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

• Published in: Royal Society Open Science
• Main Authors: Choquet, Marvin, Smolina, Irina, Dhanasiri, Anusha K. S., Blanco-Bercial, Leocadio, Kopp, Martina, Jueterbock, Alexander, Sundaram, Arvind Y. M., Hoarau, Galice
• Other Authors: Norges Forskningsråd
• Format: Article in Journal/Newspaper
• Language: English
• Published: The Royal Society 2019
• Subjects: Multidisciplinary; Calanus finmarchicus
• Online Access: http://dx.doi.org/10.1098/rsos.180608; https://royalsocietypublishing.org/doi/pdf/10.1098/rsos.180608; https://royalsocietypublishing.org/doi/full-xml/10.1098/rsos.180608

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