Li Wenli, Tucker Abraham E, Sung Way, Thomas W Kelley, Lynch Michael
Biology Department, Indiana University, Bloomington, IN 47405, USA.
Science. 2009 Nov 27;326(5957):1260-2. doi: 10.1126/science.1179302.
Rates and mechanisms of intron gain and loss have traditionally been inferred from alignments of highly conserved genes sampled from phylogenetically distant taxa. We report a population-genomic approach that detected 24 discordant intron/exon boundaries between the whole-genome sequences of two Daphnia pulex isolates. Sequencing of presence/absence loci across a collection of D. pulex isolates and outgroup Daphnia species shows that most polymorphisms are a consequence of recent gains, with parallel gains often occurring at the same locations in independent allelic lineages. More than half of the recent gains are associated with short sequence repeats, suggesting an origin via repair of staggered double-strand breaks. By comparing the allele-frequency spectrum of intron-gain alleles with that for derived single-base substitutions, we also provide evidence that newly arisen introns are intrinsically deleterious and tend to accumulate in population-genetic settings where random genetic drift is a relatively strong force.
传统上，内含子获得与丢失的速率和机制是通过对从系统发育关系较远的分类群中采样的高度保守基因进行比对来推断的。我们报告了一种群体基因组方法，该方法在两种蚤状溞分离株的全基因组序列之间检测到24个不一致的内含子/外显子边界。对一组蚤状溞分离株和外群蚤状溞物种的存在/缺失位点进行测序表明，大多数多态性是近期获得的结果，平行获得常常在独立等位基因谱系的相同位置发生。超过一半的近期获得与短序列重复相关，这表明其起源于交错双链断裂的修复。通过比较内含子获得等位基因与衍生单碱基替换的等位基因频率谱，我们还提供了证据表明新出现的内含子本质上是有害的，并且倾向于在随机遗传漂变是相对强大力量的群体遗传环境中积累。
