Data from: Types, levels, and patterns of low-copy DNA sequence divergence, and phylogenetic implications, for Gossypium genome types

To explore types, levels, and patterns of genetic divergence among diploid Gossypium (cotton) genomes, 780 cDNA, genomic DNA, and SSR loci were re-sequenced in Gossypium herbaceum (A1 genome), G. arboreum (A2), G. raimondii (D5), G. trilobum (D8), G. sturtianum (C1) and an outgroup, Gossypioides kirkii. Divergence among these genomes ranged from 7.32 polymorphic base pairs per 100 between G. kirkii and G. herbaceum (A1) to only 1.44 between G. herbaceum (A1) and G. arboreum (A2). SSR loci are least conserved with 12.71 polymorphic base pairs and 3.77 polymorphic sites per 100 base pairs, while ESTs are most conserved with 3.96 polymorphic base pairs and 2.06 sites. SSR loci also exhibit the highest percentage of 'extended polymorphisms' (spanning multiple consecutive nucleotides). The A genome lineage was particularly rapidly evolving, with the D genome also showing accelerated evolution relative to the C genome. Unexpected asymmetry in mutation rates was found, with much more transition than transversion mutation in the D genome after its divergence from a common ancestor shared with the A genome. This large quantity of orthologous DNA sequence strongly supports a phylogeny in which A-C divergence is more recent than A-D divergence, a subject that is of much importance in view of A-D polyploid formation being key to the evolution of the most productive and finest-quality cottons. Loci that are monomorphic within A or D genome types, but polymorphic between genome types, may be of practical importance for identifying locus-specific DNA markers in tetraploid cottons including leading cultivars.

为探究二倍体棉属（Gossypium）基因组间遗传分化的类型、水平与模式，本研究针对草棉（Gossypium herbaceum，A1基因组）、树棉（G. arboreum，A2）、雷蒙德氏棉（G. raimondii，D5）、三裂叶棉（G. trilobum，D8）、斯特蒂安棉（G. sturtianum，C1）以及外类群柯氏桐棉（Gossypioides kirkii）的780个互补DNA（cDNA）、基因组DNA及简单重复序列（Simple Sequence Repeats, SSR）位点开展了重测序。上述基因组间的遗传分化水平介于每100碱基对7.32个多态性碱基对（柯氏桐棉与草棉A1之间）至1.44个多态性碱基对（草棉A1与树棉A2之间）之间。其中SSR位点的保守性最低，每100碱基对中存在12.71个多态性碱基对与3.77个多态性位点；而表达序列标签（Expressed Sequence Tags, ESTs）的保守性最优，对应数值分别为3.96个多态性碱基对与2.06个位点。此外，SSR位点还展现出最高比例的“延伸型多态性”（即跨越多个连续核苷酸的多态变异）。A基因组谱系的演化速率尤为迅捷，D基因组相较于C基因组也表现出演化加速的特征。研究还发现了意料之外的突变速率不对称现象：D基因组从与A基因组共享的共同祖先分化后，其转换突变的数量远多于颠换突变。本研究获取的大量直系同源DNA序列，有力支持了“A-C分化晚于A-D分化”的系统发育关系结论——鉴于A-D多倍体形成是高产优质棉花演化的核心关键，该议题具有重要研究价值。在A或D基因组类群内部呈单态、但在基因组类群间呈现多态性的位点，对于包括主栽品种在内的四倍体棉花的位点特异性DNA标记开发，具有重要的实际应用价值。