Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype
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 d...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
PeerJ Inc.
2019-10-01
|
| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/7769.pdf |
| _version_ | 1797419011438280704 |
|---|---|
| author | Kenji Takata Hiroki Taninaka Masanori Nonaka Fumihito Iwase Taisei Kikuchi Yoshihisa Suyama Satoshi Nagai Nina Yasuda |
| author_facet | Kenji Takata Hiroki Taninaka Masanori Nonaka Fumihito Iwase Taisei Kikuchi Yoshihisa Suyama Satoshi Nagai Nina Yasuda |
| author_sort | Kenji Takata |
| collection | DOAJ |
| description | 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). |
| first_indexed | 2024-03-09T06:42:25Z |
| format | Article |
| id | doaj.art-75b26ef8bf3b40f69e170546188cae2b |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:42:25Z |
| publishDate | 2019-10-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-75b26ef8bf3b40f69e170546188cae2b2023-12-03T10:48:06ZengPeerJ Inc.PeerJ2167-83592019-10-017e776910.7717/peerj.7769Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotypeKenji Takata0Hiroki Taninaka1Masanori Nonaka2Fumihito Iwase3Taisei Kikuchi4Yoshihisa Suyama5Satoshi Nagai6Nina Yasuda7Graduate School of Agriculture, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, JapanInterdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Miyazaki, Miyazaki, JapanOkinawa Churashima Foundation Reseach Center, Motobu, Okinawa, JapanShikoku Marine Life Laboratory, Otsuki, Kochi, JapanParasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Miyazaki, JapanField Science Center, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, JapanNational Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, JapanDepartment of Marine Biology and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, JapanBackground 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).https://peerj.com/articles/7769.pdfMIG-seqIncomplete lineage sortingSpecies delimitationDeep sea coralOctocoral |
| spellingShingle | Kenji Takata Hiroki Taninaka Masanori Nonaka Fumihito Iwase Taisei Kikuchi Yoshihisa Suyama Satoshi Nagai Nina Yasuda Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype PeerJ MIG-seq Incomplete lineage sorting Species delimitation Deep sea coral Octocoral |
| title | Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype |
| title_full | Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype |
| title_fullStr | Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype |
| title_full_unstemmed | Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype |
| title_short | Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype |
| title_sort | multiplexed issr genotyping by sequencing distinguishes two precious coral species anthozoa octocorallia coralliidae that share a mitochondrial haplotype |
| topic | MIG-seq Incomplete lineage sorting Species delimitation Deep sea coral Octocoral |
| url | https://peerj.com/articles/7769.pdf |
| work_keys_str_mv | AT kenjitakata multiplexedissrgenotypingbysequencingdistinguishestwopreciouscoralspeciesanthozoaoctocoralliacoralliidaethatshareamitochondrialhaplotype AT hirokitaninaka multiplexedissrgenotypingbysequencingdistinguishestwopreciouscoralspeciesanthozoaoctocoralliacoralliidaethatshareamitochondrialhaplotype AT masanorinonaka multiplexedissrgenotypingbysequencingdistinguishestwopreciouscoralspeciesanthozoaoctocoralliacoralliidaethatshareamitochondrialhaplotype AT fumihitoiwase multiplexedissrgenotypingbysequencingdistinguishestwopreciouscoralspeciesanthozoaoctocoralliacoralliidaethatshareamitochondrialhaplotype AT taiseikikuchi multiplexedissrgenotypingbysequencingdistinguishestwopreciouscoralspeciesanthozoaoctocoralliacoralliidaethatshareamitochondrialhaplotype AT yoshihisasuyama multiplexedissrgenotypingbysequencingdistinguishestwopreciouscoralspeciesanthozoaoctocoralliacoralliidaethatshareamitochondrialhaplotype AT satoshinagai multiplexedissrgenotypingbysequencingdistinguishestwopreciouscoralspeciesanthozoaoctocoralliacoralliidaethatshareamitochondrialhaplotype AT ninayasuda multiplexedissrgenotypingbysequencingdistinguishestwopreciouscoralspeciesanthozoaoctocoralliacoralliidaethatshareamitochondrialhaplotype |