Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species - part1. Homarus americanus

Purpose: The goal of this study was to identify CNVs within SNPs data and examine adaptive population structure of American lobster populations using both SNPs and CNVs. Methods: DNA was extracted from samples collected on 1,141 wild female lobsters using muscle tissues from half of the second walking leg. Sequencing was done using a sequence capture approach so-called Rapture. The sequence capture step allows targetting a panel of informative and high quality RAD loci, which have been discovered and selected from an initial RADseq experiment. As such, these captured loci still represent a sampling of the genome-wide variation. Rapture thus represents a cost effective and flexible approach which allowed sequencing a large number of samples with a high sequencing depth, thereby enabling efficient generation of a large population genomic dataset. More specifically, we used the same 9,818 targeted loci previously used for the American lobster and all the details about the wet protocol are described in Dorant et al. (2019). All Rapture libraries were sequenced on the Ion Torrent p1v3 chip at the Plateforme d analyses genomiques of the Institute of Integrative and Systems Biology (IBIS, Universite Laval, Quebec, Canada). Two rounds of sequencing (i.e. two separated chips) were conducted for all Rapture libraries. Results: A total of 1,141 lobsters have been sequenced, yielding an average of 431 350 raw reads per sample.

本研究旨在对单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）数据中的拷贝数变异（Copy Number Variations, CNVs）进行鉴定，并结合SNPs与CNVs分析美洲龙虾种群的适应性群体结构。方法：从1141头野生雌性龙虾的第二步足一半肌肉组织中提取DNA。测序采用名为Rapture的序列捕获技术，该技术可靶向一组经初始限制性酶切位点相关DNA测序（Restriction-site Associated DNA sequencing, RADseq）实验筛选发掘的信息性、高质量RAD位点。此类捕获位点仍可表征全基因组变异的抽样情况。Rapture是一种兼具成本效益与灵活性的测序方案，可对大量样本开展高深度测序，从而高效构建大型群体基因组数据集。具体而言，本研究沿用了此前针对美洲龙虾开发的9818个靶向位点，湿实验流程的详细信息已在Dorant等人（2019）的研究中予以说明。所有Rapture文库均在加拿大魁北克拉瓦尔大学整合与系统生物学研究所（Institut de Biologie Intégrative et des Systèmes, IBIS）的基因组分析平台上，于Ion Torrent p1v3芯片上完成测序。所有Rapture文库均进行了两轮测序（即分两次使用测序芯片）。结果：共计完成1141头美洲龙虾的测序，每个样本平均获得431350条原始测序读段（reads）。