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

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Souza, CA, Murphy, N, Villacorta-Rath, C, Woodings, LN, Ilyushkina, I, Hernandez, CE, Green, BS ORCID: 0000-0001-8214-6430, Bell, JJ and Strugnell, JM 2017 , 'Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus)' , Scientific Reports, vol. 7 , pp. 1-14 , doi: 10.1038/s41598-017-06582-5.

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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 Type: Article
Authors/Creators:Souza, CA and Murphy, N and Villacorta-Rath, C and Woodings, LN and Ilyushkina, I and Hernandez, CE and Green, BS and Bell, JJ and Strugnell, JM
Keywords: genetic markers, genetic variation, marine biology, targeted resequencing, spiny rock lobster, ddRAD, Palinuridae
Journal or Publication Title: Scientific Reports
Publisher: Nature Publishing Group
ISSN: 2045-2322
DOI / ID Number: 10.1038/s41598-017-06582-5
Copyright Information:

Copyright 2016 The AuthorsLicensed under Creative Commons Attribution 4.0 International (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/

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