Genome-Wide SNP Data Revealed Notable Spatial Genetic Structure in the Deep-Sea Precious Coral Corallium japonicum

Abstract

Estimating the spatial extent of gamete and larval dispersal of deep-sea coral species, is challenging yet important for their conservation. Spatial autocorrelation analysis is useful for estimating the spatial range of dispersal of corals; however, it has not been performed for deep-sea coral species using genome-wide single nucleotide polymorphisms (SNPs). In this study, we examined the spatial genetic structure of a deep-sea coral species—the Japanese red coral, Corallium japonicum, sampled off the coast of Kochi, which lies to the southwest of the Shikoku Island in Japan; the Kochi region suffers from over-harvesting because of its high commercial value. We also examined the power of detecting significant spatial genetic structure by changing the number of loci and the proportion of missing data using both de novo analysis and mapping analysis. Similar results were obtained for both de novo and mapping analysis, although a higher number of loci were obtained by the mapping method. In addition, “many SNPs with a lot of missing data” was generally more useful than “a small number of SNPs with a small amount of missing data” to detect significant fine-scale spatial genetic structure. Our data suggested that more than 700 neutral SNPs were needed to detect significant fine-scale spatial genetic structure. The maximum first distance class that can detect significant spatial genetic structure within Kochi for the C. japonicum population was less than 11 km, suggesting that the over-harvesting of C. japonicum within a diameter of approximately 11 km in the Kochi area should be avoided, because this can cause the local extinction of this species.

Genetic population structure of the precious coral Corallium japonicum in the Northwest Pacific

“…In contrast to Corallium rubrum, which can sustain genetic differentiation even at fine spatial scales in the Mediterranean (Ledoux et al, 2010;Costantini et al, 2018;Cannas et al, 2019), C. japonicum does not appear to have fine-scale changes in population structure. This is likely related to differences in the two species' reproductive mode (C. rubrum, brooding; C. japonicum, broadcast spawning) (Takata et al, 2021).…”

“…These reads were then processed by using the pipeline ipyrad (Eaton and Overcast, 2020) with the reference-based assembly under default settings. The draft genomes of Corallium japonicum reported in Takata et al (2021) were used for the reference genome. Low-quality bases (Q < 20), adapters, and restriction sites were filtered out from each read prior to mapping to the draft genome.…”

“…In particular, single nucleotide polymorphisms (SNPs) in genomic DNA can be easily identified by using several methods such as restriction-site-associated DNA sequencing (RAD-seq; Baird et al, 2008) or multiplexed ISSR genotyping by sequencing (MIG-seq; Suyama and Matsuki, 2015). MIG-seq has attracted particular interest; although only a small number of SNP loci can be genotyped with this method, it has been used to identify population-level genetic differences and is increasingly being used to study marine organisms (Takata et al, 2019;Yorisue et al, 2020;Takata et al, 2021).…”

“…In Japanese waters, two studies have used MIG-seq to examine the population genetics of Corallium japonicum (Takata et al, 2019;Takata et al, 2021). However, these studies only examined colonies in Kochi Prefecture, and information on other regions of Japan is lacking.…”

Molecular Phylogeny and Taxonomy of the Coral Genus Cyphastrea (Cnidaria, Scleractinia, Merulinidae) in Japan, With the First Records of Two Species

“…In addition, two more morphologically unique species, C. kausti and C. hexasepta , were included in clade I. Thus, we need to search for more molecular markers or apply other methods (e.g., MIG-seq has recently been used in taxonomic studies for several coral species or coral populations [Pipithkul et al, 2021; Takata et al, 2021]) to distinguish the species included in clade I.…”