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...

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Autores principales:	Carla A. Souza, Nicholas Murphy, Cecilia Villacorta-Rath, Laura N. Woodings, Irina Ilyushkina, Cristian E. Hernandez, Bridget S. Green, James J. Bell, Jan M. Strugnell
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/985df6d530d54fd4be8c34cc2ba2999c
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spelling	oai:doaj.org-article:985df6d530d54fd4be8c34cc2ba2999c2021-12-02T11:52:20ZEfficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus)10.1038/s41598-017-06582-52045-2322https://doaj.org/article/985df6d530d54fd4be8c34cc2ba2999c2017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-06582-5https://doaj.org/toc/2045-2322Abstract 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.Carla A. SouzaNicholas MurphyCecilia Villacorta-RathLaura N. WoodingsIrina IlyushkinaCristian E. HernandezBridget S. GreenJames J. BellJan M. StrugnellNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-14 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Carla A. Souza Nicholas Murphy Cecilia Villacorta-Rath Laura N. Woodings Irina Ilyushkina Cristian E. Hernandez Bridget S. Green James J. Bell Jan M. Strugnell Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus)
description	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.
format	article
author	Carla A. Souza Nicholas Murphy Cecilia Villacorta-Rath Laura N. Woodings Irina Ilyushkina Cristian E. Hernandez Bridget S. Green James J. Bell Jan M. Strugnell
author_facet	Carla A. Souza Nicholas Murphy Cecilia Villacorta-Rath Laura N. Woodings Irina Ilyushkina Cristian E. Hernandez Bridget S. Green James J. Bell Jan M. Strugnell
author_sort	Carla A. Souza
title	Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus)
title_short	Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus)
title_full	Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus)
title_fullStr	Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus)
title_full_unstemmed	Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus)
title_sort	efficiency of ddrad target enriched sequencing across spiny rock lobster species (palinuridae: jasus)
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/985df6d530d54fd4be8c34cc2ba2999c
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Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus)

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