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，棉花）基因组间遗传分化的类型、水平与模式，本研究对草棉（Gossypium herbaceum，A1基因组）、树棉（Gossypium arboreum，A2）、雷蒙德氏棉（Gossypium raimondii，D5）、三裂棉（Gossypium trilobum，D8）、斯特提棉（Gossypium sturtianum，C1）以及外类群柯氏拟棉（Gossypioides kirkii）的780个cDNA、基因组DNA及简单序列重复（Simple Sequence Repeat，SSR）位点进行了重测序。上述基因组间的遗传分化程度介于每100个碱基对中7.32个多态性碱基（柯氏拟棉与草棉A1基因组间）至仅1.44个（草棉A1基因组与树棉A2基因组间）。简单序列重复位点的保守性最差，每100个碱基对中存在12.71个多态性碱基与3.77个多态位点；而表达序列标签（Expressed Sequence Tag，EST）的保守性最强，对应数值分别为3.96个多态性碱基与2.06个多态位点。简单序列重复位点同时拥有最高比例的"延伸型多态性"（即跨越多个连续核苷酸的多态性）。A基因组谱系的演化速度尤为迅速，而相较于C基因组，D基因组的演化速率也有所加快。研究发现了突变速率的意外不对称性：在D基因组与A基因组的共同祖先分化后，D基因组中的转换突变远多于颠换突变。该批量直系同源DNA序列强有力地支持了如下系统发育关系：A-C基因组的分化时间晚于A-D基因组分化时间。鉴于A-D多倍体的形成是培育高产优质棉花的关键演化事件，这一结论具有重要研究价值。在A或D基因组类群内呈单态、但在基因组类群间呈多态的位点，对于在包括主栽品种在内的四倍体棉花中鉴定位点特异性DNA标记具有实际应用价值。