Academic Journal
Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus)
| العنوان: | 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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| المؤلفون: | Stringer, Danielle N., Bertozzi, Terry, Meusemann, Karen, Delean, Steven, Guzik, Michelle T., Tierney, Simon M. (R19062), Mayer, Christophe, Cooper, Steven J., Javidkar, Mohammad, Zwick, Andreas, Austin, Andrew D. |
| بيانات النشر: | U.S., Public Library of Science |
| سنة النشر: | 2021 |
| المجموعة: | University of Western Sydney (UWS): Research Direct |
| مصطلحات موضوعية: | 310201 - Bioinformatic methods development, 280102 - Expanding knowledge in the biological sciences |
| الوصف: | 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 (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. |
| نوع الوثيقة: | article in journal/newspaper |
| وصف الملف: | |
| اللغة: | English |
| Relation: | ARC LP140100555; http://purl.org/au-research/grants/arc/LP140100555; PLoS One--1932-6203-- Vol. 16 Issue. 9 No. e0256861 pp: - |
| DOI: | 10.1371/journal.pone.0256861 |
| الاتاحة: | https://doi.org/10.1371/journal.pone.0256861 https://hdl.handle.net/1959.7/uws:62724 |
| Rights: | © 2021 Stringer et al. 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. |
| رقم الانضمام: | edsbas.7F25D75E |
| قاعدة البيانات: | BASE |
| DOI: | 10.1371/journal.pone.0256861 |
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