Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA.
BMC Evol Biol. 2011 Jun 16;11:168. doi: 10.1186/1471-2148-11-168.
Genome wide analysis of variation within a species can reveal the evolution of fundamental biological processes such as mutation, recombination, and natural selection. We compare genome wide sequence differences between two independent isolates of the nematode Caenorhabditis elegans (CB4856 and CB4858) and the reference genome (N2).
The base substitution pattern when comparing N2 against CB4858 reveals a transition over transversion bias (1.32:1) that is not present in CB4856. In CB4856, there is a significant bias in the direction of base substitution. The frequency of A or T bases in N2 that are G or C bases in CB4856 outnumber the opposite frequencies for transitions as well as transversions. These differences were not observed in the N2/CB4858 comparison. Similarly, we observed a strong bias for deletions over insertions in CB4856 (1.44: 1) that is not present in CB4858. In both CB4856 and CB4858, there is a significant correlation between SNP rate and recombination rate on the autosomes but not on the X chromosome. Furthermore, we identified numerous significant hotspots of variation in the CB4856-N2 comparison.In both CB4856 and CB4858, based on a measure of the strength of selection (ka/ks), all the chromosomes are under negative selection and in CB4856, there is no difference in the strength of natural selection in either the autosomes versus X or between any of the chromosomes. By contrast, in CB4858, ka/ks values are smaller in the autosomes than in the X chromosome. In addition, in CB4858, ka/ks values differ between chromosomes.
The clear bias of deletions over insertions in CB4856 suggests that either the CB4856 genome is becoming smaller or the N2 genome is getting larger. We hypothesize the hotspots found represent alleles that are shared between CB4856 and CB4858 but not N2. Because the ka/ks ratio in the X chromosome is higher than the autosomes on average in CB4858, purifying selection is reduced on the X chromosome.
对物种内变异的全基因组分析可以揭示突变、重组和自然选择等基本生物学过程的演化。我们比较了两个独立的秀丽隐杆线虫（CB4856 和 CB4858）品系与参考基因组（N2）之间的全基因组序列差异。
将 N2 与 CB4858 进行比较时，碱基取代模式显示转换超过颠换的偏向性（1.32:1），而在 CB4856 中不存在这种偏向性。在 CB4856 中，碱基取代的方向存在显著偏向性。在 N2 中，A 或 T 碱基变成 G 或 C 碱基的频率超过了转换和颠换的相反频率。在 N2/CB4858 的比较中没有观察到这些差异。同样，我们观察到 CB4856 中缺失相对于插入的强烈偏向性（1.44:1），而在 CB4858 中不存在这种偏向性。在 CB4856 和 CB4858 中，常染色体上 SNP 率和重组率之间存在显著相关性，但在 X 染色体上不存在。此外，我们在 CB4856-N2 比较中鉴定出许多显著的变异热点。在 CB4856 和 CB4858 中，基于选择强度的度量（ka/ks），所有染色体都受到负选择的影响，而在 CB4856 中，常染色体与 X 染色体之间或任何染色体之间的自然选择强度没有差异。相比之下，在 CB4858 中，常染色体上的 ka/ks 值小于 X 染色体上的 ka/ks 值。此外，在 CB4858 中，染色体之间的 ka/ks 值存在差异。
CB4856 中缺失相对于插入的明显偏向性表明，要么 CB4856 基因组正在变小，要么 N2 基因组正在变大。我们假设发现的热点代表了 CB4856 和 CB4858 之间共享但与 N2 不共享的等位基因。由于 CB4858 中 X 染色体上的 ka/ks 比值平均高于常染色体，因此 X 染色体上的纯化选择减少。
