（棉花）细胞核中同时存在两个基因组（AT和DT基因组），这使得了解其基因组的组成、进化和功能变得复杂。这两个基因组源自参与祖先异源多倍体化的A基因组和D基因组二倍体祖先。为了更好地理解异源多倍体基因组，我们对现存的包含A1（草棉）、A2（亚洲棉）或D5（雷蒙德氏棉）基因组的二倍体近缘种的基因组进行了重测序。我们对每个二倍体物种的多个样本进行深度重测序并进行了比较分析，在A二倍体和D二倍体基因组之间鉴定出2400万个单核苷酸多态性（SNP）。这些分析有助于在所有检测到的多态性位点构建A基因组和D基因组之间保守SNP的稳健索引。该索引广泛适用于其他二倍体和异源多倍体棉花样本的 reads 映射工作。进一步分析还揭示了相对于D基因组参考序列，A基因组中推定的重复和缺失位置。大约25400个缺失区域包括978个基因超过50%的缺失，其中许多基因与淀粉合成有关。在多倍体基因组中，我们还检测到1472个同源染色体之间的转换事件，包括与113个基因重叠的事件。对棉花基因组的持续表征将进一步提高我们对棉花纤维和农艺产量进行调控的能力。
