Das Zoologische Forschungsmuseum Alexander Koenig

ist ein Forschungsmuseum der Leibniz Gemeinschaft

Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods

AutorInnen: 
Stringer, D. N., Bertozzi, T., Meusemann, K., Delean, S., Guzik, M. T., Tierney, S. M., Mayer, C., Cooper, S. J. B., Javidkar, M., Zwick, A., Austin, A. D.
Erscheinungsjahr: 
2021
Vollständiger Titel: 
Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods
ZFMK-Autorinnen / ZFMK-Autoren: 
Publiziert in: 
PLoS ONE
Publikationstyp: 
Zeitschriftenaufsatz
DOI Name: 
doi.org/10.1371/journal.pone.0256861
Keywords: 
Hybrid enrichment, Exon capture, Isopods
Bibliographische Angaben: 
Stringer, D. N., Bertozzi, T., Meusemann, K., Delean, S., Guzik, M. T., Tierney, S. M., Mayer, C., Cooper, S. J. B., Javidkar, M., Zwick, A., Austin, A. D. (2021): Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus). - PLOS ONE 16 (9): e0256861. https://doi.org/10.1371/journal.pone.0256861.
Abstract: 

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.