Target-capture probes for phylogenomics of the Caenogastropoda
Goulding, Tricia; Strong, Ellen; Quattrini, Andrea (2023), Target-capture probes for phylogenomics of the Caenogastropoda , Dryad, Dataset, https://doi.org/10.5061/dryad.b2rbnzskw
Target-capture approaches have facilitated a rapid growth in the field of phylogenomics but few probe sets exist for mollusks, an exceptionally rich phylum with unparalleled ecological and morphological diversity. We designed and tested the first universal probe set using Phyluce to capture ultraconserved elements (UCEs) and exon loci from the Subclass Caenogastropoda – one of six major lineages of gastropods. The probe set consists of 29,441 probes (8,872 for UCEs and 20,569 for exons) designed to target 1,142 UCE loci and 1,933 exon loci (3,075 total). In silico analyses of our probe set yielded an average of 2,110 loci from genomes and 1,389 loci from transcriptomes of diverse caenogastropods, respectively. After screening these loci to remove those that matched multiple contigs, an average of 1,686 loci from genomes and 785 loci from transcriptomes were retained. Phylogenetic analyses of the loci extracted from transcriptomes produced well-supported trees very similar to those published based on transcriptomic analyses. Although there are few caenogastropod genomes to analyze, phylogenetic relationships estimated from the analysis of loci extracted from genomes recover similar phylogenetic relationships and indicate that the loci targeted with this probe set are informative for resolving deep phylogenetic relationships. An in vitro analysis of the probe set with the Epitoniidae, a diverse caenogastropod family of uncertain affinity and with poorly resolved evolutionary relationships, recovered an average of 1,710 loci and produced a well-resolved phylogeny. Although preliminary, the analysis of loci captured by our probe set for a small number of epitoniid taxa produced a well-resolved tree indicating that this probe set is also able to resolve relationships at shallower hierarchical scales. Together, the in silico and in vitro analyses indicate that target-capture enrichment with this probe set is a useful tool for reconstructing phylogenetic relationships across taxonomic levels and evolutionary time scales.
Please see the README document ("README_Caenogastropod_probeset.md") and the accompanying published article: Goulding, T.C., Strong, E.E., and Quattrini, A. 2023. Target-capture probes for phylogenomics of the Caenogastropoda. Molecular Ecology Resources. Accepted.