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Wang W, Cao B, Xu Z, Jia Z, Yu S, Tian P, Niu W, Xiao J. The complete mitochondrial genome of Montiporavietnamensis (Scleractinia, Acroporidae). Biodivers Data J 2022; 10:e91531. [PMID: 36761536 PMCID: PMC9848517 DOI: 10.3897/bdj.10.e91531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/02/2022] [Indexed: 11/12/2022] Open
Abstract
Montiporavietnamensis Veron, 2000 (Cnidaria, Anthozoa, Scleractinia, Acroporidae) is an uncommon, but distinctive species of stony coral. The complete mitochondrial genome of M.vietnamensis was sequenced in this study for the first time, based on 32 pairs of primers newly designed according to seven species in the family Acroporidae. The mitogenome of M.vietnamensis has a circular form and is 17,885 bp long, including 13 protein-coding genes (PCGs), 2 tRNA (tRNAMet, tRNATrp), 2 rRNA genes and a putative control-region. The base composition of the complete mitogenome was 24.8% A, 14.2% C, 24.2% G and 36.8% T, with a higher AT content (61.6%) than GC content (38.4%). Based on 13 protein-coding genes, a Maximum Likelihood phylogenetic analysis showed that M.vietnamensis is clustered in the genus Montipora which belongs to the family Acroporidae. More stony coral species should be sequenced for basic molecular information and to help confirm the taxonomic status and evolutionary relationships of Scleractinia in the future.
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Affiliation(s)
- Wei Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Bingbing Cao
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Ziqing Xu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Zhiyu Jia
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Shuangen Yu
- Key Laboratory of Mariculture of Ministry of Education, College of Fisheries, Ocean University of China, Qingdao, ChinaKey Laboratory of Mariculture of Ministry of Education, College of Fisheries, Ocean University of ChinaQingdaoChina
| | - Peng Tian
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Wentao Niu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Jiaguang Xiao
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
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Kashimoto R, Hisata K, Shinzato C, Satoh N, Shoguchi E. Expansion and Diversification of Fluorescent Protein Genes in Fifteen Acropora Species during the Evolution of Acroporid Corals. Genes (Basel) 2021; 12:genes12030397. [PMID: 33799612 PMCID: PMC8001845 DOI: 10.3390/genes12030397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 11/16/2022] Open
Abstract
In addition to a purple, non-fluorescent chromoprotein (ChrP), fluorescent proteins (FPs) account for the vivid colors of corals, which occur in green (GFP), cyan (CFP), and red (RFP) FPs. To understand the evolution of the coral FP gene family, we examined the genomes of 15 Acropora species and three confamilial taxa. This genome-wide survey identified 219 FP genes. Molecular phylogeny revealed that the 15 Acropora species each have 9–18 FP genes, whereas the other acroporids examined have only two, suggesting a pronounced expansion of the FP genes in the genus Acropora. The data estimates of FP gene duplication suggest that the last common ancestor of the Acropora species that survived in the period of high sea surface temperature (Paleogene period) has already gained 16 FP genes. Different evolutionary histories of lineage-specific duplication and loss were discovered among GFP/CFPs, RFPs, and ChrPs. Synteny analysis revealed core GFP/CFP, RFP, and ChrP gene clusters, in which a tandem duplication of the FP genes was evident. The expansion and diversification of Acropora FPs may have contributed to the present-day richness of this genus.
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Affiliation(s)
- Rio Kashimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; (K.H.); (N.S.); (E.S.)
- Correspondence:
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; (K.H.); (N.S.); (E.S.)
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564, Japan;
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; (K.H.); (N.S.); (E.S.)
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; (K.H.); (N.S.); (E.S.)
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Kurniawan R, Ariestasari A, Silalahi RS, Karlina I, Febrianto T, Kurniawan D, Amrifo V, Abrar M, Syakti AD. Identification Acroporidae and Favidae by a newly approach called Reef Identification Knowhow Application-Reconstructed by 3D Imagery (RIKA-R3DI) Method. MethodsX 2019; 6:1084-1100. [PMID: 31193328 PMCID: PMC6526297 DOI: 10.1016/j.mex.2019.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 05/04/2019] [Indexed: 10/26/2022] Open
Abstract
With an increase on coral reefs vulnerability worldwide, an efficient and an integrated monitoring technique are required. Photographic and video methods are now becoming more attractive rather than conventional technique to optimize diver time. In this research, the level of effectiveness of RIKA-R3DI method was evaluated using Agisoft Photoscan. The method was based on the reconstructed images in three dimensional image assisted by a computer with Agisoft Photoscan to facilitate data processing. This research aims to identify Acroporidae and Favidae as the models of coral reef-building species. The samples were collected from the waters of Beralas Pasir Island, Bintan Regency. Visual engineering was conducted in the form of 3D viewing with attention to the corallite shape and size, as well as the color of the corals. The result was successful in identifying 4 species, i.e. Acropora microphthalma, A. sarmentosa, Favia maritima, F. vietnamensis. The keys benefit of this methodologies are: •The RIKA-R3DI method allows to reduce diving time during direct visual observation.•The method has high accuracy and is non-invasive, since it does not touch directly to the coral.•The application of RIKA-R3DI can be used to identified the coral species and evaluate the coral health status base on the percent coverage.
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Affiliation(s)
- Rika Kurniawan
- Marine Science and Fisheries Faculty - Raja Ali Haji Maritime University, Jl. Politeknik Senggarang-Tanjungpinang, Riau Islands Province, 29100, Indonesia
| | - Aprilia Ariestasari
- Marine Science and Fisheries Faculty - Raja Ali Haji Maritime University, Jl. Politeknik Senggarang-Tanjungpinang, Riau Islands Province, 29100, Indonesia
| | - Roiko Sunarwan Silalahi
- Marine Science and Fisheries Faculty - Raja Ali Haji Maritime University, Jl. Politeknik Senggarang-Tanjungpinang, Riau Islands Province, 29100, Indonesia
| | - Ita Karlina
- Marine Science and Fisheries Faculty - Raja Ali Haji Maritime University, Jl. Politeknik Senggarang-Tanjungpinang, Riau Islands Province, 29100, Indonesia
| | - Try Febrianto
- Marine Science and Fisheries Faculty - Raja Ali Haji Maritime University, Jl. Politeknik Senggarang-Tanjungpinang, Riau Islands Province, 29100, Indonesia
| | - Dedy Kurniawan
- Marine Science and Fisheries Faculty - Raja Ali Haji Maritime University, Jl. Politeknik Senggarang-Tanjungpinang, Riau Islands Province, 29100, Indonesia
| | - Viktor Amrifo
- Fisheries and Marine Science Faculty - Riau University, Kampus Bina Widya Km 12,5, Simpang Baru, Pekanbaru, 28293, Indonesia
| | - Muhammad Abrar
- Research Center for Oceanography, Indonesian Institute of Sciences, Jl. Pasir Putih I Ancol Timur, 14430, Jakarta Utara, Indonesia
| | - Agung Dhamar Syakti
- Marine Science and Fisheries Faculty - Raja Ali Haji Maritime University, Jl. Politeknik Senggarang-Tanjungpinang, Riau Islands Province, 29100, Indonesia.,Center for Maritime Biosciences Studies - Institute for Sciences and Community Service, Jenderal Soedirman University, Kampus Karangwangkal, Jl. dr. Suparno, Purwokerto, 53123, Indonesia
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Abstract
Here, for the first time, we sequenced the complete mitogenome of Alveopora japonica Eguchi, 1968 (Scleractinia: Acroporidae). Genome size was 17,886 bp with 13 protein-coding, two rRNA, and two tRNA genes. This gene composition was identical to the typical scleractinian pattern. Our results strongly support the recent transfer of this coral species to the family Acroporidae.
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Affiliation(s)
- In-Young Cho
- National Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
| | - Sung-Jin Hwang
- Department of Eco-Biological Science, Woosuk University, Jincheon-eup, Republic of Korea
| | - Keun-Yong Kim
- Korea Maritime and Ocean University, Busan, Republic of Korea
| | - Moongeun Yoon
- National Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
| | - Il Hun Kim
- National Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
| | - Min-Seop Kim
- National Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
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Abstract
The complete mitogenome of the hexacorallia, Montipora aequituberculata has been amplified and sequenced. The mitogenome consists of 17,886 bp, with 13 protein-coding genes, 2 ribosomal RNA genes, 2 transfer RNA genes and a control region. It has been observed that ND5 gene is split into two parts by a large fragment of genes, which commonly presented in scleractinian coral. The overall base composition of the H-strand was A, 24.91%; G, 24.1%; C, 14.2%; and T, 36.8%, with a slight AT bias of 61.7%. The control region was 627 bp in length and located between 12S rRNA and COIII gene. Based on the neighbour-joining (NJ) tree, M. aequituberculata was grouped with M. cactus, Anacropora matthai and Acropora tenuis, and formed a clade of Acroporidae. In conclusion, the complete mitogenome of M. aequituberculata data may provide more informative for phylogenetic approach for corals phylogeny.
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Affiliation(s)
- Yu-Min Ju
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan, Republic of China
| | - Sheng-Tai Hsiao
- Marine Fisheries Division, Fisheries Research Institute, Keelung, Taiwan, Republic of China
| | - Fu-Wen Kuo
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan, Republic of China
| | - Jui-Hsien Wu
- Eastern Marine Biology Research Center, Fisheries Research Institute, Council of Agriculture, Taitung, Taiwan, Republic of China
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