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Xiao J, Tian P, Guo F, Yu S, Wang W, Wang X, Niu W. Characterization of the complete mitochondrial genome of Diploastrea heliopora and phylogeny of the scleractinia species which have group I introns in their COI genes. Saudi J Biol Sci 2021; 28:7054-7060. [PMID: 34867006 PMCID: PMC8626255 DOI: 10.1016/j.sjbs.2021.07.086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/04/2022] Open
Abstract
Mitochondrial genome DNA is a powerful marker for resolving phylogenetic relationships among scleractinian corals. Here, we decode the complete mitochondrial genome of Diploastrea heliopora (Lamarck, 1816) for the first time. The general features are 18 363 bp in length, and conventionally, with 13 protein coding genes, two ribosomal RNAs, and two transfer RNAs. Gene arrangement and distribution are similar to other scleractinian corals. Moreover, the COI gene of D. heliopora is broken up into two parts by a complex group I intron. This intron is 1076 bases in length and contains helical structures (P1-P10, except P2) and four conserved regions (P, Q, R, and S). The mitochondrial genome of D. heliopora has asymmetric base composition (13.03% C, 20.29% G, 25.91% A, and 40.77% for T). Based on concatenated protein coding genes, ML and BI trees show similar phylogenetic relationship: D. heliopora clustered closely with Sclerophyllia maxima and Echinophyllia aspera into the robust branch. The data and conclusion in this study are reference for further phylogenetic studies of corals.
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Affiliation(s)
- Jiaguang Xiao
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Peng Tian
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Feng Guo
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Shuangen Yu
- Fisheries College, Ocean University of China, Qingdao 266003, China
| | - Wei Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xiaolei Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Wentao Niu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
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Colin L, Yesson C, Head CEI. Complete mitochondrial genomes of three reef forming Acropora corals (Acroporidae, Scleractinia) from Chagos Archipelago, Indian Ocean. Biodivers Data J 2021; 9:e72762. [PMID: 34707458 PMCID: PMC8497460 DOI: 10.3897/bdj.9.e72762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/25/2021] [Indexed: 11/12/2022] Open
Abstract
We present the first mitochondrial genomes from Chagos Archipelago, Indian Ocean, of three putative species of reef forming Acropora (Acropora aff. tenuis, Acroporaaff.cytherea and Acropora aff. orbicularis). The circular genome consists respectively of 18,334 bp, 18,353 bp and 18,584 bp. All mitochondrial genomes recovered comprise 13 protein-coding genes, two transfer RNA genes and two ribosomal RNA genes, with an overall GC content ranging from 37.9% to 38.0%. These new genomic data contribute to our increased understanding of genus Acropora and its species boundaries, ultimately aiding species monitoring and conservation efforts.
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Affiliation(s)
- Luigi Colin
- Institute of Zoology, Zoological Society of London, Regent's Park, NW1 4RY, London, United Kingdom Institute of Zoology, Zoological Society of London, Regent's Park, NW1 4RY London United Kingdom
| | - Chris Yesson
- Institute of Zoology, Zoological Society of London, Regent's Park, NW1 4RY, London, United Kingdom Institute of Zoology, Zoological Society of London, Regent's Park, NW1 4RY London United Kingdom
| | - Catherine E I Head
- Institute of Zoology, Zoological Society of London, Regent's Park, NW1 4RY, London, United Kingdom Institute of Zoology, Zoological Society of London, Regent's Park, NW1 4RY London United Kingdom.,Department of Zoology, University of Oxford, John Krebs Field Station, Wytham, OX2 8JQ, Oxford, United Kingdom Department of Zoology, University of Oxford, John Krebs Field Station, Wytham, OX2 8JQ Oxford United Kingdom.,St Peter's College, New Inn Hall Street, OX1 2DL, Oxford, United Kingdom St Peter's College, New Inn Hall Street, OX1 2DL Oxford United Kingdom
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Niu W, Xiao J, Tian P, Yu S, Guo F, Wang J, Huang D. Characterization of the complete mitochondrial genome sequences of three Merulinidae corals and novel insights into the phylogenetics. PeerJ 2020; 8:e8455. [PMID: 32002337 PMCID: PMC6984341 DOI: 10.7717/peerj.8455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 12/24/2019] [Indexed: 11/20/2022] Open
Abstract
Over the past few decades, modern coral taxonomy, combining morphology and molecular sequence data, has resolved many long-standing questions about scleractinian corals. In this study, we sequenced the complete mitochondrial genomes of three Merulinidae corals (Dipsastraea rotumana, Favites pentagona, and Hydnophora exesa) for the first time using next-generation sequencing. The obtained mitogenome sequences ranged from 16,466 bp (D. rotumana) to 18,006 bp (F. pentagona) in length, and included 13 unique protein-coding genes (PCGs), two transfer RNA genes, and two ribosomal RNA genes . Gene arrangement, nucleotide composition, and nucleotide bias of the three Merulinidae corals were canonically identical to each other and consistent with other scleractinian corals. We performed a Bayesian phylogenetic reconstruction based on 13 protein-coding sequences of 86 Scleractinia species. The results showed that the family Merulinidae was conventionally nested within the robust branch, with H. exesa clustered closely with F. pentagona and D. rotumana clustered closely with Favites abdita. This study provides novel insight into the phylogenetics of species within the family Merulinidae and the evolutionary relationships among different Scleractinia genera.
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Affiliation(s)
- Wentao Niu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Jiaguang Xiao
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Peng Tian
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Shuangen Yu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Feng Guo
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Jianjia Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Dingyong Huang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
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Niu W, Yu S, Tian P, Xiao J. Complete mitochondrial genome of Echinophylliaaspera (Scleractinia, Lobophylliidae): Mitogenome characterization and phylogenetic positioning. Zookeys 2018; 793:1-14. [PMID: 30405308 PMCID: PMC6218560 DOI: 10.3897/zookeys.793.28977] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/20/2018] [Indexed: 11/23/2022] Open
Abstract
Lack of mitochondrial genome data of Scleractinia is hampering progress across genetic, systematic, phylogenetic, and evolutionary studies concerning this taxon. Therefore, in this study, the complete mitogenome sequence of the stony coral Echinophylliaaspera (Ellis & Solander, 1786), has been decoded for the first time by next generation sequencing and genome assembly. The assembled mitogenome is 17,697 bp in length, containing 13 protein coding genes (PCGs), two transfer RNAs and two ribosomal RNAs. It has the same gene content and gene arrangement as in other Scleractinia. All genes are encoded on the same strand. Most of the PCGs use ATG as the start codon except for ND2, which uses ATT as the start codon. The A+T content of the mitochondrial genome is 65.92% (25.35% A, 40.57% T, 20.65% G, and 13.43% for C). Bayesian and maximum likelihood phylogenetic analysis have been performed using PCGs, and the result shows that E.aspera clustered closely with Sclerophylliamaxima (Sheppard & Salm, 1988), both of which belong to Lobophylliidae, when compared with species belonging to Merulinidae and other scleractinian taxa used as outgroups. The complete mitogenome of E.aspera provides essential and important DNA molecular data for further phylogenetic and evolutionary analyses of corals.
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Affiliation(s)
- Wentao Niu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, ChinaLaboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic AdministrationXiamenChina
| | - Shuangen Yu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, ChinaLaboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic AdministrationXiamenChina
| | - Peng Tian
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, ChinaLaboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic AdministrationXiamenChina
| | - Jiaguang Xiao
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, ChinaLaboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic AdministrationXiamenChina
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Johnston EC, Forsman ZH, Flot JF, Schmidt-Roach S, Pinzón JH, Knapp ISS, Toonen RJ. A genomic glance through the fog of plasticity and diversification in Pocillopora. Sci Rep 2017; 7:5991. [PMID: 28729652 PMCID: PMC5519588 DOI: 10.1038/s41598-017-06085-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/07/2017] [Indexed: 01/01/2023] Open
Abstract
Scleractinian corals of the genus Pocillopora (Lamarck, 1816) are notoriously difficult to identify morphologically with considerable debate on the degree to which phenotypic plasticity, introgressive hybridization and incomplete lineage sorting obscure well-defined taxonomic lineages. Here, we used RAD-seq to resolve the phylogenetic relationships among seven species of Pocillopora represented by 15 coral holobiont metagenomic libraries. We found strong concordance between the coral holobiont datasets, reads that mapped to the Pocillopora damicornis (Linnaeus, 1758) transcriptome, nearly complete mitochondrial genomes, 430 unlinked high-quality SNPs shared across all Pocillopora taxa, and a conspecificity matrix of the holobiont dataset. These datasets also show strong concordance with previously published clustering of the mitochondrial clades based on the mtDNA open reading frame (ORF). We resolve seven clear monophyletic groups, with no evidence for introgressive hybridization among any but the most recently derived sister species. In contrast, ribosomal and histone datasets, which are most commonly used in coral phylogenies to date, were less informative and contradictory to these other datasets. These data indicate that extant Pocillopora species diversified from a common ancestral lineage within the last ~3 million years. Key to this evolutionary success story may be the high phenotypic plasticity exhibited by Pocillopora species.
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Affiliation(s)
- Erika C Johnston
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA.
| | - Zac H Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Jean-François Flot
- Université libre de Bruxelles (ULB), Avenue F.D. Roosevelt 50, B-1050, Bruxelles, Belgium
| | - Sebastian Schmidt-Roach
- Australian Institute of Marine Science, 4810, Townsville, Australia
- Carl von Ossietzky University of Oldenburg, 26129, Oldenburg, Germany
| | - Jorge H Pinzón
- Department of Psychiatry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ingrid S S Knapp
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
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Coral hybridization or phenotypic variation? Genomic data reveal gene flow between Porites lobata and P. Compressa. Mol Phylogenet Evol 2017; 111:132-148. [DOI: 10.1016/j.ympev.2017.03.023] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 03/26/2017] [Accepted: 03/26/2017] [Indexed: 11/18/2022]
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