Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms

Despite the increasing accessibility of high-throughput sequencing,
obtaining high-quality genomic data on non-model organisms without
proximate well-assembled and annotated genomes remains challenging. Here
we describe a workflow that takes advantage of distant genomic resources
and ingroup transcriptomes to select and jointly enrich long open reading
frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for
integrative studies of microevolutionary and macroevolutionary dynamics.
This workflow is applied to samples of the African unionid bivalve tribe
Coelaturini (Parreysiinae) at basin and continent-wide scales. Our results
indicate that ORFs are efficiently captured without prior identification
of intron-exon boundaries. The enrichment of UCEs was less successful but
nevertheless produced substantial datasets. Exploratory continent-wide
phylogenetic analyses with ORF supercontigs (> 515,000 parsimony
informative sites) resulted in a fully resolved phylogeny, the backbone of
which was also retrieved with UCEs (> 11,000 informative sites).
Variant calling on ORFs and UCEs of Coelaturini from the Malawi Basin
produced ~2,000 SNPs per population pair. Estimates of nucleotide
diversity and population differentiation were similar for ORFs and UCEs.
They were low compared to previous estimates in mollusks, but comparable
to those in recently diversifying Malawi cichlids and other taxa at an
early stage of speciation. Skimming off-target sequence data from the same
enriched libraries of Coelaturini from the Malawi Basin, we reconstructed
the maternally-inherited mitogenome, which displays the gene order
inferred for the most recent common ancestor of Unionidae. Overall, our
workflow and results provide exciting perspectives for integrative genomic
studies of microevolutionary and macroevolutionary dynamics in non-model
organisms.