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

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 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.

Novel genomic resources for shelled pteropods: a draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance

“…The high number of SNPs may be indicative of high levels of genetic variation, congruent with predictions for marine zooplankton with large population sizes [12]. The number of SNPs recovered (Table 4) and percentage of properly paired reads mapping uniquely to the targets (Table 3) are comparable to the results from a similar protocol on copepods [26].…”

“…However, RADseq protocols require between 50 ng and 1 μg of high-quality DNA, with higher amounts being recommended for better performance [24], and has faced substantial challenges in other planktonic organisms e.g. [25,26]. Furthermore, RADseq may not be cost efficient for species with large genomes [26].…”

“…[25,26]. Furthermore, RADseq may not be cost efficient for species with large genomes [26]. Target capture enrichment [27][28][29] overcomes this limitation in DNA starting amount and quality, by using single-stranded DNA probes to selectively hybridise to specific genomic regions that are then recovered and sequenced [30].…”

“…In this study, we designed target capture probes for the shelled pteropod Limacina bulimoides based on the method developed in Choquet et al [26], to address population genomic questions using a genome-wide approach. We obtained the draft genome of L. bulimoides to develop a set of target capture probes, and tested the success of these probes through the number of single nucleotide polymorphisms (SNPs) recovered in the focal species.…”

Insights from a general, full-likelihood Bayesian approach to inferring shared evolutionary events from genomic data: Inferring shared demographic events is challenging

“…For the mutation-scaled effective size of the descendant population (N D e µ), we used an offset gamma distribution with a shape of 4, offset of 0.0001, and mean of 0.0021 after accounting for the offset ( Table 2). The mean of this distribution corresponds to an average number of differences per character between individuals in the population (i.e., nucleotide diversity) of 0.0084, which is comparable to estimates from genomic data of populations of zooplankton (Choquet et al, 2019), stickleback fish (Hohenlohe et al, 2010), and humans (Auton et al, 2015). For the distribution of event times, we used a gamma distribution with a shape of 4, offset of 0.0001, and a mean of 0.002 (after accounting for the offset; Table 2).…”