Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus)

Abstract

Double digest restriction site-associated DNA sequencing (ddRADseq) and target capture sequencing methods are used to explore population and phylogenetic questions in non-model organisms. ddRADseq offers a simple and reliable protocol for population genomic studies, however it can result in a large amount of missing data due to allelic dropout. Target capture sequencing offers an opportunity to increase sequencing coverage with little missing data and consistent orthologous loci across samples, although this approach has generally been applied to conserved markers for deeper evolutionary questions. Here, we combine both methods to generate high quality sequencing data for population genomic studies of all marine lobster species from the genus Jasus. We designed probes based on ddRADseq libraries of two lobster species (Jasus edwardsii and Sagmariasus verreauxi) and evaluated the captured sequencing data in five other Jasus species. We validated 4,465 polymorphic loci amongst these species using a cost effective sequencing protocol, of which 1,730 were recovered from all species, and 4,026 were present in at least three species. The method was also successfully applied to DNA samples obtained from museum specimens. This data will be further used to assess spatial-temporal genetic variation in Jasus species found in the Southern Hemisphere.

Assessing changes in genomic divergence following a century of human‐mediated secondary contact among wild and captive‐bred ducks

“…For the 69 samples, a total of 2,202 markers (140,477 base pairs (bp) across the Z sex (99 markers; 6,122 bp) and 28 autosomal (2,103 markers; 134,355 bp) chromosomes (Figure ) passed quality filtering. Given an original bait‐capture array of 3,446 ddRAD‐seq loci, we were able to achieve a recovery rate of 64%, which is similar to reported recovery rates using RAD‐based bait arrays (Souza et al, ). Additionally, we succeeded with off‐target recovery of 641 base pairs of the mtDNA control region for 69 samples, with >90% of sites represented by >10× coverage.…”

“…Figure S1) passed quality filtering. Given an original bait-capture array of 3,446 ddRAD-seq loci, we were able to achieve a recovery rate of 64%, which is similar to reported recovery rates using RAD-based bait arrays (Souza et al, 2017).…”

Advancing our understanding of the connectivity, evolution and management of marine lobsters through genetics

“…Tanner et al 2017) -but there has been little progress in this area to date. Recently, target capture sequencing (based on probes developed from double digest restriction site-associated DNA sequencing [ddRADseq]) was demonstrated to be successful in capturing sequence data across all Jasus species and Sagmariasus (Souza et al 2017). Such targeted capture methods do not necessarily require samples with high quality DNA and will therefore likely enable sequencing of rare and difficult to obtain taxa held within museum collections.…”

“…So far, studies on lobsters have used molecular methods, such as RADseq, that do not 498 require reference genomes (e.g. Benestan et al 2015;Souza et al 2017;Villacorta-Rath et al 499 2018). Recent developments in bioinformatic tools such as assembly algorithms have 500 improved the de novo assembly quality and SNP calling for organisms lacking a reference genome (Davey et al 2011;Rochette and Catchen 2017).…”

Genome-wide sequencing uncovers cryptic diversity and mito-nuclear discordance in theOctopus vulgarisspecies complex

“…Despite these advantages for resolving phylogenetic relationships among closely related taxa, a shortcoming of RADseq studies is that an increase in phylogenetic distance also increases locus loss due to mutations at restriction sites 18,36 . However, complimenting ddRADseq with target capture sequencing has shown promise for addressing allelic dropout 42 .…”