Extended genomic regions flanking ultraconserved elements allow efficient species identification and intraspecific diversity assessment in coral

Genetically informed conservation is critically important to ensure that interventions benefit the population of interest. In corals, preserving genetic diversity and accurate species identification are crucial for the sexual propagation. While various methods exist for species identification and measuring intraspecific variation, obtaining and analysing molecular data that enables rapid yet informed decisions on broodstock choice and progeny quality assurance remains challenging. Here we present a novel approach towards resource effective intraspecific genetic profiling by targeting extended genomic regions around ultra-conserved elements (UCEs). By sorting loci by parsimony informativeness and using a locus window size as small as 5000 bp upstream and downstream of the UCE, we identified a subset of 500 UCE-associated loci that can accurately resolve phylogenetic relationships among species and assess intraspecific variation with accuracy comparable to a whole-genome dataset, while. This method was validated using existing population genomic data from six species of staghorn coral (Acropora hyacinthus, Acropora tersa, Acropora pectinata, Acropora sp. "VI-3", Acropora kenti and Acropora cf. spathulata). The phylogeny produced by the UCE subset is congruent with the phylogeny based on complete data. With the moderate number and length of target genomic region sizes providing a balance between resolution and sequencing effort, this study provides a proof-of-concept approach towards developing fast, scalable, and cost-effective workflows using a real-time long-read sequencers such as Oxford Nanopore Technologies. The methodology has the broad potential to be applied to support genetic assessment across taxa where taxonomic uncertainty is common, improving confidence in experimental frameworks and conservation decisions.