Data from: 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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AbstractLatest 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 10 415 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 FST 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., Usage notesPython scripts - File formatting - Sequence CaptureAll relevant scripts used to format files, analyse data and obtain results from sequence capture experiment on two sympatric populations of whitefish ecotypes in the process of speciation.MEC-13-0265_seq-capt.tar.gzWhitefish sequence capture assemblyFasta file containing 2,228 genes de novo assembled after conducting a targeted enrichment and re-sequencing experiment on two sympatric populations of whitefish (Coregonus clupeaformis) currently in the process of speciation.assembled_genes.fasta
摘要 进化生物学领域的最新技术进展，为解析物种分化过程中复杂的遗传结构带来了全新挑战。湖白鲑的同域种群正是研究该科学问题的关键模式系统之一。尽管随机基因型分型测序方法与测序技术成本的不断降低为相关研究提供了便利，但对编码区变异的解析仍存在诸多难点，尤其对于鲑科这类近期发生全基因组复制的类群而言，全基因组重测序会大幅提升分析复杂度。为此，我们设计了一款靶向2773个注释基因的序列捕获芯片，以解析同域分布的矮型白鲑与正常型白鲑之间的基因组分化特征与分化程度。在成功捕获的2728个基因中，经初步基础过滤后，共鉴定出2182个编码区与10415个非编码区的推定单核苷酸多态性位点（single-nucleotide polymorphisms, SNPs）。基于2203个经过质量优化筛选的SNPs开展全基因组扫描，在210个候选基因中鉴定出267个异常分化SNPs，这些位点所在的基因组区域可能与白鲑的物种分化及生殖隔离相关。研究发现不同SNP位点的FST估值存在高度异质性；编码区多态性整体处于较低水平，且异常分化位点中非编码突变占主导。不同位点间的分化模式异质性证实了在存在基因流的物种形成过程中，基因组具有多孔性特征。鉴于仅有少量蛋白编码突变被鉴定为高度分化，结合此前的转录组学研究，本研究结果表明，调控区域的变异相较于蛋白编码突变，在白鲑种群分化过程中可能发挥了更为关键的作用。本研究首次证明，对于基因组庞大且尚未完成全基因组测序的非模式物种而言，大规模靶向重测序技术具备良好的应用效能。 使用说明 Python脚本 文件格式化 序列捕获实验相关脚本 本研究针对正处于物种形成过程中的两种同域分布白鲑生态型开展序列捕获实验，所有用于文件格式化、数据分析及结果获取的相关Python脚本均包含于此。 MEC-13-0265_seq-capt.tar.gz 白鲑序列捕获组装文件 该FASTA文件包含了2228个从头组装的基因序列，这些基因来自针对两种正处于物种形成过程中的同域分布白鲑（Coregonus clupeaformis）开展的靶向富集与重测序实验。 assembled_genes.fasta
