Supplementary material from "Towards population genomics in non-model species with large genomes; a case study of the marine zooplankton Calanus finmarchicus "

• Main Authors: Choquet, Marvin, Smolina, Irina, Anusha K. S. Dhanasiri, Blanco-Bercial, Leocadio, Kopp, Martina, Jueterbock, Alexander, Sundaram, Arvind Y. M., Galice Hoarau
• Format: Article in Journal/Newspaper
• Language: unknown
• Published: Figshare 2019
• Subjects: 60102 Bioinformatics; FOS Computer and information sciences; 60408 Genomics; FOS Biological sciences; Calanus finmarchicus
• Online Access: https://dx.doi.org/10.6084/m9.figshare.c.4382240; https://rs.figshare.com/collections/Supplementary_material_from_Towards_population_genomics_in_non-model_species_with_large_genomes_a_case_study_of_the_marine_zooplankton_i_Calanus_finmarchicus_i_/4382240

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.