Cargando…
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...
Autores principales: | , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8448321/ https://www.ncbi.nlm.nih.gov/pubmed/34534224 http://dx.doi.org/10.1371/journal.pone.0256861 |
_version_ | 1784569213854154752 |
---|---|
author | Stringer, Danielle N. Bertozzi, Terry Meusemann, Karen Delean, Steven Guzik, Michelle T. Tierney, Simon M. Mayer, Christoph Cooper, Steven J. B. Javidkar, Mohammad Zwick, Andreas Austin, Andrew D. |
author_facet | Stringer, Danielle N. Bertozzi, Terry Meusemann, Karen Delean, Steven Guzik, Michelle T. Tierney, Simon M. Mayer, Christoph Cooper, Steven J. B. Javidkar, Mohammad Zwick, Andreas Austin, Andrew D. |
author_sort | Stringer, Danielle N. |
collection | PubMed |
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 | Online Article Text |
id | pubmed-8448321 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-84483212021-09-18 Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus) Stringer, Danielle N. Bertozzi, Terry Meusemann, Karen Delean, Steven Guzik, Michelle T. Tierney, Simon M. Mayer, Christoph Cooper, Steven J. B. Javidkar, Mohammad Zwick, Andreas Austin, Andrew D. PLoS One Research Article 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. Public Library of Science 2021-09-17 /pmc/articles/PMC8448321/ /pubmed/34534224 http://dx.doi.org/10.1371/journal.pone.0256861 Text en © 2021 Stringer et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Stringer, Danielle N. Bertozzi, Terry Meusemann, Karen Delean, Steven Guzik, Michelle T. Tierney, Simon M. Mayer, Christoph Cooper, Steven J. B. Javidkar, Mohammad Zwick, Andreas Austin, Andrew D. Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus) |
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_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_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_sort | development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (philosciidae: haloniscus) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8448321/ https://www.ncbi.nlm.nih.gov/pubmed/34534224 http://dx.doi.org/10.1371/journal.pone.0256861 |
work_keys_str_mv | AT stringerdaniellen developmentandevaluationofacustombaitdesignbasedon469singlecopyproteincodinggenesforexoncaptureofisopodsphilosciidaehaloniscus AT bertozziterry developmentandevaluationofacustombaitdesignbasedon469singlecopyproteincodinggenesforexoncaptureofisopodsphilosciidaehaloniscus AT meusemannkaren developmentandevaluationofacustombaitdesignbasedon469singlecopyproteincodinggenesforexoncaptureofisopodsphilosciidaehaloniscus AT deleansteven developmentandevaluationofacustombaitdesignbasedon469singlecopyproteincodinggenesforexoncaptureofisopodsphilosciidaehaloniscus AT guzikmichellet developmentandevaluationofacustombaitdesignbasedon469singlecopyproteincodinggenesforexoncaptureofisopodsphilosciidaehaloniscus AT tierneysimonm developmentandevaluationofacustombaitdesignbasedon469singlecopyproteincodinggenesforexoncaptureofisopodsphilosciidaehaloniscus AT mayerchristoph developmentandevaluationofacustombaitdesignbasedon469singlecopyproteincodinggenesforexoncaptureofisopodsphilosciidaehaloniscus AT cooperstevenjb developmentandevaluationofacustombaitdesignbasedon469singlecopyproteincodinggenesforexoncaptureofisopodsphilosciidaehaloniscus AT javidkarmohammad developmentandevaluationofacustombaitdesignbasedon469singlecopyproteincodinggenesforexoncaptureofisopodsphilosciidaehaloniscus AT zwickandreas developmentandevaluationofacustombaitdesignbasedon469singlecopyproteincodinggenesforexoncaptureofisopodsphilosciidaehaloniscus AT austinandrewd developmentandevaluationofacustombaitdesignbasedon469singlecopyproteincodinggenesforexoncaptureofisopodsphilosciidaehaloniscus |