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

Abstract

Background: Pteropods are planktonic gastropods that are considered as bio-indicators to monitor impacts of ocean acidification on marine ecosystems. In order to gain insight into their adaptive potential to future environmental changes, it is critical to use adequate molecular tools to delimit species and population boundaries and to assess their genetic connectivity. We developed a set of target capture probes to investigate genetic variation across their large-sized genome using a population genomics approach. Target capture is less limited by DNA amount and quality than other genome-reduced representation protocols, and has the potential for application on closely related species based on probes designed from one species. Results: We generated the first draft genome of a pteropod, Limacina bulimoides, resulting in a fragmented assembly of 2.9 Gbp. Using this assembly and a transcriptome as a reference, we designed a set of 2899 genomewide target capture probes for L. bulimoides. The set of probes includes 2812 single copy nuclear targets, the 28S rDNA sequence, ten mitochondrial genes, 35 candidate biomineralisation genes, and 41 non-coding regions. The capture reaction performed with these probes was highly efficient with 97% of the targets recovered on the focal species. A total of 137,938 single nucleotide polymorphism markers were obtained from the captured sequences across a test panel of nine individuals. The probes set was also tested on four related species: L. trochiformis, L. lesueurii, L. helicina, and Heliconoides inflatus, showing an exponential decrease in capture efficiency with increased genetic distance from the focal species. Sixty-two targets were sufficiently conserved to be recovered consistently across all five species. Conclusion: The target capture protocol used in this study was effective in capturing genome-wide variation in the focal species L. bulimoides, suitable for population genomic analyses, while providing insights into conserved genomic regions in related species. The present study provides new genomic resources for pteropods and supports the use of target capture-based protocols to efficiently characterise genomic variation in small non-model organisms with large genomes.

Oceanic dispersal barriers in a holoplanktonic gastropod

“…Holoplanktonic organisms are useful to gain insight into global biogeographical patterns in pelagic dispersal (Álvarez-Noriega et al, 2020;Bradbury et al, 2008), as their dispersal potential is not confounded by settlement processes that involve complex biophysical interactions with coastal or benthic habitats (Pineda et al, 2009;Prairie et al, 2012;Weersing & Toonen, 2009). To gain further insight into the nature and drivers of dispersal barriers in the open ocean, as well as to identify signals of selection across the genome, a broader range of ecological observations and in-depth analyses of genome-wide diversity in zooplankton will be necessary (Bucklin et al, 2018;Choo et al, 2020;Choquet et al, 2019;Gagnaire et al, 2015). This is important because marine zooplankton are key players in pelagic food webs and useful indicators as rapid responders to environmental variation and climate change (Beaugrand et al, 2009).…”

Sequencing of Transcriptome and Small RNA Revealed the Xenobiotic Metabolism-Related Genes and Potential Regulatory miRNA in Asian Tramp Snail

“…Mollusca is the second most species-rich phylum after Arthropoda in the animal kingdom, yet only a few genomic information has been published so far. For gastropods, the already sequenced genomes could be found in the sea hare A. californica ( Moroz et al, 2006 ); the freshwater snail B. glabrata ( Adema et al, 2017 ), Radix auricularia ( Schell et al, 2017 ), and Lymnaea stagnalis (unpublished; genome data are available in the NCBI database: GCA_900036025.1); the sea snail Patella vulgata ( Kenny et al, 2015 ), Conus tribblei ( Barghi et al, 2016 ), and L. gigantea ( Simakov et al, 2013 ); and the shelled pteropod Limacina bulimoides ( Choo et al, 2020 ). In this study, out of 23,481 annotated unigenes against the NR protein database, 13,775 unigenes (58%) have strong homology with A. californica .…”

Molluscan phylogenomics requires strategically selected genomes

“…Furthermore, some groups are currently only represented by highly fragmented, relatively incomplete genomes (e.g. pteropod gastropods represented by Limacina bulimoides with 60.2% BUSCO score and palaeoheterodont bivalves represented by Venustaconcha ellipsiformis with 68% BUSCO score, [33,34]) and would benefit from high-quality genome assemblies. We suggest that the main priority in selecting new genome sequencing projects should be to fill these gaps across Mollusca as a whole and to increase the taxon sampling group by group.…”