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Background   Heliopora coerulea , the blue coral, is the octocoral characterized by its blue skeleton. Recently, two  Heliopora  species were delimited by DNA markers: HC-A and HC-B. To clarify the genomic divergence of these  Heliopora  species (HC-A and HC-B) from sympatric and allopatric populations in Okinawa, Japan, we used a high throughput reduced representation genomic DNA sequencing approach (ezRAD).    Results  We found 6742 biallelic SNPs shared among all target populations, which successfully distinguished the HC-A and HC-B species in both the sympatric and allopatric populations, with no evidence of hybridization between the two. In addition, we detected 410 fixed SNPs linking functional gene differences, including heat resilience and reproductive timing, between HC-A and HC-B.    Conclusions  We confirmed clear genomic divergence between  Heliopora  species and found possible genes related to stress-responses and reproduction, which may shed light on the speciation process and ecological divergence of coral species.

RADseq population genomics confirms divergence across closely related species in blue coral (Heliopora coerulea)