Genomic evidence of population genetic differentiation in deep-sea squat lobster Shinkaia crosnieri (crustacea: Decapoda: Anomura) from Northwestern Pacific hydrothermal vent and cold seep
Genomic evidence of population genetic differentiation in deep-sea squat lobster Shinkaia crosnieri (crustacea: Decapoda: Anomura) from Northwestern Pacific hydrothermal vent and cold seep
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西北太平洋热液喷口和冷泉深海蹲龙虾 Shinkaia crosnieri（甲壳纲：十足目：Anomura）种群遗传分化的基因组证据
DOI：
10.1016/j.dsr.2019.103188
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发表时间：
2020-02-01
影响因子：
2.4
通讯作者：
Sha, Zhongli
中科院分区：
文献类型：
--
作者：
Cheng, Jiao;Hui, Min;Sha, Zhongli
galatheid蹲龙虾，Shinkaia crosnieri Baba和威廉姆斯，1998年，是既居住在深海热液喷口又居住在冷泉的少数优势物种之一。本研究以线粒体细胞色素c氧化酶亚基I（mtDNA COI）和核基因组单核苷酸多态性（SNP）为遗传标记，研究了S.中国南海冲绳热液喷口和冷渗漏的crosnieri种群。线粒体COI序列分析表明，深海喷口的S. crosnieri与冷泉居群在遗传上存在差异。为了深入了解驱动这种遗传断裂的进化力量，我们进行了限制性位点相关DNA分析，以评估S. crosnieri居住在这两种环境中的全基因组规模，并评估选择过程中塑造这种模式的作用。利用组装的S. crosnieri作为参考，在30个S. crosnieri标本。基于SNPs的结构和主成分分析支持喷口和渗漏种群之间的遗传分化。S. crosnieri群体的确认，通过使用F-sT为基础的离群值测试，这导致54个潜在的本地选择的SNP，表明自然选择作为该物种的遗传分化的驱动因素的重要作用，确定增加的人口分歧。进一步的研究表明，含有异常SNPs的候选基因参与了多种生物学过程，包括免疫、转座子和代谢过程。总的来说，我们的研究结果表明，在喷口和渗漏S之间存在显着的遗传差异。crosnieri种群在西北太平洋的分布，并为了解潜在的遗传基础提供了线索。crosnieri在殖民到深海化学合成生态系统。
The galatheid squat lobster, Shinkaia crosnieri Baba and Williams, 1998, is one of the few dominant species inhabiting both deep-sea hydrothermal vents and cold seeps. Here, we used mitochondrial cytochrome c oxidase subunit I (mtDNA COI) and nuclear genome-wide single nucleotide polymorphism (SNP) as genetic markers to investigate genetic connectivity of S. crosnieri populations from a hydrothermal vent of Okinawa Through and a cold seep of the South China Sea. MtDNA COI sequence analyses indicated that deep-sea vent population of S. crosnieri was genetically divergent from cold seep population. To obtain deep insights into the evolutionary forces driving this genetic break, we performed restriction-site associated DNA analysis to evaluate the extent of genetic differentiation in S. crosnieri inhabiting both environments on a genome-wide scale, and to assess the role of selective processes in shaping this pattern. Using the assembled survey genome of S. crosnieri as a reference, 12,963 SNPs were identified for 30 S. crosnieri specimens. The structural and principle component analyses based on SNPs supported genetic differentiation between the vent and seep populations. Evidence for local adaptation of S. crosnieri populations was confirmed by identifying increased population divergence using F-sT-based outlier tests, which resulted in 54 potentially locally selected SNPs, indicative of an important role for natural selection as a driver of genetic divergence in this species. Further studies revealed that candidate genes containing outlier SNPs were involved in diverse biological processes, including immunity, transposon and metabolic processes. Overall, our results demonstrated significant genetic divergence between the vent and seep S. crosnieri populations in the Northwestern Pacific and provided clues to understand potential genetic basis underlying local adaptation in S. crosnieri during colonization into deep-sea chemosynthetic ecosystems.