Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype

Kenji Takata; Hiroki Taninaka; Masanori Nonaka; Fumihito Iwase; Taisei Kikuchi; Yoshihisa Suyama; Satoshi Nagai; Nina Yasuda

doi:10.7717/peerj.7769

Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype

PeerJ. 2019 Oct 4:7:e7769. doi: 10.7717/peerj.7769. eCollection 2019.

Authors

Kenji Takata^{1

2}, Hiroki Taninaka³, Masanori Nonaka⁴, Fumihito Iwase⁵, Taisei Kikuchi⁶, Yoshihisa Suyama⁷, Satoshi Nagai⁸, Nina Yasuda²

Affiliations

¹ Graduate School of Agriculture, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, Japan.
² Department of Marine Biology and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, Japan.
³ Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Miyazaki, Miyazaki, Japan.
⁴ Okinawa Churashima Foundation Reseach Center, Motobu, Okinawa, Japan.
⁵ Shikoku Marine Life Laboratory, Otsuki, Kochi, Japan.
⁶ Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Miyazaki, Japan.
⁷ Field Science Center, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan.
⁸ National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan.

Abstract

Background: Precious corals known as coralliid corals (Anthozoa: Octocorallia) play an important role in increasing the biodiversity of the deep sea. Currently, these corals are highly threatened because of overfishing that has been brought on by an increased demand and elevated prices for them.The deep sea precious corals Pleurocorallium elatius and P. konojoi are distributed in Japanese waters and have distinct morphological features: (1) the terminal branches of the colony form of P. elatius are very fine, while those of P. konojoi are blunt and rounded, (2) the autozooids of P. elatius are arranged in approximately four rows, while those of P. konojoi are clustered in groups. However, previous genetic analysis using mtDNA and nuclear DNA did not indicate monophyly. Therefore, it is important to clarify their species status to allow for their conservation.

Methodology: We collected a total of 87 samples (60 of Corallium japonicum and 27 of P. konojoi) from around the Ryukyu Islands and Shikoku Island, which are geographically separated by approximately 1,300 km. We used a multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) and obtained 223 SNPs with which to perform STRUCTURE analysis and principle coordinate analysis (PCoA). In addition, two relatively polymorphic mtDNA regions were sequenced and compared.

Results: P. elatius and P. konojoi share a same mtDNA haplotype, which has been previously reported. However, MIG-seq analysis clearly distinguished the two species based on PCoA and STRUCTURE analysis, including 5% of species-specific fixed SNPs.

Conclusion: This study indicated that P. elatius and P. konojoi are different species and therefore both species should be conserved separately. Our findings highlight the importance of the conservation of these two species, especially P. elatius, whose population has been dramatically depleted over the last 100 years. The study also demonstrated the effectiveness and robustness of MIG-seq for defining closely related octocoral species that were otherwise indistinguishable using traditional genetic markers (mtDNA and EF).

Keywords: Deep sea coral; Incomplete lineage sorting; MIG-seq; Octocoral; Species delimitation.

Grants and funding

This study was supported by the Japan Society for the Promotion of Science (JSPS) Grant-in-aid for young scientists (A) (17H04996),16H04722, a Grant-in-Aid for Research Fellows (201921342), and the Sumitomo Foundation Fiscal 2018 Grant for Environmental Research Projects and the Program to Disseminate Tenure Tracking System from the Ministry of Education, Culture, Sports, Science and Technology (MEXT). Additional support was granted by the Japan Society for the Promotion of Science (JSPS) KAKENHI (Grant Number 16H04722). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.