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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dc.contributor.authorStringer, D.
dc.contributor.authorBertozzi, T.
dc.contributor.authorMeusemann, K.
dc.contributor.authorDelean, J.
dc.contributor.authorGuzik, M.
dc.contributor.authorTierney, S.
dc.contributor.authorMayer, C.
dc.contributor.authorCooper, S.
dc.contributor.authorZwick, A.
dc.contributor.authorAustin, A.
dc.contributor.editorZHANG, F.
dc.date.issued2021
dc.description.abstractTranscriptome-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.
dc.description.statementofresponsibilityDanielle N. Stringer, Terry Bertozzi, Karen Meusemann, Steven Delean, Michelle T. Guzik, Simon M. Tierney ... et al.
dc.identifier.citationPLoS ONE, 2021; 16(9):1-24
dc.identifier.doi10.1371/journal.pone.0256861
dc.identifier.issn1932-6203
dc.identifier.issn1932-6203
dc.identifier.orcidStringer, D. [0000-0002-6562-5031]
dc.identifier.orcidBertozzi, T. [0000-0001-6665-3395]
dc.identifier.orcidDelean, J. [0000-0003-1116-5014]
dc.identifier.orcidTierney, S. [0000-0002-8812-6753]
dc.identifier.orcidCooper, S. [0000-0002-7843-8438]
dc.identifier.orcidAustin, A. [0000-0002-9602-2276]
dc.identifier.urihttps://hdl.handle.net/2440/132962
dc.language.isoen
dc.publisherPublic Library of Science
dc.relation.granthttp://purl.org/au-research/grants/arc/LP0669062
dc.relation.granthttp://purl.org/au-research/grants/arc/LP140100555
dc.rights© 2021 Stringer et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.source.urihttps://doi.org/10.1371/journal.pone.0256861
dc.subjectAnimals
dc.subjectIsopoda
dc.subjectGenetics, Population
dc.subjectPhylogeny
dc.subjectGene Expression
dc.subjectOpen Reading Frames
dc.subjectGenome
dc.subjectIntrons
dc.subjectExons
dc.subjectGenetic Loci
dc.subjectHigh-Throughput Nucleotide Sequencing
dc.subjectArthropod Proteins
dc.subjectDatasets as Topic
dc.titleDevelopment and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus)
dc.typeJournal article
pubs.publication-statusPublished

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