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

Souza, Carla A., Murphy, Nicholas, Villacorta-Rath, Cecilia, Woodings, Laura N., Ilyushkina, Irina, Hernandez, Cristian E., Green, Bridget S., Bell, James J., and Strugnell, Jan (2017) Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus). Scientific Reports, 7 (1).

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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.

Item ID: 52244
Item Type: Article (Refereed Research - C1)
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ISSN: 2045-2322
Funders: Australian Research Council (ARC), Tasmanian Rock Lobster Fisherman's Association, Department of Primary Industries, Park Water and Environment, Seafood Innovations, New Zealand, New Zealand Rock Lobster Industry Council, Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil (CNPq), La Trobe University (LTU), Holsworth Wildlife Research Endowment, New South Wales Department of Primary Industries, IMAS
Projects and Grants: ARC Discovery Project grant DP150101491, ARC Linkage Project grant LP120200164, Fisheries Research & Development Corporation grant 2015-025, CNPq postdoctoral grant, LTU Securing, Food, Water and the Environment Grant
Date Deposited: 22 Mar 2018 05:14
FoR Codes: 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060411 Population, Ecological and Evolutionary Genetics @ 100%
SEO Codes: 83 ANIMAL PRODUCTION AND ANIMAL PRIMARY PRODUCTS > 8302 Fisheries - Wild Caught > 830206 Wild Caught Rock Lobster @ 100%
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