Asellus aquaticus genome and VCF file from samples obtained on Gotland, Sweden

Organisms well suited for the study of ecotype formation have wide distribution ranges, where they adapt to multiple drastically different habitats repeatedly over space and time. Here we study such ecotypes in a Crustacean model, Asellus aquaticus, a commonly occurring isopod found in freshwater habitats as diverse as streams, caves and lakes. Previous studies focusing on cave versus surface ecotypes have attributed depigmentation, eye loss and prolonged antennae to several south European cave systems. Likewise, surveys across multiple Swedish lakes have identified the presence of dark-pigmented \"reed\" and light-pigmented \"stonewort\" ecotypes, which can be found within the same lake. In this study, we sequenced the first draft genome of A. aquaticus, and subsequently use this to map reads and call variants in surface stream, cave and two lake ecotypes. In addition, the draft genome was combined with a RADseq approach to perform a QTL mapping study using a laboratory bred F2 and F4 cave...

适合开展生态型形成（ecotype formation）研究的生物类群通常拥有广泛的分布范围，可在不同时空尺度下反复适应多种截然不同的栖息生境。本研究以甲壳动物（Crustacean）模型物种——水虱（Asellus aquaticus）为研究对象，该物种是广泛分布于溪流、洞穴与湖泊等多样淡水生境的等足类甲壳动物。此前针对洞穴与地表生态型的相关研究已证实，欧洲南部多个洞穴系统中的该类种群演化出了色素脱失、眼部退化以及触角延长的特征。与之类似，针对瑞典多个湖泊的调查发现，同一湖泊中同时存在深色素“芦苇”生态型与浅色素“轮藻”生态型。本研究首次完成了水虱（Asellus aquaticus）的全基因组草图测序，并以此为参考基因组比对测序读段（reads）、检出地表溪流、洞穴以及两种湖泊生态型种群的遗传变异。此外，本研究将该基因组草图与限制性位点关联DNA测序（RADseq，Restriction-site Associated DNA sequencing）技术相结合，利用实验室培育的F2及F4代洞穴种群开展数量性状基因座（QTL，Quantitative Trait Locus）定位研究。