Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus).

Transcriptome-based exon capture approaches, along with next-generation sequencing, are allowing for the rapid and cost-effective production of extensive and informative phylogenomic datasets from non-model organisms for phylogenetics and population genetics research. These approaches generally empl...

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Autores principales:	Danielle N Stringer, Terry Bertozzi, Karen Meusemann, Steven Delean, Michelle T Guzik, Simon M Tierney, Christoph Mayer, Steven J B Cooper, Mohammad Javidkar, Andreas Zwick, Andrew D Austin
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c18d713e7e274d9aa5dd419474a275c4
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spelling	oai:doaj.org-article:c18d713e7e274d9aa5dd419474a275c42021-12-02T20:14:33ZDevelopment and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus).1932-620310.1371/journal.pone.0256861https://doaj.org/article/c18d713e7e274d9aa5dd419474a275c42021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0256861https://doaj.org/toc/1932-6203Transcriptome-based exon capture approaches, along with next-generation sequencing, are allowing for the rapid and cost-effective production of extensive and informative phylogenomic datasets from non-model organisms for phylogenetics and population genetics research. These approaches generally employ a reference genome to infer the intron-exon structure of targeted loci and preferentially select longer exons. However, in the absence of an existing and well-annotated genome, we applied this exon capture method directly, without initially identifying intron-exon boundaries for bait design, to a group of highly diverse Haloniscus (Philosciidae), paraplatyarthrid and armadillid isopods, and examined the performance of our methods and bait design for phylogenetic inference. Here, we identified an isopod-specific set of single-copy protein-coding loci, and a custom bait design to capture targeted regions from 469 genes, and analysed the resulting sequence data with a mapping approach and newly-created post-processing scripts. We effectively recovered a large and informative dataset comprising both short (<100 bp) and longer (>300 bp) exons, with high uniformity in sequencing depth. We were also able to successfully capture exon data from up to 16-year-old museum specimens along with more distantly related outgroup taxa, and efficiently pool multiple samples prior to capture. Our well-resolved phylogenies highlight the overall utility of this methodological approach and custom bait design, which offer enormous potential for application to future isopod, as well as broader crustacean, molecular studies.Danielle N StringerTerry BertozziKaren MeusemannSteven DeleanMichelle T GuzikSimon M TierneyChristoph MayerSteven J B CooperMohammad JavidkarAndreas ZwickAndrew D AustinPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 9, p e0256861 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Danielle N Stringer Terry Bertozzi Karen Meusemann Steven Delean Michelle T Guzik Simon M Tierney Christoph Mayer Steven J B Cooper Mohammad Javidkar Andreas Zwick Andrew D Austin Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus).
description	Transcriptome-based exon capture approaches, along with next-generation sequencing, are allowing for the rapid and cost-effective production of extensive and informative phylogenomic datasets from non-model organisms for phylogenetics and population genetics research. These approaches generally employ a reference genome to infer the intron-exon structure of targeted loci and preferentially select longer exons. However, in the absence of an existing and well-annotated genome, we applied this exon capture method directly, without initially identifying intron-exon boundaries for bait design, to a group of highly diverse Haloniscus (Philosciidae), paraplatyarthrid and armadillid isopods, and examined the performance of our methods and bait design for phylogenetic inference. Here, we identified an isopod-specific set of single-copy protein-coding loci, and a custom bait design to capture targeted regions from 469 genes, and analysed the resulting sequence data with a mapping approach and newly-created post-processing scripts. We effectively recovered a large and informative dataset comprising both short (<100 bp) and longer (>300 bp) exons, with high uniformity in sequencing depth. We were also able to successfully capture exon data from up to 16-year-old museum specimens along with more distantly related outgroup taxa, and efficiently pool multiple samples prior to capture. Our well-resolved phylogenies highlight the overall utility of this methodological approach and custom bait design, which offer enormous potential for application to future isopod, as well as broader crustacean, molecular studies.
format	article
author	Danielle N Stringer Terry Bertozzi Karen Meusemann Steven Delean Michelle T Guzik Simon M Tierney Christoph Mayer Steven J B Cooper Mohammad Javidkar Andreas Zwick Andrew D Austin
author_facet	Danielle N Stringer Terry Bertozzi Karen Meusemann Steven Delean Michelle T Guzik Simon M Tierney Christoph Mayer Steven J B Cooper Mohammad Javidkar Andreas Zwick Andrew D Austin
author_sort	Danielle N Stringer
title	Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus).
title_short	Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus).
title_full	Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus).
title_fullStr	Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus).
title_full_unstemmed	Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus).
title_sort	development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (philosciidae: haloniscus).
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/c18d713e7e274d9aa5dd419474a275c4
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Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus).

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