A polyvalent and universal tool for genomic studies in gastropod
molluscs (Heterobranchia: Tectipleura)
Abstract
Molluscs are the second most diverse animal phylum and heterobranch
gastropods present ~44,000 species. These comprise
fascinating creatures with a huge morphological and ecological
disparity. Such great diversity comes with even larger phylogenetic
uncertainty and many taxa have been largely neglected in molecular
assessments. Genomic tools have provided resolution to deep cladogenic
events but generating large numbers of transcriptomes/genomes is
expensive and usually requires fresh material. Here we leverage a target
enrichment approach to design and synthesize a probe set based on
available genomes and transcriptomes across Heterobranchia. Our probe
set contains 57,606 70mer baits and targets a total of 2,259
ultra-conserved elements (UCEs). Post-sequencing capture efficiency was
tested against 31 marine heterobranchs from major groups, including
Acochlidia, Acteonoidea, Aplysiida, Cephalaspidea, Pleurobranchida,
Pteropoda, Runcinida, Sacoglossa, and Umbraculida. The combined Trinity
and Velvet assemblies recovered up to 2,211 UCEs in Tectipleura and up
to 1,978 in Nudipleura, the most distantly related taxon to our core
study group. Total alignment length was 525,599 bp and contained 52%
informative sites and 21% missing data. Maximum-likelihood and Bayesian
inference approaches recovered the monophyly of all orders tested as
well as the larger clades Nudipleura, Panpulmonata, and
Euopisthobranchia. The successful enrichment of diversely preserved
material and DNA concentrations demonstrate the polyvalent nature of
UCEs, and the universality of the probe set designed. We believe this
probe set will enable multiple, interesting lines of research, that will
benefit from an inexpensive and largely informative tool that will,
additionally, benefit from the access to museum collections to gather
genomic data.