VenomCap: An exon-capture probe set for the targeted sequencing of snake venom genes.

Autor: Travers SL; Department of Genetics, Rutgers University, Piscataway, New Jersey, USA., Hutter CR; Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA., Austin CC; Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA., Donnellan SC; South Australian Museum, Adelaide, Australia.; Australian Museum Research Institute, Australian Museum, Sydney, Australia., Buehler MD; Department of Biological Sciences and Auburn Museum of Natural History, Auburn University, Auburn, Alabama, USA., Ellison CE; Department of Genetics, Rutgers University, Piscataway, New Jersey, USA., Ruane S; Life Sciences Section, Negaunee Integrative Research Center, Field Museum, Chicago, Illinois, USA.
Jazyk: angličtina
Zdroj: Molecular ecology resources [Mol Ecol Resour] 2024 Nov; Vol. 24 (8), pp. e14020. Date of Electronic Publication: 2024 Sep 19.
DOI: 10.1111/1755-0998.14020
Abstrakt: Snake venoms are complex mixtures of toxic proteins that hold significant medical, pharmacological and evolutionary interest. To better understand the genetic diversity underlying snake venoms, we developed VenomCap, a novel exon-capture probe set targeting toxin-coding genes from a wide range of elapid snakes, with a particular focus on the ecologically diverse and medically important subfamily Hydrophiinae. We tested the capture success of VenomCap across 24 species, representing all major elapid lineages. We included snake phylogenomic probes in the VenomCap capture set, allowing us to compare capture performance between venom and phylogenomic loci and to infer elapid phylogenetic relationships. We demonstrated VenomCap's ability to recover exons from ~1500 target markers, representing a total of 24 known venom gene families, which includes the dominant gene families found in elapid venoms. We find that VenomCap's capture results are robust across all elapids sampled, and especially among hydrophiines, with respect to measures of target capture success (target loci matched, sensitivity, specificity and missing data). As a cost-effective and efficient alternative to full genome sequencing, VenomCap can dramatically accelerate the sequencing and analysis of venom gene families. Overall, our tool offers a model for genomic studies on snake venom gene diversity and evolution that can be expanded for comprehensive comparisons across the other families of venomous snakes.
(© 2024 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
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