Max-Planck Institute for Developmental Biology, Department for Evolutionary Biology, Spemannstrasse 37, D-72076 Tübingen, Germany.
G3 (Bethesda). 2012 Sep;2(9):1027-34. doi: 10.1534/g3.112.003129. Epub 2012 Sep 1.
Modern evolutionary biology requires integrative approaches that combine life history, population structure, ecology, and development. The nematode Pristionchus pacificus has been established as a model system in which these aspects can be studied in one organism. P. pacificus has well-developed genetic, genomic, and transgenic tools and its ecologic association with scarab beetles is well described. A recent study provided first mutation rate estimates based on mitochondrial genome sequencing and mutation accumulation line experiments that help resolve rather ancient evolutionary branches. Here, we analyzed the tandem-repeat pattern and studied spontaneous mutation rates for microsatellite markers by using the previously generated mutation accumulation lines. We found that 0.59%-3.83% of the genome is composed of short tandem repeats. We developed 41 microsatellite markers, randomly chosen throughout the genome and analyzed them in 82 mutation accumulation lines after 142 generations. A total of 31 mutations were identified in these lines. There was a strong correlation between allele size and mutation rate in P. pacificus, similar to Caenorhabditis elegans. In contrast to C. elegans, however, there is no evidence for a bias toward multistep mutations. The mutation spectrum of microsatellite loci in P. pacificus shows more insertions than deletions, indicating a tendency toward lengthening, a process that might have contributed to the increase in genome size. The mutation rates obtained for individual microsatellite markers provide guidelines for divergence time estimates that can be applied in P. pacificus next-generation sequencing approaches of wild isolates.
现代进化生物学需要综合的方法，将生活史、种群结构、生态学和发育结合起来。秀丽隐杆线虫（Pristionchus pacificus）已被确立为一个模型系统，可以在一个生物体中研究这些方面。秀丽隐杆线虫具有发达的遗传、基因组和转基因工具，其与金龟子科甲虫的生态联系也得到了很好的描述。最近的一项研究提供了基于线粒体基因组测序和突变积累系实验的第一个突变率估计值，这有助于解决相当古老的进化分支问题。在这里，我们分析了串联重复模式，并使用先前产生的突变积累系研究了微卫星标记的自发突变率。我们发现，基因组的 0.59%-3.83%由短串联重复组成。我们开发了 41 个微卫星标记，随机选择整个基因组，并在 142 代后分析了 82 个突变积累系中的这些标记。在这些系中总共鉴定出 31 个突变。秀丽隐杆线虫的等位基因大小与突变率之间存在很强的相关性，类似于秀丽隐杆线虫（Caenorhabditis elegans）。然而，与秀丽隐杆线虫不同的是，没有证据表明存在多步突变的偏向性。微卫星位点在秀丽隐杆线虫中的突变谱显示插入多于缺失，表明存在变长的趋势，这一过程可能导致了基因组大小的增加。个别微卫星标记的突变率为提供了在 P. pacificus 下一代测序方法中应用于野生分离株的分歧时间估计的指导方针。
