Choquet Marvin, Smolina Irina, Dhanasiri Anusha K S, Blanco-Bercial Leocadio, Kopp Martina, Jueterbock Alexander, Sundaram Arvind Y M, Hoarau Galice
Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
Bermuda Institute of Ocean Sciences, St George's, Bermuda.
R Soc Open Sci. 2019 Feb 13;6(2):180608. doi: 10.1098/rsos.180608. eCollection 2019 Feb.
Advances in next-generation sequencing technologies and the development of genome-reduced representation protocols have opened the way to genome-wide population studies in non-model species. However, species with large genomes remain challenging, hampering the development of genomic resources for a number of taxa including marine arthropods. Here, we developed a genome-reduced representation method for the ecologically important marine copepod (haploid genome size of 6.34 Gbp). We optimized a capture enrichment-based protocol based on 2656 single-copy genes, yielding a total of 154 087 high-quality SNPs in including 62 372 in common among the three locations tested. The set of capture probes was also successfully applied to the congeneric . Preliminary analyses of these markers revealed similar levels of genetic diversity between the two species, while populations of showed stronger genetic structure compared to . Using this powerful set of markers, we did not detect any evidence of hybridization between and . Finally, we propose a shortened version of our protocol, offering a promising solution for population genomics studies in non-model species with large genomes.
新一代测序技术的进步以及基因组简化表征方案的发展，为非模式物种的全基因组群体研究开辟了道路。然而，具有大基因组的物种仍然具有挑战性，阻碍了包括海洋节肢动物在内的许多分类群的基因组资源开发。在此，我们为具有重要生态意义的海洋桡足类动物（单倍体基因组大小为6.34 Gbp）开发了一种基因组简化表征方法。我们基于2656个单拷贝基因优化了一种基于捕获富集的方案，在三个测试地点共产生了154087个高质量单核苷酸多态性（SNP），其中62372个是共同的。该捕获探针集也成功应用于同属物种。对这些标记的初步分析显示，两个物种之间的遗传多样性水平相似，而与相比，的种群显示出更强的遗传结构。使用这一强大的标记集，我们没有检测到与之间杂交的任何证据。最后，我们提出了我们方案的一个简化版本，为具有大基因组的非模式物种的群体基因组学研究提供了一个有前景的解决方案。
