Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis)
Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis)
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DOI：
10.1111/mec.12447
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发表时间：
2013-10-01
影响因子：
4.9
通讯作者：
Bernatchez, Louis
中科院分区：
文献类型：
--
作者：
Hebert, Francois Olivier;Renaut, Sebastien;Bernatchez, Louis
进化生物学的最新技术发展为记录物种分化过程中复杂的遗传结构带来了新的挑战。湖白鱼的同域种群是研究这一问题的关键系统之一。尽管随机基因型测序方法的价值和测序技术成本的降低，但研究编码区域的变异仍然具有挑战性，特别是在最近重复基因组的情况下，如鲑鱼，因为这极大地复杂化了全基因组重测序。因此，我们设计了一个针对2773个注释基因的序列捕获阵列，以记录同域侏儒鱼和正常白鱼之间基因组差异的性质和程度。在成功捕获的2728个基因中，应用第一组基本过滤器共鉴定出2182个编码单核苷酸多态性和10415个非编码推定单核苷酸多态性。通过对2203个snp进行高质量筛选的基因组扫描，在210个候选基因中发现了267个异常snp，这些候选基因位于可能与白鱼分化和生殖隔离有关的基因组区域。我们发现SNP位点之间的F-ST估计高度异质。总体上编码多态性水平较低，非编码突变在异常值中占主导地位。基因座间差异的异质性模式证实了基因组在基因流动的物种形成过程中的多孔性。考虑到很少有蛋白质编码突变被鉴定为高度分化，我们的研究结果以及之前的转录组学研究表明，在白鱼种群分化过程中，调控区域的变化很可能比蛋白质编码突变发挥更大的作用。这项研究首次证明了对具有如此大且未测序基因组的非模式物种进行大规模靶向重测序的效率。
Latest technological developments in evolutionary biology bring new challenges in documenting the intricate genetic architecture of species in the process of divergence. Sympatric populations of lake whitefish represent one of the key systems to investigate this issue. Despite the value of random genotype-by-sequencing methods and decreasing cost of sequencing technologies, it remains challenging to investigate variation in coding regions, especially in the case of recently duplicated genomes as in salmonids, as this greatly complicates whole genome resequencing. We thus designed a sequence capture array targeting 2773 annotated genes to document the nature and the extent of genomic divergence between sympatric dwarf and normal whitefish. Among the 2728 genes successfully captured, a total of 2182 coding and 10415 noncoding putative single-nucleotide polymorphisms (SNPs) were identified after applying a first set of basic filters. A genome scan with a quality-refined selection of 2203 SNPs identified 267 outlier SNPs in 210 candidate genes located in genomic regions potentially involved in whitefish divergence and reproductive isolation. We found highly heterogeneous F-ST estimates among SNP loci. There was an overall low level of coding polymorphism, with a predominance of noncoding mutations among outliers. The heterogeneous patterns of divergence among loci confirm the porous nature of genomes during speciation with gene flow. Considering that few protein-coding mutations were identified as highly divergent, our results, along with previous transcriptomic studies, imply that changes in regulatory regions most likely had a greater role in the process of whitefish population divergence than protein-coding mutations. This study is the first to demonstrate the efficiency of large-scale targeted resequencing for a nonmodel species with such a large and unsequenced genome.