Towards population genomics in non-model species with large genomes: a case study of the marine zooplankton<i>Calanus finmarchicus</i>

Abstract

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 <i>Calanus finmarchicus</i> (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 <i>C. finmarchicus</i> including 62 372 in common among the three locations tested. The set of capture probes was also successfully applied to the congeneric <i>C. glacialis</i>. Preliminary analyses of these markers revealed similar levels of genetic diversity between the two <i>Calanus</i> species, while populations of <i>C. glacialis</i> showed stronger genetic structure compared to <i>C. finmarchicus</i>. Using this powerful set of markers, we did not detect any evidence of hybridization between <i>C. finmarchicus</i> and <i>C. glacialis</i>. Finally, we propose a shortened version of our protocol, offering a promising solution for population genomics studies in non-model species with large genomes.