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Addamo AM, Modrell MS, Taviani M, Machordom A. Unravelling the relationships among Madrepora Linnaeus, 1758, Oculina Lamark, 1816 and Cladocora Ehrenberg, 1834 (Cnidaria: Anthozoa: Scleractinia). INVERTEBR SYST 2024; 38:IS23027. [PMID: 38744497 DOI: 10.1071/is23027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 03/18/2024] [Indexed: 05/16/2024]
Abstract
Despite the widespread use of integrative taxonomic approaches, many scleractinian coral genera and species remain grouped in polyphyletic families, classified as incertae sedis or simply understudied. Oculinidae Gray, 1847 represents a family for which many taxonomic questions remain unresolved, particularly those related to some of the current genera, such as Oculina Lamark, 1816 or recently removed genera, including Cladocora Ehrenberg, 1834 and Madrepora Linnaeus, 1758. Cladocora is currently assigned to the family Cladocoridae Milne Edwards & Haime, 1857 and a new family, Bathyporidae Kitahara, Capel, Zilberberg & Cairns, 2024, was recently raised to accommodate Madrepora . However, the name Bathyporidae is not valid because this was not formed on the basis of a type genus name. To resolve taxonomic questions related to these three genera, the evolutionary relationships are explored through phylogenetic analyses of 18 molecular markers. The results of these analyses support a close relationship between the species Oculina patagonica and Cladocora caespitosa , indicating that these may belong to the same family (and possibly genus), and highlighting the need for detailed revisions of Oculina and Cladocora . By contrast, a distant relationship is found between these two species and Madrepora oculata , with the overall evidence supporting the placement of Madrepora in the resurrected family Madreporidae Ehrenberg, 1834. This study advances our knowledge of coral systematics and highlights the need for a comprehensive review of the genera Oculina , Cladocora and Madrepora .
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Affiliation(s)
- Anna M Addamo
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), E-28006 Madrid, Spain; and European Commission, Joint Research Centre (JRC), I-21027 Ispra, Italy; and Climate Change Research Centre (CCRC), University of Insubria, I-21100 Varese, Italy; and Present address: Faculty of Biosciences and Aquaculture, Nord University, NO-8049 Bodø, Norway
| | - Melinda S Modrell
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), E-28006 Madrid, Spain
| | - Marco Taviani
- Istituto di Scienze Marine, Consiglio Nazionale delle Ricerche (ISMAR-CNR), I-40129 Bologna, Italy; and Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Annie Machordom
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), E-28006 Madrid, Spain
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2
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Vaga CF, Seiblitz IGL, Stolarski J, Capel KCC, Quattrini AM, Cairns SD, Huang D, Quek RZB, Kitahara MV. 300 million years apart: the extreme case of macromorphological skeletal convergence between deltocyathids and a turbinoliid coral (Anthozoa, Scleractinia). INVERTEBR SYST 2024; 38:IS23053. [PMID: 38744500 DOI: 10.1071/is23053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/18/2024] [Indexed: 05/16/2024]
Abstract
The integration of morphological and molecular lines of evidence has enabled the family Deltocyathidae to be erected to accommodate Deltocyathus species that were previously ascribed to the family Caryophylliidae. However, although displaying the same morphological characteristics as other species of Deltocyathus , molecular data suggested that D. magnificus was phylogenetically distant from Deltocyathidae, falling within the family Turbinoliidae instead. To elucidate the enigmatic evolutionary history of this species and skeletal microstructural features, the phylogenetic relationships of Deltocyathidae and Turbinoliidae were investigated using nuclear ultraconserved and exon loci and complete mitochondrial genomes. Both nuclear and mitochondrial phylogenomic reconstructions confirmed the position of D. magnificus within turbinolids. Furthermore, a novel mitochondrial gene order was uncovered for Deltocyathidae species. This gene order was not present in Turbinoliidae or in D. magnificus that both have the scleractinian canonical gene order, further indicating the taxonomic utility of mitochondrial gene order. D. magnificus is therefore formally moved to the family Turbinoliidae and accommodated in a new genus (Dennantotrochus Kitahara, Vaga & Stolarski, gen. nov.). Surprisingly, turbinolids and deltocyathids do not differ in microstructural organisation of the skeleton that consists of densely packed, individualised rapid accretion deposits and thickening deposits composed of fibres perpendicular to the skeleton surface. Therefore, although both families are clearly evolutionarily divergent, macromorphological features indicate a case of skeletal convergence while these may still share conservative biomineralisation mechanisms. ZooBank: urn:lsid:zoobank.org:pub:5F1C0E25-3CC6-4D1F-B1F0-CD9D0014678E.
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Affiliation(s)
- C F Vaga
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA; and Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - I G L Seiblitz
- Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - J Stolarski
- Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, PL-00-818 Warsaw, Poland
| | - K C C Capel
- Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Invertebrate Department, National Museum of Rio de Janeiro, Federal University of Rio de Janeiro, 20940-040, Rio de Janeiro, Brazil
| | - A M Quattrini
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA
| | - S D Cairns
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA
| | - D Huang
- Lee Kong Chian Natural History Museum, National University of Singapore, Conservatory Drive, Singapore 117377, Singapore; and Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - R Z B Quek
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; and Yale-NUS College, National University of Singapore, Singapore 138527, Singapore
| | - M V Kitahara
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA; and Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
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3
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Capel KCC, Zilberberg C, Carpes RM, Morrison CL, Vaga CF, Quattrini AM, Zb Quek R, Huang D, Cairns SD, Kitahara MV. How long have we been mistaken? Multi-tools shedding light into the systematics of the widespread deep-water genus Madrepora Linnaeus, 1758 (Scleractinia). Mol Phylogenet Evol 2024; 191:107994. [PMID: 38113961 DOI: 10.1016/j.ympev.2023.107994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/02/2023] [Accepted: 12/12/2023] [Indexed: 12/21/2023]
Abstract
Deep-water coral reefs are found worldwide and harbor biodiversity levels that are comparable to their shallow-water counterparts. However, the genetic diversity and population structure of deep-water species remain poorly explored, and historical taxonomical issues still need to be resolved. Here we used microsatellite markers as well as ultraconserved elements (UCE) and exons to shed light on the population structure, genetic diversity, and phylogenetic position of the genus Madrepora, which contains M. oculata, one of the most widespread scleractinian species. Population structure of 107 samples from three Southwestern Atlantic sedimentary basins revealed the occurrence of a cryptic species, herein named M. piresae sp. nov. (authored by Kitahara, Capel and Zilberberg), which can be found in sympatry with M. oculata. Phylogeny reconstructions based on 134 UCEs and exon regions corroborated the population genetic data, with the recovery of two well-supported groups, and reinforced the polyphyly of the family Oculinidae. In order to better accommodate the genus Madrepora, while reducing taxonomical confusion associated with the name Madreporidae, we propose the monogeneric family Bathyporidae fam. nov. (authored by Kitahara, Capel, Zilberberg and Cairns). Our findings advance the knowledge on the widespread deep-water genus Madrepora, resolve a long-standing question regarding the phylogenetic position of the genus, and highlight the need of a worldwide review of the genus.
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Affiliation(s)
- Kátia C C Capel
- Center for Marine Biology, University of São Paulo, São Sebastião, São Paulo, Brazil; Instituto Coral Vivo, Rua dos Coqueiros, 87, 45807-000 Santa Cruz Cabrália, BA, Brazil.
| | - Carla Zilberberg
- Instituto Coral Vivo, Rua dos Coqueiros, 87, 45807-000 Santa Cruz Cabrália, BA, Brazil; Department of Zoology, Institute of Biodiversity and Sustainability - Nupem, Federal University of Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Raphael M Carpes
- Department of Zoology, Institute of Biodiversity and Sustainability - Nupem, Federal University of Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Cheryl L Morrison
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research Laboratory, Kearneysville, United States
| | - Claudia F Vaga
- Center for Marine Biology, University of São Paulo, São Sebastião, São Paulo, Brazil; Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil; Department of Invertebrate Zoology, Smithsonian Institution, Washington DC, United States
| | - Andrea M Quattrini
- Department of Invertebrate Zoology, Smithsonian Institution, Washington DC, United States
| | - Randolph Zb Quek
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore; Lee Kong Chian Natural History Museum, National University of Singapore, Singapore
| | - Stephen D Cairns
- Department of Invertebrate Zoology, Smithsonian Institution, Washington DC, United States
| | - Marcelo V Kitahara
- Center for Marine Biology, University of São Paulo, São Sebastião, São Paulo, Brazil; Instituto Coral Vivo, Rua dos Coqueiros, 87, 45807-000 Santa Cruz Cabrália, BA, Brazil; Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil; Department of Invertebrate Zoology, Smithsonian Institution, Washington DC, United States.
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The Complete Mitochondrial Genome of Homophyllia bowerbanki (Scleractinia, Lobophylliidae): The First Sequence for the Genus Homophyllia. Genes (Basel) 2023; 14:genes14030695. [PMID: 36980967 PMCID: PMC10048006 DOI: 10.3390/genes14030695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
Reef-building coral species of the order Scleractinia play an important role in shallow tropical seas by providing an environmental base for the ecosystem. The molecular data of complete mitochondrial genome have become an important source for evaluating phylogenetic and evolutionary studies of Scleractinia. Here, the complete mitogenome of Homophyllia bowerbanki (Milne Edwards and Haime, 1857), collected from Nansha Islands of the South China Sea, was sequenced for the first time through a next-generation sequencing method. H. bowerbanki is the first species of its genus for which the mitogenome was sequenced. This mitogenome was 18,154 bp in size and included two transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and two ribosomal RNA genes (rRNAs). It showed a similar gene structure and gene order to the other typical scleractinians. All 17 genes were encoded on the H strand and the total GC content was 33.86% in mitogenome. Phylogenetic analysis (maximum likelihood tree method) showed that H. bowerbanki belonged to the “Robust” clade and clustered together with other two species in the family Lobophylliidae based on 13 PCGs. The mitogenome can provide significant molecular information to clarify the evolutionary and phylogenetic relationships between stony corals and to facilitate their taxonomic classification; it can also support coral species monitoring and conservation efforts.
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Tian P, Jia Z, Cao B, Wang W, Xiao J, Niu W. Complete mitochondrial genome sequences of Physogyralichtensteini (Milne Edwards & Haime, 1851) and Plerogyrasinuosa (Dana, 1846) (Scleractinia, Plerogyridae): characterisation and phylogenetic analysis. Zookeys 2022; 1114:21-34. [PMID: 36761708 PMCID: PMC9848633 DOI: 10.3897/zookeys.1114.85028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/11/2022] [Indexed: 11/12/2022] Open
Abstract
In this study, the whole mitochondrial genomes of Physogyralichtensteini and Plerogyrasinuosa have been sequenced for the first time. The length of their assembled mitogenome sequences were 17,286 bp and 17,586 bp, respectively, both including 13 protein-coding genes, two tRNAs, and two rRNAs. Their mitogenomes offered no distinct structure and their gene order were the same as other typical scleractinians. Based on 13 protein-coding genes, a maximum likelihood phylogenetic analysis showed that Physogyralichtensteini and Plerogyrasinuosa are clustered in the family Plerogyridae, which belongs to the "Robust" clade. The 13 tandem mitogenome PCG sequences used in this research can provide important molecular information to clarify the evolutionary relationships amongst stony corals, especially at the family level. On the other hand, more advanced markers and more species need to be used in the future to confirm the evolutionary relationships of all the scleractinians.
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Affiliation(s)
- Peng Tian
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Zhiyu Jia
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Bingbing Cao
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Wei Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Jiaguang Xiao
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Wentao Niu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, ChinaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
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Seiblitz IGL, Vaga CF, Capel KCC, Cairns SD, Stolarski J, Quattrini AM, Kitahara MV. Caryophylliids (Anthozoa, Scleractinia) and mitochondrial gene order: insights from mitochondrial and nuclear phylogenomics. Mol Phylogenet Evol 2022; 175:107565. [PMID: 35787457 DOI: 10.1016/j.ympev.2022.107565] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 10/17/2022]
Abstract
Molecularly, the family Caryophylliidae is polyphyletic and different sets of genetic data converge towards a consensus that a taxonomic review of this family is necessary. Overall, the order of genes in the mitochondrial genome (mitogenome) together with DNA sequences have been used to successfully untangle evolutionary relationships in several groups of organisms. Published mitogenomes of two caryophylliid genera (Desmophyllum and Solenosmilia) present a transposition of the gene block containing cob, nad2, and nad6, which is located between nad5 5' exon and trnW, while that of Polycyathus chaishanensis presents the same gene order as the majority of scleractinian corals. In molecular-based evolutionary reconstructions, caryophylliids that have the mitochondrial gene rearrangement were recovered as a monophyletic lineage ("true" caryophylliids), while members of the genus Polycyathus were placed in a different position. In this study, additional mitogenomes of this family were assembled and included in evolutionary reconstructions of Scleractinia in order to improve our understanding on whether the mitogenome gene rearrangement is limited to and, therefore, could be a synapomorphy of the actual members of Caryophylliidae. Specimens of Caryophyllia scobinosa, Premocyathus sp., Heterocyathus sulcatus, and Trochocyathus caryophylloides, as well as Desmophyllum pertusum and Solenosmilia variabilis from the Southwest Atlantic were sequenced using Illumina platforms. Then, mitochondrial genomes were assembled and annotated, and nuclear datasets were recovered in-silico from assembled contigs using a previously published set of baits. Evolutionary reconstructions were performed using mitochondrial and nuclear datasets and based on Maximum Likelihood and Bayesian Inference. Obtained mitogenomes are circular and range between 15,816 and 18,225 bp in size and from 30.76% to 36.63% in GC content. The gene rearrangement is only seen in C. scobinosa, D. pertusum, Premocyathus sp., and S. variabilis, which were recovered as a monophyletic clade in both mitochondrial and nuclear phylogenies. On the other hand, the "caryophylliids" with the canonical mitogenome gene order were not recovered within this clade. Differences in features of the skeleton of "true" caryophylliids in comparison to traditional members of the family were observed and offer further support that the gene rearrangement might be seen as a synapomorphy of family Caryophylliidae.
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Affiliation(s)
- I G L Seiblitz
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil.
| | - C F Vaga
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - K C C Capel
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Marine Science, Federal University of São Paulo, 11070-100 Santos, Brazil
| | - S D Cairns
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163 United States of America
| | - J Stolarski
- Institute of Paleobiology, Polish Academy of Sciences, PL-00-818 Warsaw, Poland
| | - A M Quattrini
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163 United States of America
| | - M V Kitahara
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Marine Science, Federal University of São Paulo, 11070-100 Santos, Brazil.
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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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The Mitochondrial Genome of the Sea Anemone Stichodactyla haddoni Reveals Catalytic Introns, Insertion-Like Element, and Unexpected Phylogeny. Life (Basel) 2021; 11:life11050402. [PMID: 33924866 PMCID: PMC8146996 DOI: 10.3390/life11050402] [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: 03/31/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 01/15/2023] Open
Abstract
A hallmark of sea anemone mitochondrial genomes (mitogenomes) is the presence of complex catalytic group I introns. Here, we report the complete mitogenome and corresponding transcriptome of the carpet sea anemone Stichodactyla haddoni (family Stichodactylidae). The mitogenome is vertebrate-like in size, organization, and gene content. Two mitochondrial genes encoding NADH dehydrogenase subunit 5 (ND5) and cytochrome c oxidase subunit I (COI) are interrupted with complex group I introns, and one of the introns (ND5-717) harbors two conventional mitochondrial genes (ND1 and ND3) within its sequence. All the mitochondrial genes, including the group I introns, are expressed at the RNA level. Nonconventional and optional mitochondrial genes are present in the mitogenome of S. haddoni. One of these gene codes for a COI-884 intron homing endonuclease and is organized in-frame with the upstream COI exon. The insertion-like orfA is expressed as RNA and translocated in the mitogenome as compared with other sea anemones. Phylogenetic analyses based on complete nucleotide and derived protein sequences indicate that S. haddoni is embedded within the family Actiniidae, a finding that challenges current taxonomy.
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Seiblitz IGL, Capel KCC, Stolarski J, Quek ZBR, Huang D, Kitahara MV. The earliest diverging extant scleractinian corals recovered by mitochondrial genomes. Sci Rep 2020; 10:20714. [PMID: 33244171 PMCID: PMC7693180 DOI: 10.1038/s41598-020-77763-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/11/2020] [Indexed: 11/08/2022] Open
Abstract
Evolutionary reconstructions of scleractinian corals have a discrepant proportion of zooxanthellate reef-building species in relation to their azooxanthellate deep-sea counterparts. In particular, the earliest diverging "Basal" lineage remains poorly studied compared to "Robust" and "Complex" corals. The lack of data from corals other than reef-building species impairs a broader understanding of scleractinian evolution. Here, based on complete mitogenomes, the early onset of azooxanthellate corals is explored focusing on one of the most morphologically distinct families, Micrabaciidae. Sequenced on both Illumina and Sanger platforms, mitogenomes of four micrabaciids range from 19,048 to 19,542 bp and have gene content and order similar to the majority of scleractinians. Phylogenies containing all mitochondrial genes confirm the monophyly of Micrabaciidae as a sister group to the rest of Scleractinia. This topology not only corroborates the hypothesis of a solitary and azooxanthellate ancestor for the order, but also agrees with the unique skeletal microstructure previously found in the family. Moreover, the early-diverging position of micrabaciids followed by gardineriids reinforces the previously observed macromorphological similarities between micrabaciids and Corallimorpharia as well as its microstructural differences with Gardineriidae. The fact that both families share features with family Kilbuchophylliidae ultimately points towards a Middle Ordovician origin for Scleractinia.
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Affiliation(s)
- Isabela G L Seiblitz
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil.
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil.
| | - Kátia C C Capel
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
| | | | | | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Marcelo V Kitahara
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
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10
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Dubin A, Chi SI, Emblem Å, Moum T, Johansen SD. Deep-water sea anemone with a two-chromosome mitochondrial genome. Gene 2019; 692:195-200. [PMID: 30641219 DOI: 10.1016/j.gene.2018.12.074] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/10/2018] [Accepted: 12/20/2018] [Indexed: 10/27/2022]
Abstract
Mitochondrial genome organization of sea anemones appears conserved among species and families, and is represented by a single circular DNA molecule of 17 to 21 kb. The mitochondrial gene content corresponds to the same 13 protein components of the oxidative phosphorylation (OxPhos) system as in vertebrates. Hallmarks, however, include a highly reduced tRNA gene repertoire and the presence of autocatalytic group I introns. Here we demonstrate that the mitochondrial genome of the deep-water sea anemone Protanthea simplex deviates significantly from that of other known sea anemones. The P. simplex mitochondrial genome contains a heavily scrambled order of genes that are coded on both DNA strands and organized along two circular mito-chromosomes, MCh-I and MCh-II. We found MCh-I to be representative of the prototypic sea anemone mitochondrial genome, encoding 12 OxPhos proteins, two ribosomal RNAs, two transfer RNAs, and a group I intron. In contrast, MCh-II was found to be a laterally transferred plasmid-like DNA carrying the conserved cytochrome oxidase II gene and a second allele of the small subunit ribosomal RNA gene.
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Affiliation(s)
- Arseny Dubin
- Genomics group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
| | - Sylvia Ighem Chi
- Department of Medical Biology, Faculty of Health Sciences, UiT - Arctic University of Norway, Tromsø, Norway.
| | - Åse Emblem
- Department of Medical Biology, Faculty of Health Sciences, UiT - Arctic University of Norway, Tromsø, Norway; Research Laboratory and Department of Laboratory Medicine, Nordland Hospital, Bodø, Norway.
| | - Truls Moum
- Genomics group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
| | - Steinar D Johansen
- Genomics group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway; Department of Medical Biology, Faculty of Health Sciences, UiT - Arctic University of Norway, Tromsø, Norway.
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11
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Zoantharian mitochondrial genomes contain unique complex group I introns and highly conserved intergenic regions. Gene 2017; 628:24-31. [DOI: 10.1016/j.gene.2017.07.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 06/03/2017] [Accepted: 07/10/2017] [Indexed: 11/20/2022]
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Capel KCC, Migotto AE, Zilberberg C, Lin MF, Forsman Z, Miller DJ, Kitahara MV. Complete mitochondrial genome sequences of Atlantic representatives of the invasive Pacific coral species Tubastraea coccinea and T. tagusensis (Scleractinia, Dendrophylliidae): Implications for species identification. Gene 2016; 590:270-7. [PMID: 27234370 DOI: 10.1016/j.gene.2016.05.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/17/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
Abstract
Members of the azooxanthellate coral genus Tubastraea are invasive species with particular concern because they have become established and are fierce competitors in the invaded areas in many parts of the world. Pacific Tubastraea species are spreading fast throughout the Atlantic Ocean, occupying over 95% of the available substrate in some areas and out-competing native endemic species. Approximately half of all known coral species are azooxanthellate but these are seriously under-represented compared to zooxanthellate corals in terms of the availability of mitochondrial (mt) genome data. In the present study, the complete mt DNA sequences of Atlantic individuals of the invasive scleractinian species Tubastraea coccinea and Tubastraea tagusensis were determined and compared to the GenBank reference sequence available for a Pacific "T. coccinea" individual. At 19,094bp (compared to 19,070bp for the GenBank specimen), the mt genomes assembled for the Atlantic T. coccinea and T. tagusensis were among the longest sequence determined to date for "Complex" scleractinians. Comparisons of genomes data showed that the "T. coccinea" sequence deposited on GenBank was more closely related to that from Dendrophyllia arbuscula than to the Atlantic Tubastraea spp., in terms of genome length and base pair similarities. This was confirmed by phylogenetic analysis, suggesting that the former was misidentified and might actually be a member from the genus Dendrophyllia. In addition, although in general the COX1 locus has a slow evolutionary rate in Scleractinia, it was the most variable region of the Tubastraea mt genome and can be used as markers for genus or species identification. Given the limited data available for azooxanthellate corals, the results presented here represent an important contribution to our understanding of phylogenetic relationships and the evolutionary history of the Scleractinia.
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Affiliation(s)
- K C C Capel
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - A E Migotto
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
| | - C Zilberberg
- Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - M F Lin
- Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, Australia; Biodiversity Research Centre, Academia Sinica, Taipei, Taiwan; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Z Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i, USA
| | - D J Miller
- Comparative Genomics Centre and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - M V Kitahara
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil; Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil.
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Addamo AM, Vertino A, Stolarski J, García-Jiménez R, Taviani M, Machordom A. Merging scleractinian genera: the overwhelming genetic similarity between solitary Desmophyllum and colonial Lophelia. BMC Evol Biol 2016; 16:108. [PMID: 27193263 PMCID: PMC4870751 DOI: 10.1186/s12862-016-0654-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/12/2016] [Indexed: 12/16/2022] Open
Abstract
Background In recent years, several types of molecular markers and new microscale skeletal characters have shown potential as powerful tools for phylogenetic reconstructions and higher-level taxonomy of scleractinian corals. Nonetheless, discrimination of closely related taxa is still highly controversial in scleractinian coral research. Here we used newly sequenced complete mitochondrial genomes and 30 microsatellites to define the genetic divergence between two closely related azooxanthellate taxa of the family Caryophylliidae: solitary Desmophyllum dianthus and colonial Lophelia pertusa. Results In the mitochondrial control region, an astonishing 99.8 % of nucleotides between L. pertusa and D. dianthus were identical. Variability of the mitochondrial genomes of the two species is represented by only 12 non-synonymous out of 19 total nucleotide substitutions. Microsatellite sequence (37 loci) analysis of L. pertusa and D. dianthus showed genetic similarity is about 97 %. Our results also indicated that L. pertusa and D. dianthus show high skeletal plasticity in corallum shape and similarity in skeletal ontogeny, micromorphological (septal and wall granulations) and microstructural characters (arrangement of rapid accretion deposits, thickening deposits). Conclusions Molecularly and morphologically, the solitary Desmophyllum and the dendroid Lophelia appear to be significantly more similar to each other than other unambiguous coral genera analysed to date. This consequently leads to ascribe both taxa under the generic name Desmophyllum (priority by date of publication). Findings of this study demonstrate that coloniality may not be a robust taxonomic character in scleractinian corals. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0654-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Maria Addamo
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Agostina Vertino
- Dipartimento di Scienze dell'Ambiente e del Territorio e di Scienze della Terra, Università di Milano Bicocca (UNIMIB), Piazza della Scienza 4, 20126, Milan, Italy.,Department of Geology Renard Centre of Marine Geology, Universiteit Ghent, Krijgslaan 281, B-9000, Ghent, Belgium
| | - Jaroslaw Stolarski
- Polskiej Akademii Nauk, Instytut Paleobiologii, Twarda 51/55, PL-00-818, Warsaw, Poland
| | - Ricardo García-Jiménez
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Marco Taviani
- Consiglio Nazionale delle Ricerche, Istituto di Scienze Marine (ISMAR), Via Gobetti 101, 40129, Bologna, Italy.,Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, 02543, MA, USA.,Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Annie Machordom
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain.
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Lin MF, Kitahara MV, Luo H, Tracey D, Geller J, Fukami H, Miller DJ, Chen CA. Mitochondrial genome rearrangements in the scleractinia/corallimorpharia complex: implications for coral phylogeny. Genome Biol Evol 2016; 6:1086-95. [PMID: 24769753 PMCID: PMC4040992 DOI: 10.1093/gbe/evu084] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Corallimorpharia is a small Order of skeleton-less animals that is closely related to the reef-building corals (Scleractinia) and of fundamental interest in the context of understanding the potential impacts of climate change in the future on coral reefs. The relationship between the nominal Orders Corallimorpharia and Scleractinia is controversial—the former is either the closest outgroup to the Scleractinia or alternatively is derived from corals via skeleton loss. This latter scenario, the “naked coral” hypothesis, is strongly supported by analyses based on mitochondrial (mt) protein sequences, whereas the former is equally strongly supported by analyses of mt nucleotide sequences. The “naked coral” hypothesis seeks to link skeleton loss in the putative ancestor of corallimorpharians with a period of elevated oceanic CO2 during the Cretaceous, leading to the idea that these skeleton-less animals may be harbingers for the fate of coral reefs under global climate change. In an attempt to better understand their evolutionary relationships, we examined mt genome organization in a representative range (12 species, representing 3 of the 4 extant families) of corallimorpharians and compared these patterns with other Hexacorallia. The most surprising finding was that mt genome organization in Corallimorphus profundus, a deep-water species that is the most scleractinian-like of all corallimorpharians on the basis of morphology, was much more similar to the common scleractinian pattern than to those of other corallimorpharians. This finding is consistent with the idea that C. profundus represents a key position in the coral <-> corallimorpharian transition.
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Affiliation(s)
- Mei-Fang Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Shi X, Tian P, Lin R, Lan W, Niu W, Zheng X. Complete mitochondrial genome of disc coralTurbinaria peltata(Scleractinia, Dendrophylliidae). ACTA ACUST UNITED AC 2014; 27:962-3. [DOI: 10.3109/19401736.2014.926506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Emblem Å, Okkenhaug S, Weiss ES, Denver DR, Karlsen BO, Moum T, Johansen SD. Sea anemones possess dynamic mitogenome structures. Mol Phylogenet Evol 2014; 75:184-93. [DOI: 10.1016/j.ympev.2014.02.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 01/31/2014] [Accepted: 02/17/2014] [Indexed: 11/24/2022]
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Kitahara MV, Lin MF, Forêt S, Huttley G, Miller DJ, Chen CA. The "naked coral" hypothesis revisited--evidence for and against scleractinian monophyly. PLoS One 2014; 9:e94774. [PMID: 24740380 PMCID: PMC3989238 DOI: 10.1371/journal.pone.0094774] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 03/20/2014] [Indexed: 12/01/2022] Open
Abstract
The relationship between Scleractinia and Corallimorpharia, Orders within Anthozoa distinguished by the presence of an aragonite skeleton in the former, is controversial. Although classically considered distinct groups, some phylogenetic analyses have placed the Corallimorpharia within a larger Scleractinia/Corallimorpharia clade, leading to the suggestion that the Corallimorpharia are “naked corals” that arose via skeleton loss during the Cretaceous from a Scleractinian ancestor. Scleractinian paraphyly is, however, contradicted by a number of recent phylogenetic studies based on mt nucleotide (nt) sequence data. Whereas the “naked coral” hypothesis was based on analysis of the sequences of proteins encoded by a relatively small number of mt genomes, here a much-expanded dataset was used to reinvestigate hexacorallian phylogeny. The initial observation was that, whereas analyses based on nt data support scleractinian monophyly, those based on amino acid (aa) data support the “naked coral” hypothesis, irrespective of the method and with very strong support. To better understand the bases of these contrasting results, the effects of systematic errors were examined. Compared to other hexacorallians, the mt genomes of “Robust” corals have a higher (A+T) content, codon usage is far more constrained, and the proteins that they encode have a markedly higher phenylalanine content, leading us to suggest that mt DNA repair may be impaired in this lineage. Thus the “naked coral” topology could be caused by high levels of saturation in these mitochondrial sequences, long-branch effects or model violations. The equivocal results of these extensive analyses highlight the fundamental problems of basing coral phylogeny on mitochondrial sequence data.
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MESH Headings
- Amino Acids/genetics
- Animals
- Anthozoa/classification
- Anthozoa/genetics
- Base Composition/genetics
- Codon/genetics
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- Genome, Mitochondrial/genetics
- Mitochondrial Proteins/genetics
- Phylogeny
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Transfer, Met/genetics
- RNA, Transfer, Trp/genetics
- Sequence Analysis, DNA
- Species Specificity
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Affiliation(s)
- Marcelo V. Kitahara
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Santos, São Paulo, Brazil
- Centro de Biologia Marinha (CEBIMar), Universidade de São Paulo, São Sebastião, São Paulo, Brazil
| | - Mei-Fang Lin
- School of Pharmacy and Molecular Sciences, James Cook University, Townsville, Queensland, Australia
- Biodiversity Research Centre, Academia Sinica, Taipei, Taiwan
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Sylvain Forêt
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Gavin Huttley
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - David J. Miller
- School of Pharmacy and Molecular Sciences, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- * E-mail: (CAC); (DJM)
| | - Chaolun Allen Chen
- Biodiversity Research Centre, Academia Sinica, Taipei, Taiwan
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
- Taiwan International Graduate Program (TIGP)-Biodiversity, Academia Sinica, Taipei, Taiwan
- * E-mail: (CAC); (DJM)
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Wang M, Sun J, Li J, Qiu JW. Complete mitochondrial genome of the brain coral Platygyra carnosus. ACTA ACUST UNITED AC 2013; 24:194-5. [PMID: 23688266 DOI: 10.3109/19401736.2012.744981] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Despite the importance of many species of Faviidae as structural-forming corals, only five species in three genera had a sequenced mitochondrial genome. We report the sixth complete mitochondrial genome in this family from the brain coral Platygyra carnosus, which is 16,463 bp in length and AT rich (67.0%). It has the typical coral mitochondrial gene arrangement, consisting of 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 2 transfer RNA (tRNA) genes (tRNA-Met and tRNA-Trp). The ND5 gene is interrupted by a large group I intron which contains 10 protein-coding genes and 12S rRNA. Compared with related species from the same family, the three non-coding regions that are longer than 200 bp are less conserved in sequences than the coding regions, indicating potential markers for population genetic studies.
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Affiliation(s)
- Mingling Wang
- Department of Biology, Hong Kong Baptist University, Hong Kong, People's Republic of China
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