Transcriptome-based target-enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia)

Area of Science:

• Marine Biology
• Genomics
• Evolutionary Biology

Background:

• Stony corals (Scleractinia) are ecologically and economically vital but their evolutionary relationships are poorly understood.
• Existing taxonomic and genetic data are insufficient for robust phylogenetic reconstruction.
• Limited availability of informative genetic markers hinders detailed phylogenomic analyses.

Purpose of the Study:

• To develop a novel set of DNA enrichment baits for phylogenomic analysis in stony corals.
• To increase the number and quality of genetic loci available for Scleractinia phylogeny.
• To facilitate more accurate and comprehensive evolutionary studies of stony corals.

Main Methods:

• Designed 15,919 DNA enrichment baits targeting 605 orthogroups across 1,139 exon regions.
• Included barcoding baits for COI and histone H3 genes for quality control.
• Performed hybrid capture on 18 coral species and analyzed captured loci through stringent filtering.

Main Results:

• Successfully captured an average of 74% of targeted loci per species.
• Developed a final probe set of 13,479 baits targeting 452 loci across 865 exon regions.
• Phylogenomic analyses (Maximum Likelihood, Bayesian, species tree) yielded congruent and highly supported evolutionary trees.

Conclusions:

• The developed phylogenomic method enables consistent capture of orthologous loci across diverse coral taxa.
• This approach facilitates data integration from multiple studies, enhancing future phylogenetic sampling of Scleractinia.
• The study provides a robust framework for resolving stony coral evolutionary history.