Hexacorallian UCEs and where to find them: genomic mapping and assessment of ultraconserved elements

The targeted capture and enrichment of conserved regions across the nuclear genome has become a popular genome reduction method to sequence thousands of loci for phylogenomics and downstream species delimitation purposes. The approach that targets ultraconserved elements (UCEs) and exons has provided taxonomic resolution across deep and shallow timescales for many taxa that have previously proved to be particularly recalcitrant with traditional markers. However, basic information such as the genomic location and locus type (e.g., exonic, intronic) of the UCE loci targeted are often lacking for newly developed probe designs. Here, we identify UCE loci on Hexacorallia (corals and anemones) genomes using the recently designed hexa-v2 probe set and characterise the identified UCE loci by mapping the targeted capture probe set to annotated chromosome-level genome assemblies where possible. We also examine their efficacy in reconstructing phylogenetic relationships across the subclass. Based on publicly available genome assemblies and annotations, we show that hexacorallian UCE loci targeted by the hexa-v2 probe set are primarily exon-associated in the probe region and intron-associated in the flanking regions, are located throughout the genomes and across chromosomes and are effective in reconstructing hexacorallian phylogenetic relationships.