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

• Published in: BMC genomics Vol. 21; no. 1; pp. 11 - 14
• Main Authors: Choo, Le Qin, Bal, Thijs M. P., Choquet, Marvin, Smolina, Irina, Ramos-Silva, Paula, Marlétaz, Ferdinand, Kopp, Martina, Hoarau, Galice, Peijnenburg, Katja T. C. A.
• Format: Journal Article
• Language: English
• Published: London BioMed Central 03.01.2020; BMC
• Subjects: Acidification; Animal Genetics and Genomics; Animals; Assembly; Biogeochemistry; Biomedical and Life Sciences; Deoxyribonucleic acid; Design; DNA; DNA probes; Environmental changes; Exon capture; Gastropoda - genetics; Gastropoda - metabolism; Gene expression; Genes; Genetic distance; Genetic diversity; Genome; Genome - genetics; Genomes; Genomic analysis; Genomics; Genomics - trends; Hydrogen-Ion Concentration; Indicator species; Life Sciences; Limacina bulimoides; Marine Biology; Marine ecosystems; Marine zooplankton; Microarrays; Microbial Genetics and Genomics; Mitochondria; Multicellular invertebrate genomics; Non-model organism; Nucleotides; Ocean acidification; Oceans and Seas; Phylogeny; Plant Genetics and Genomics; Polymorphism; Polymorphism, Single Nucleotide - genetics; Population; Probes; Proteomics; Research Article; Seawater - chemistry; Single-nucleotide polymorphism; Species; Species Specificity; Targeted sequencing; Transcriptome - genetics; Exon capture; Targeted sequencing; Genome; Marine zooplankton; Non-model organism
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-019-6372-z

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 genome-wide 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.