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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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2
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Hayes JM, Abdul-Rahman NH, Gerdes MJ, Musah RA. Coral Genus Differentiation Based on Direct Analysis in Real Time-High Resolution Mass Spectrometry-Derived Chemical Fingerprints. Anal Chem 2021; 93:15306-15314. [PMID: 34761917 DOI: 10.1021/acs.analchem.1c02519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coral reefs are one of the most biologically diverse ecosystems, and the accurate identification of the species is essential for diversity assessment and conservation. Current genus determination approaches are time-consuming and resource-intensive and can be highly subjective. To explore the hypothesis that the small-molecule profiles of coral are genus-specific and can be used as a rapid tool to catalogue and distinguish between coral genera, the small-molecule chemical fingerprints of the species Acanthastrea echinata, Catalaphyllia jardinei, Duncanopsammia axifuga, Echinopora lamellosa, Euphyllia divisa, Euphyllia paraancora, Euphyllia paradivisa, Galaxea fascicularis, Herpolitha limax, Montipora confusa, Monitpora digitata, Montipora setosa, Pachyseris rugosa, Pavona cactus, Plerogyra sinuosa, Pocillopora acuta, Seriatopora hystrix, Sinularia dura, Turbinaria peltata, Turbinaria reniformis, Xenia elongata, and Xenia umbellata were generated using direct analysis in real time-high resolution mass spectrometry (DART-HRMS). It is demonstrated here that the mass spectrum-derived small-molecule profiles for coral of different genera are distinct. Multivariate statistical analysis processing of the DART-HRMS data enabled rapid genus-level differentiation based on the chemical composition of the coral. Coral samples were analyzed with no sample preparation required, making the approach rapid and efficient. The resulting spectra were subjected to kernel discriminant analysis (KDA), which furnished accurate genus differentiation of the coral. Leave-one-out cross-validation (LOOCV) was carried out to determine the classification accuracy of each model and confirm that this approach can be used for coral genus attribution with prediction accuracies ranging from 86.67 to 97.33%. The advantages and application of the statistical analysis to DART-HRMS-derived coral chemical signatures for genus-level differentiation are discussed.
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Affiliation(s)
- Jessica M Hayes
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Nana-Hawwa Abdul-Rahman
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Michael J Gerdes
- CapitalCorals Inc., 20 Colvin Avenue, Albany, New York 12206, United States
| | - Rabi A Musah
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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3
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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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4
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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: 6] [Impact Index Per Article: 1.5] [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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Xiao M, Brugler MR, Broe MB, Gusmão LC, Daly M, Rodríguez E. Mitogenomics suggests a sister relationship of Relicanthus daphneae (Cnidaria: Anthozoa: Hexacorallia: incerti ordinis) with Actiniaria. Sci Rep 2019; 9:18182. [PMID: 31796816 PMCID: PMC6890759 DOI: 10.1038/s41598-019-54637-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/07/2019] [Indexed: 11/09/2022] Open
Abstract
Relicanthus daphneae (formerly Boloceroides daphneae) was first described in 2006 as a giant sea anemone based on morphology. In 2014, its classification was challenged based on molecular data: using five genes, Relicanthus was resolved sister to zoanthideans, but with mixed support. To better understand the evolutionary relationship of Relicanthus with other early-branching metazoans, we present 15 newly-sequenced sea anemone mitochondrial genomes and a mitogenome-based phylogeny including all major cnidarian groups, sponges, and placozoans. Our phylogenetic reconstruction reveals a moderately supported sister relationship between Relicanthus and the Actiniaria. Morphologically, the cnidae of Relicanthus has apical flaps, the only existing synapomorphy for sea anemones. Based on both molecular and morphological results, we propose a third suborder (Helenmonae) within the Actiniaria to accommodate Relicanthus. Although Relicanthus shares the same gene order and content with other available actiniarian mitogenomes, it is clearly distinct at the nucleotide level from anemones within the existing suborders. The phylogenetic position of Relicanthus could reflect its association with the periphery of isolated hydrothermal vents, which, although patchy and ephemeral, harbor unique chemosynthetic communities that provide a relatively stable food source to higher trophic levels over long evolutionary timescales. The ability to colonize the deep sea and the periphery of new vent systems may be facilitated by Relicanthus’ large and extremely yolky eggs.
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Affiliation(s)
- Madelyne Xiao
- Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
| | - Mercer R Brugler
- Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.,Biological Sciences Department, NYC College of Technology (CUNY), 285 Jay Street, Brooklyn, NY, 11201, USA
| | - Michael B Broe
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 300 Aronoff Laboratory, Columbus, OH, 43210, USA
| | - Luciana C Gusmão
- Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
| | - Marymegan Daly
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 300 Aronoff Laboratory, Columbus, OH, 43210, USA.
| | - Estefanía Rodríguez
- Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
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6
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De Palmas S, Soto D, Denis V, Ho MJ, Chen CA. Molecular assessment of Pocillopora verrucosa (Scleractinia; Pocilloporidae) distribution along a depth gradient in Ludao, Taiwan. PeerJ 2018; 6:e5797. [PMID: 30386700 PMCID: PMC6204238 DOI: 10.7717/peerj.5797] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/20/2018] [Indexed: 01/17/2023] Open
Abstract
It can be challenging to identify scleractinian corals from the genus Pocillopora Lamarck 1816 in the field because of their large range of inter- and intra-specific morphological variation that co-occur with changes in the physical environment. This task is made more arduous in the context of a depth gradient, where light and water current could greatly affect the morphology of the corallum. Pocillopora verrucosa (Ellis & Solander 1786) in Taiwan was previously reported exclusively from shallow waters (<10 m in depth), but a recent observation of this species in the mesophotic zone (>40 m in depth) questions this bathymetric distribution. We used the mitochondrial open reading frame and the histone 3 molecular markers to investigate the vertical and horizontal spatial distribution of P. verrucosa around Ludao (Green Island), Taiwan. We genotyped 101 P. verrucosa-like colonies collected from four depth zones, ranging from 7 to 45 m, at three sites around the island. Of the 101 colonies sampled, 85 were genotyped as P. verrucosa, 15 as P. meandrina, and one specimen as an undescribed Pocillopora species. P. verrucosa was found at all depths, while P. meandrina and the undescribed Pocillopora specimen were limited to 15 m depth. P. verrucosa has a large bathymetric distribution around Ludao and could benefit from the refuge that the mesophotic zone offers. This study illustrates the difficulty of identifying Pocillopora corals in the field and emphasizes the relevance of molecular taxonomy as an important and complementary tool to traditional taxonomy for clarifying vertical and horizontal species distribution. Our results also illustrate the need in conservation biology to target species genetic diversity rather than just species diversity.
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Affiliation(s)
- Stéphane De Palmas
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Derek Soto
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Vianney Denis
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Ming-Jay Ho
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Green Island Marine Research Station, Academia Sinica, Ludao, Taitung County, Taiwan
| | - Chaolun Allen Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan.,Institute of Oceanography, National Taiwan University, Taipei, Taiwan
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7
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Brugler MR, González-Muñoz RE, Tessler M, Rodríguez E. An EPIC journey to locate single-copy nuclear markers in sea anemones. ZOOL SCR 2018. [DOI: 10.1111/zsc.12309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mercer R. Brugler
- Division of Invertebrate Zoology; American Museum of Natural History; New York New York
- Biological Sciences Department; NYC College of Technology (CUNY); Brooklyn New York
| | - Ricardo E. González-Muñoz
- Laboratorio de Biología de Cnidarios; Instituto de Investigaciones Marinas y Costeras (IIMyC); CONICET; Universidad Nacional de Mar del Plata; Mar del Plata Argentina
- Instituto de Ciencias del Mar y Limnología (ICMyL); Posgrado en Ciencias del Mar y Limnología (PCMyL); UNAM, Ciudad Universitaria; Ciudad de México México
| | - Michael Tessler
- Division of Invertebrate Zoology; American Museum of Natural History; New York New York
| | - Estefanía Rodríguez
- Division of Invertebrate Zoology; American Museum of Natural History; New York New York
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8
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Underwood JN, Richards ZT, Miller KJ, Puotinen ML, Gilmour JP. Genetic signatures through space, time and multiple disturbances in a ubiquitous brooding coral. Mol Ecol 2018; 27:1586-1602. [DOI: 10.1111/mec.14559] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 02/22/2018] [Accepted: 02/24/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Jim N. Underwood
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
| | - Zoe T. Richards
- Trace and Environmental DNA Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
- Department of Aquatic Zoology Western Australian Museum Perth WA Australia
| | - Karen J. Miller
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
| | - Marji L. Puotinen
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
| | - James P. Gilmour
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
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9
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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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10
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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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11
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Warner PA, van Oppen MJH, Willis BL. Unexpected cryptic species diversity in the widespread coralSeriatopora hystrixmasks spatial-genetic patterns of connectivity. Mol Ecol 2015; 24:2993-3008. [DOI: 10.1111/mec.13225] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/25/2015] [Accepted: 04/29/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Patricia A. Warner
- AIMS@JCU; Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld 4811 Australia
- College of Marine and Environmental Sciences; James Cook University; Townsville Qld 4811 Australia
| | - Madeleine J. H. van Oppen
- AIMS@JCU; Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld 4811 Australia
- Australian Institute of Marine Science; PMB3, Townsville MC; Townsville Qld 4810 Australia
| | - Bette L. Willis
- AIMS@JCU; Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld 4811 Australia
- College of Marine and Environmental Sciences; James Cook University; Townsville Qld 4811 Australia
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Shi X, Lin R, Zheng X, Liu X, Niu W. Complete mitochondrial genome of leaf coral Pavona decussata (Scleractinia, Agariciidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3126-7. [PMID: 25630728 DOI: 10.3109/19401736.2015.1007296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The leaf coral Pavona decussate is a wide-spread shallow-water species of genus Pavona within Agariciidae. In our study, the entire mitochondrial nucleotide sequence of P. decussate was determined. The sequence was 18,378 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes (small and large mitochondrial ribosomal RNA) and 2 transfer RNA genes (tRNA(Met) and tRNA(Trp)). The overall base composition of the mitogenome was 23.8% A, 35.4% T, 25.4% G, and 15.4% C, with a high AT content of 59.3%, which is typical for invertebrate mtDNA. It shared 97.9%, 96.2% and 89.3% mitogenome sequence with P. clavus, Agaricia humilis and Astreopora myriophthalma, respectively.
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Affiliation(s)
- Xiaofeng Shi
- a Laboratory of Marine Biology and Ecology , Third Institute of Oceanography, State Oceanic Administration , Xiamen , P.R. China and
| | - Rongcheng Lin
- a Laboratory of Marine Biology and Ecology , Third Institute of Oceanography, State Oceanic Administration , Xiamen , P.R. China and
| | - Xinqing Zheng
- a Laboratory of Marine Biology and Ecology , Third Institute of Oceanography, State Oceanic Administration , Xiamen , P.R. China and
| | - Xinming Liu
- b Guangxi Academy of Oceanography , Nanning , P.R. China
| | - Wentao Niu
- a Laboratory of Marine Biology and Ecology , Third Institute of Oceanography, State Oceanic Administration , Xiamen , P.R. China and
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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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14
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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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15
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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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Brugler MR, Opresko DM, France SC. The evolutionary history of the order Antipatharia (Cnidaria: Anthozoa: Hexacorallia) as inferred from mitochondrial and nuclear DNA: implications for black coral taxonomy and systematics. Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12060] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mercer R. Brugler
- Department of Biology; University of Louisiana at Lafayette; PO Box 42451 Lafayette LA USA
| | - Dennis M. Opresko
- Smithsonian Institution; National Museum of Natural History; Washington, DC USA
| | - Scott C. France
- Department of Biology; University of Louisiana at Lafayette; PO Box 42451 Lafayette LA USA
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DNA barcoding reveals the coral "laboratory-rat", Stylophora pistillata encompasses multiple identities. Sci Rep 2013; 3:1520. [PMID: 23519209 PMCID: PMC3605610 DOI: 10.1038/srep01520] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 03/05/2013] [Indexed: 02/07/2023] Open
Abstract
Stylophora pistillata is a widely used coral “lab-rat” species with highly variable morphology and a broad biogeographic range (Red Sea to western central Pacific). Here we show, by analysing Cytochorme Oxidase I sequences, from 241 samples across this range, that this taxon in fact comprises four deeply divergent clades corresponding to the Pacific-Western Australia, Chagos-Madagascar-South Africa, Gulf of Aden-Zanzibar-Madagascar, and Red Sea-Persian/Arabian Gulf-Kenya. On the basis of the fossil record of Stylophora, these four clades diverged from one another 51.5-29.6 Mya, i.e., long before the closure of the Tethyan connection between the tropical Indo-West Pacific and Atlantic in the early Miocene (16–24 Mya) and should be recognised as four distinct species. These findings have implications for comparative ecological and/or physiological studies carried out using Stylophora pistillata as a model species, and highlight the fact that phenotypic plasticity, thought to be common in scleractinian corals, can mask significant genetic variation.
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Osigus HJ, Eitel M, Bernt M, Donath A, Schierwater B. Mitogenomics at the base of Metazoa. Mol Phylogenet Evol 2013; 69:339-51. [PMID: 23891951 DOI: 10.1016/j.ympev.2013.07.016] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 05/29/2013] [Accepted: 07/09/2013] [Indexed: 11/25/2022]
Abstract
Unraveling the base of metazoan evolution is of crucial importance for rooting the metazoan Tree of Life. This subject has attracted substantial attention for more than a century and recently fueled a burst of modern phylogenetic studies. Conflicting scenarios from different studies and incongruent results from nuclear versus mitochondrial markers challenge current molecular phylogenetic approaches. Here we analyze the presently most comprehensive data sets of mitochondrial genomes from non-bilaterian animals to illuminate the phylogenetic relationships among early branching metazoan phyla. The results of our analyses illustrate the value of mitogenomics and support previously known topologies between animal phyla but also identify several problematic taxa, which are sensitive to long branch artifacts or missing data.
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Affiliation(s)
- Hans-Jürgen Osigus
- Stiftung Tierärztliche Hochschule Hannover, ITZ, Ecology and Evolution, Buenteweg 17d, D-30559 Hannover, Germany.
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Uda K, Komeda Y, Fujita T, Iwasaki N, Bavestrello G, Giovine M, Cattaneo-Vietti R, Suzuki T. Complete mitochondrial genomes of the Japanese pink coral (Corallium elatius) and the Mediterranean red coral (Corallium rubrum): a reevaluation of the phylogeny of the family Coralliidae based on molecular data. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2013; 8:209-19. [PMID: 23792378 DOI: 10.1016/j.cbd.2013.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/23/2013] [Accepted: 05/26/2013] [Indexed: 11/30/2022]
Abstract
Precious corals are soft corals belonging to the family Coralliidae (Anthozoa: Octocorallia: Alcyonacea) and class Anthozoa, whose skeletal axes are used for jewelry. The family Coralliidae includes ca. 40 species and was originally thought to comprise of the single genus Corallium. In 2003, Corallium was split into two genera, Corallium and Paracorallium, and seven species were moved to this newly identified genus on the bases of morphological features. Previously, we determined the complete mitochondrial genome sequence of two precious corals Paracorallium japonicum and Corallium konojoi, in order to clarify their systematic positions. The two genomes showed high nucleotide sequence identity, but their gene order arrangements were not identical. Here, we determined three complete mitochondrial genome sequences from the one specimen of Mediterranean Corallium rubrum and two specimens of Corallium elatius coming from Kagoshima (South Japan). The circular mitochondrial genomes of C. rubrum and C. elatius are 18,915bp and 18,969-18,970bp in length, respectively, and encode 14 typical octocorallian protein-coding genes (nad1-6, nad4L, cox1-3, cob, atp6, atp8, and mtMutS, which is an octocoral-specific mismatch repair gene homologue), two ribosomal RNA genes (rns and rnl), and one transfer RNA (trnM). The overall nucleotide differences between C. konojoi and each C. elatius haplotype (T2007 and I2011) are only 10 and 11 nucleotides, respectively; this degree of similarity indicates that C. elatius and C. konojoi are very closely related species. Notably, the C. rubrum mitochondrial genome shows more nucleotide sequence identity to P. japonicum (99.5%) than to its congeneric species C. konojoi (95.3%) and C. elatius (95.3%). Moreover, the gene order arrangement of C. rubrum was the same as that of P. japonicum, while that of C. elatius was the same as C. konojoi. Phylogenetic analysis based on three mitochondrial genes from 24 scleraxonian species shows that the family Coralliidae is separated into two distinct groups, recovering Corallium as a paraphyletic genus. Our results indicate that the currently accepted generic classification of Coralliidae should be reconsidered.
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Affiliation(s)
- Kouji Uda
- Laboratories of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan.
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Flot JF, Dahl M, André C. Lophelia pertusa corals from the Ionian and Barents seas share identical nuclear ITS2 and near-identical mitochondrial genome sequences. BMC Res Notes 2013; 6:144. [PMID: 23578100 PMCID: PMC3637110 DOI: 10.1186/1756-0500-6-144] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 03/22/2013] [Indexed: 11/10/2022] Open
Abstract
Background Lophelia pertusa is a keystone cold-water coral species with a widespread distribution. Due to the lack of a mitochondrial marker variable enough for intraspecific analyses, the population structure of this species has only been studied using ITS and microsatellites so far. We therefore decided to sequence and compare complete mitochondrial genomes from two distant L. pertusa populations putatively isolated from each other (in the Barents Sea off Norway and in the Mediterranean Sea off Italy) in the hope of finding regions variable enough for population genetic and phylogeographic studies. Results The mitogenomes of two L. pertusa individuals collected in the Mediterranean and Barents seas differed at only one position, which was a non-synonymous substitution, but comparison with another recently published L. pertusa mitochondrial genome sequence from Norway revealed 18 nucleotide differences. These included two synonymous and nine non-synonymous substitutions in protein-coding genes (dN/dS > 1): hence, the mitogenome of L. pertusa may be experiencing positive selection. To test for the presence of cryptic species, the mitochondrial control region and the nuclear ITS2 were sequenced for five individuals from each site: Italian and Norwegian populations turned out to share haplotypes of both markers, indicating that they belonged to the same species. Conclusions L. pertusa corals collected 7,500 km apart shared identical nuclear ITS2 and near-identical mitogenomes, supporting the hypothesis of a recent connection between Lophelia reefs in the Mediterranean and in the Northern Atlantic. Multi-locus or population genomic approaches will be required to shed further light on the genetic connectivity between L. pertusa reefs across Europe; nevertheless, ITS2 and the mitochondrial control region may be useful markers for investigating the phylogeography and species boundaries of the keystone genus Lophelia across its worldwide area of distribution.
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21
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Pante E, Saucier EH, France SC. Molecular and morphological data support reclassification of the octocoral genus Isidoides. INVERTEBR SYST 2013. [DOI: 10.1071/is12053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The rare octocoral genus Isidoides Nutting, 1910 was originally placed in the Gorgonellidae (now the Ellisellidae), even though it showed a remarkable similarity to the Isidae (now the Isididae). Isidoides was not classified in the Isididae mostly because the type specimen lacked skeletal nodes, a defining characteristic of that family. The genus was later assigned to the Chrysogorgiidae based on sclerite morphology. Specimens were recently collected in the south-western Pacific, providing material for genetic analysis and detailed characterisation of the morphology, and allowing us to consider the systematic placement of this taxon within the suborder Calcaxonia. A previously reported phylogeny allowed us to reject monophyly with the Chrysogorgiidae, and infer a close relationship with the Isididae subfamily Keratoisidinae. While scanning for molecular variation across mitochondrial genes, we discovered a novel gene order that is, based on available data, unique among metazoans. Despite these new data, the systematic placement of Isidoides is still unclear, as (1) the phylogenetic relationships among Isididae subfamilies remain poorly resolved, (2) genetic distances between mitochondrial mtMutS sequences from Isidoides and Keratoisidinae are characteristic of intra-familial distances, and (3) mitochondrial gene rearrangements may occur among confamilial genera. For these reasons, and because a revision of the Isididae is beyond the scope of this contribution, we amend the familial placement of Isidoides to incertae sedis.
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Mitogenome polymorphism in a single branch sample revealed by SOLiD deep sequencing of the Lophelia pertusa coral genome. Gene 2012; 506:344-9. [DOI: 10.1016/j.gene.2012.06.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Accepted: 06/19/2012] [Indexed: 11/22/2022]
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23
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Lin MF, Kitahara MV, Tachikawa H, Fukami H, Miller DJ, Chen CA. Novel organization of the mitochondrial genome in the deep-sea coral, Madrepora oculata (Hexacorallia, Scleractinia, Oculinidae) and its taxonomic implications. Mol Phylogenet Evol 2012; 65:323-8. [PMID: 22760028 DOI: 10.1016/j.ympev.2012.06.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 05/29/2012] [Accepted: 06/04/2012] [Indexed: 11/18/2022]
Abstract
Madrepora is one of the most ecologically important genera of reef-building scleractinians in the deep sea, occurring from tropical to high-latitude regions. Despite this, the taxonomic affinities and relationships within the genus Madrepora remain unclear. To clarify these issues, we sequenced the mitochondrial (mt) genome of the most widespread Madrepora species, M. oculata, and compared this with data for other scleractinians. The architecture of the M. oculata mt genome was very similar to that of other scleractinians, except for a novel gene rearrangement affecting only cox2 and cox3. This pattern of gene organization was common to four geographically distinct M. oculata individuals as well as the congeneric species M. minutiseptum, but was not shared by other genera that are closely related on the basis of cox1 sequence analysis nor other oculinids, suggesting that it might be unique to Madrepora.
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Affiliation(s)
- Mei-Fang Lin
- Biodiversity Research Center, Academia Sinica, Nangang, Taipei 115, Taiwan
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24
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Maikova OO, Stepnova GN, Belikov SI. Variations in noncoding sequences of the mitochondrial DNA in sponges from family Lubomirskiidae. DOKL BIOCHEM BIOPHYS 2012; 442:46-8. [DOI: 10.1134/s1607672912010140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Indexed: 11/23/2022]
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Kim S, Kim J, Choi HG, Park JK, Min GS. Complete mitochondrial genome of the northern mauxia shrimpAcetes chinensis(Decapoda, Dendrobranchiata, Sergestoidae). ACTA ACUST UNITED AC 2012; 23:28-30. [DOI: 10.3109/19401736.2011.643878] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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26
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Bongaerts P, Riginos C, Hay KB, van Oppen MJH, Hoegh-Guldberg O, Dove S. Adaptive divergence in a scleractinian coral: physiological adaptation of Seriatopora hystrix to shallow and deep reef habitats. BMC Evol Biol 2011; 11:303. [PMID: 22004364 PMCID: PMC3203877 DOI: 10.1186/1471-2148-11-303] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 10/17/2011] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Divergent natural selection across environmental gradients has been acknowledged as a major driver of population and species divergence, however its role in the diversification of scleractinian corals remains poorly understood. Recently, it was demonstrated that the brooding coral Seriatopora hystrix and its algal endosymbionts (Symbiodinium) are genetically partitioned across reef environments (0-30 m) on the far northern Great Barrier Reef. Here, we explore the potential mechanisms underlying this differentiation and assess the stability of host-symbiont associations through a reciprocal transplantation experiment across habitats ('Back Reef', 'Upper Slope' and 'Deep Slope'), in combination with molecular (mtDNA and ITS2-DGGE) and photo-physiological analyses (respirometry and HPLC). RESULTS The highest survival rates were observed for native transplants (measured 14 months after transplantation), indicating differential selective pressures between habitats. Host-symbiont assemblages remained stable during the experimental duration, demonstrating that the ability to "shuffle" or "switch" symbionts is restricted in S. hystrix. Photo-physiological differences were observed between transplants originating from the shallow and deep habitats, with indirect evidence of an increased heterotrophic capacity in native deep-water transplants (from the 'Deep Slope' habitat). Similar photo-acclimatisation potential was observed between transplants originating from the two shallow habitats ('Back Reef' and 'Upper Slope'), highlighting that their genetic segregation over depth may be due to other, non-photo-physiological traits under selection. CONCLUSIONS This study confirms that the observed habitat partitioning of S. hystrix (and associated Symbiodinium) is reflective of adaptive divergence along a depth gradient. Gene flow appears to be reduced due to divergent selection, highlighting the potential role of ecological mechanisms, in addition to physical dispersal barriers, in the diversification of scleractinian corals and their associated Symbiodinium.
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Affiliation(s)
- Pim Bongaerts
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
- ARC Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Kyra B Hay
- Heron Island Research Station, The University of Queensland, Heron Island, QLD 4680, Australia
| | | | - Ove Hoegh-Guldberg
- ARC Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, QLD 4072, Australia
- Global Change Institute, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Sophie Dove
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
- ARC Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, QLD 4072, Australia
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Flot JF, Blanchot J, Charpy L, Cruaud C, Licuanan WY, Nakano Y, Payri C, Tillier S. Incongruence between morphotypes and genetically delimited species in the coral genus Stylophora: phenotypic plasticity, morphological convergence, morphological stasis or interspecific hybridization? BMC Ecol 2011; 11:22. [PMID: 21970706 PMCID: PMC3269986 DOI: 10.1186/1472-6785-11-22] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 10/04/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Morphological data suggest that, unlike most other groups of marine organisms, scleractinian corals of the genus Stylophora are more diverse in the western Indian Ocean and in the Red Sea than in the central Indo-Pacific. However, the morphology of corals is often a poor predictor of their actual biodiversity: hence, we conducted a genetic survey of Stylophora corals collected in Madagascar, Okinawa, the Philippines and New Caledonia in an attempt to find out the true number of species in these various locations. RESULTS A molecular phylogenetic analysis of the mitochondrial ORF and putative control region concurs with a haploweb analysis of nuclear ITS2 sequences in delimiting three species among our dataset: species A and B are found in Madagascar whereas species C occurs in Okinawa, the Philippines and New Caledonia. Comparison of ITS1 sequences from these three species with data available online suggests that species C is also found on the Great Barrier Reef, in Malaysia, in the South China Sea and in Taiwan, and that a distinct species D occurs in the Red Sea. Shallow-water morphs of species A correspond to the morphological description of Stylophora madagascarensis, species B presents the morphology of Stylophora mordax, whereas species C comprises various morphotypes including Stylophora pistillata and Stylophora mordax. CONCLUSIONS Genetic analysis of the coral genus Stylophora reveals species boundaries that are not congruent with morphological traits. Of the four hypotheses that may explain such discrepancy (phenotypic plasticity, morphological stasis, morphological convergence, and interspecific hybridization), the first two appear likely to play a role but the fourth one is rejected since mitochondrial and nuclear markers yield congruent species delimitations. The position of the root in our molecular phylogenies suggests that the center of origin of Stylophora is located in the western Indian Ocean, which probably explains why this genus presents a higher biodiversity in the westernmost part of its area of distribution than in the "Coral Triangle".
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Affiliation(s)
- Jean-François Flot
- Courant Research Center "Geobiology", University of Göttingen, Goldschmidtstraße 3, 37077 Göttingen, Germany
- CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, 91057 Evry Cedex, France
- UMR UPMC-CNRS-MNHN-IRD 7138, Département Systématique et Évolution, Muséum National d'Histoire Naturelle, Case Postale 26, 57 rue Cuvier, 75231 Paris Cedex 05, France
- URBO, Department of Biology, University of Namur, Rue de Bruxelle 61, 5000 Namur, Belgium
| | - Jean Blanchot
- UMR LOBP, Centre d'Océanologie de Marseille, Campus de Luminy, Case 901, 13288 Marseille Cedex 09, France
| | - Loïc Charpy
- UMR LOBP, Centre IRD de Tahiti, BP 529, 98713 Papeete, French Polynesia
| | - Corinne Cruaud
- CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, 91057 Evry Cedex, France
| | - Wilfredo Y Licuanan
- Br. Alfred Shields FSC Marine Station and Biology Department, De La Salle University, Manila 1004, Philippines
| | - Yoshikatsu Nakano
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 3422, Japan
| | - Claude Payri
- UR COREUS, IRD, B.P. A5, 98848 Nouméa, New Caledonia
| | - Simon Tillier
- UMR UPMC-CNRS-MNHN-IRD 7138, Département Systématique et Évolution, Muséum National d'Histoire Naturelle, Case Postale 26, 57 rue Cuvier, 75231 Paris Cedex 05, France
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Mitogenome rearrangement in the cold-water scleractinian coral Lophelia pertusa (Cnidaria, Anthozoa) involves a long-term evolving group I intron. Mol Phylogenet Evol 2011; 61:495-503. [PMID: 21820066 DOI: 10.1016/j.ympev.2011.07.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Revised: 07/13/2011] [Accepted: 07/14/2011] [Indexed: 11/21/2022]
Abstract
Group I introns are genetic insertion elements that invade host genomes in a wide range of organisms. In metazoans, however, group I introns are extremely rare, so far only identified within mitogenomes of hexacorals and some sponges. We sequenced the complete mitogenome of the cold-water scleractinian coral Lophelia pertusa, the dominating deep sea reef-building coral species in the North Atlantic Ocean. The mitogenome (16,150 bp) has the same gene content but organized in a unique gene order compared to that of other known scleractinian corals. A complex group I intron (6460 bp) inserted in the ND5 gene (position 717) was found to host seven essential mitochondrial protein genes and one ribosomal RNA gene. Phylogenetic analysis supports a vertical inheritance pattern of the ND5-717 intron among hexacoral mitogenomes with no examples of intron loss. Structural assessments of the Lophelia intron revealed an unusual organization that lacks the universally conserved ωG at the 3' end, as well as a highly compact RNA core structure with overlapping ribozyme and protein coding capacities. Based on phylogenetic and structural analyses we reconstructed the evolutionary history of ND5-717, from its ancestral protist origin, through intron loss in some early metazoan lineages, and into a compulsory feature with functional implications in hexacorals.
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Zhang J, Wu X, Xie M, Xu X, Li A. The mitochondrial genome ofPolylabris halichoeres(Monogenea: Microcotylidae). ACTA ACUST UNITED AC 2011; 22:3-5. [DOI: 10.3109/19401736.2011.588223] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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van Oppen MJH, Bongaerts P, Underwood JN, Peplow LM, Cooper TF. The role of deep reefs in shallow reef recovery: an assessment of vertical connectivity in a brooding coral from west and east Australia. Mol Ecol 2011; 20:1647-60. [PMID: 21410573 DOI: 10.1111/j.1365-294x.2011.05050.x] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Uda K, Komeda Y, Koyama H, Koga K, Fujita T, Iwasaki N, Suzuki T. Complete mitochondrial genomes of two Japanese precious corals, Paracorallium japonicum and Corallium konojoi (Cnidaria, Octocorallia, Coralliidae): notable differences in gene arrangement. Gene 2011; 476:27-37. [PMID: 21310221 DOI: 10.1016/j.gene.2011.01.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 01/28/2011] [Accepted: 01/31/2011] [Indexed: 10/18/2022]
Abstract
Precious coral are taxonomically a group of corals that belong to the family Coralliidae within the order Alcyonacea, subclass Octocorallia, and class Anthozoa, whose skeletal axes are used for jewelry. They are distributed in the Mediterranean Sea and in waters adjacent to Japan, Taiwan, Midway Island and the Hawaiian Islands. The genus Corallium of the family Coralliidae was recently divided into two genera, Corallium and Paracorallium, based on morphological observations, but insufficient molecular evidence to support this classification has been presented to date. We determined for the first time the complete mitochondrial genome sequence of two precious corals P. japonicum and C. konojoi, in order to clarify their systematic positions. The circular mitochondrial genomes of P. japonicum and C. konojoi are 18,913bp and 18,969bp in length, respectively, and encode 13 typical energy pathway protein coding genes (nad1-6, nad4L, cox1-3, cob, atp6 and atp8), two ribosomal RNA genes (rns and rnl), a transfer RNA (trnM) and a mismatch repair gene homologue msh1. The two genomes have an overall nucleotide sequence identity of 97.5%, which is comparable to that between Acanella eburnea and Keratoisidinae sp. belonging to Octocorallia. Surprisingly, however, their gene arrangements were not identical. Phylogenetic analyses using seven complete mitochondrial genome sequences belonging to species in the subclass Octocorallia indicated that within the subclass, at least three gene order rearrangement events occurred during evolution. Our results support the validity of the morphological classification that separated the family Coralliidae into two genera, Corallium and Paracorallium.
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Affiliation(s)
- Kouji Uda
- Laboratories of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan.
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Bongaerts P, Riginos C, Ridgway T, Sampayo EM, van Oppen MJH, Englebert N, Vermeulen F, Hoegh-Guldberg O. Genetic divergence across habitats in the widespread coral Seriatopora hystrix and its associated Symbiodinium. PLoS One 2010; 5:e10871. [PMID: 20523735 PMCID: PMC2877717 DOI: 10.1371/journal.pone.0010871] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Accepted: 05/04/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Coral reefs are hotspots of biodiversity, yet processes of diversification in these ecosystems are poorly understood. The environmental heterogeneity of coral reef environments could be an important contributor to diversification, however, evidence supporting ecological speciation in corals is sparse. Here, we present data from a widespread coral species that reveals a strong association of host and symbiont lineages with specific habitats, consistent with distinct, sympatric gene pools that are maintained through ecologically-based selection. METHODOLOGY/PRINCIPAL FINDINGS Populations of a common brooding coral, Seriatopora hystrix, were sampled from three adjacent reef habitats (spanning a approximately 30 m depth range) at three locations on the Great Barrier Reef (n = 336). The populations were assessed for genetic structure using a combination of mitochondrial (putative control region) and nuclear (three microsatellites) markers for the coral host, and the ITS2 region of the ribosomal DNA for the algal symbionts (Symbiodinium). Our results show concordant genetic partitioning of both the coral host and its symbionts across the different habitats, independent of sampling location. CONCLUSIONS/SIGNIFICANCE This study demonstrates that coral populations and their associated symbionts can be highly structured across habitats on a single reef. Coral populations from adjacent habitats were found to be genetically isolated from each other, whereas genetic similarity was maintained across similar habitat types at different locations. The most parsimonious explanation for the observed genetic partitioning across habitats is that adaptation to the local environment has caused ecological divergence of distinct genetic groups within S. hystrix.
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Affiliation(s)
- Pim Bongaerts
- Global Change Institute, The University of Queensland, St Lucia, Queensland, Australia.
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MitoZoa: A curated mitochondrial genome database of metazoans for comparative genomics studies. Mitochondrion 2010; 10:192-9. [DOI: 10.1016/j.mito.2010.01.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 12/14/2009] [Accepted: 01/08/2010] [Indexed: 11/23/2022]
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Wagner D, Brugler MR, Opresko DM, France SC, Montgomery AD, Toonen RJ. Using morphometrics, in situ observations and genetic characters to distinguish among commercially valuable Hawaiian black coral species; a redescription of Antipathes grandis Verrill, 1928 (Antipatharia:Antipathidae). INVERTEBR SYST 2010. [DOI: 10.1071/is10004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The commercially valuable Hawaiian black coral Antipathes grandis Verrill, 1928 is redescribed based on reexamination of the holotype from the Bernice P. Bishop Museum and field collections of 34 specimens from depths of 27–127 m. The first scanning electron micrographs of A. grandis skeletal spines are provided, along with a series of in situ colour photographs and morphometric measurements of spines and polyps. Three colour morphotypes were collected in the field (red, pale red, and white), none of which could be differentiated based on morphological or genetic characters (two mitochondrial and two nuclear markers). In situ observations are used in conjunction with morphological and genetic characters to distinguish among the commercially valuable Hawaiian black coral species A. grandis and A. griggi Opresko, 2009. A. grandis is differentiated from A. griggi by its finer and more irregular branching, smaller and more closely-spaced polyps, and conical spines that are smaller and not characterised by bifurcations towards their apex. Morphologically, the species most closely resembling A. grandis is A. caribbeana Opresko, 1996 from the Caribbean. Among analysed congenerics, DNA sequences of A. grandis were likewise most similar to those of A. caribbeana for three of the four molecular markers used in this study. A combination of low genetic variability, incomplete taxonomic sampling, and unexpected similarity between A. caribbeana and the unbranched whip coral Stichopathes cf. occidentalis (Gray, 1860), hindered our ability to determine the sister relationship of A. grandis. However, in no phylogenetic reconstruction did A. grandis group sister to its sympatric congener A. griggi.
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Comparative mitochondrial genomics of freshwater mussels (Bivalvia: Unionoida) with doubly uniparental inheritance of mtDNA: gender-specific open reading frames and putative origins of replication. Genetics 2009; 183:1575-89. [PMID: 19822725 DOI: 10.1534/genetics.109.110700] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Doubly uniparental inheritance (DUI) of mitochondrial DNA in marine mussels (Mytiloida), freshwater mussels (Unionoida), and marine clams (Veneroida) is the only known exception to the general rule of strict maternal transmission of mtDNA in animals. DUI is characterized by the presence of gender-associated mitochondrial DNA lineages that are inherited through males (male-transmitted or M types) or females (female-transmitted or F types), respectively. This unusual system constitutes an excellent model for studying basic aspects of mitochondrial DNA inheritance and the evolution of mtDNA genomes in general. Here we compare published mitochondrial genomes of unionoid bivalve species with DUI, with an emphasis on characterizing unassigned regions, to identify regions of the F and M mtDNA genomes that could (i) play a role in replication or transcription of the mtDNA molecule and/or (ii) determine whether a genome will be transmitted via the female or the male gamete. Our results reveal the presence of one F-specific and one M-specific open reading frames (ORFs), and we hypothesize that they play a role in the transmission and/or gender-specific adaptive functions of the M and F mtDNA genomes in unionoid bivalves. Three major unassigned regions shared among all F and M unionoid genomes have also been identified, and our results indicate that (i) two of them are potential heavy-strand control regions (O(H)) for regulating replication and/or transcription and that (ii) multiple and potentially bidirectional light-strand origins of replication (O(L)) are present in unionoid F and M mitochondrial genomes. We propose that unassigned regions are the most promising candidate sequences in which to find regulatory and/or gender-specific sequences that could determine whether a mitochondrial genome will be maternally or paternally transmitted.
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Exploring the utility of an indel-rich, mitochondrial intergenic region as a molecular barcode for bamboo corals (Octocorallia: Isididae). Mar Genomics 2009; 2:183-92. [DOI: 10.1016/j.margen.2009.10.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 08/19/2009] [Accepted: 10/08/2009] [Indexed: 11/24/2022]
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More evidence for pervasive paraphyly in scleractinian corals: Systematic study of Southeast Asian Faviidae (Cnidaria; Scleractinia) based on molecular and morphological data. Mol Phylogenet Evol 2009; 50:102-16. [PMID: 19000930 DOI: 10.1016/j.ympev.2008.10.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Revised: 10/04/2008] [Accepted: 10/17/2008] [Indexed: 11/22/2022]
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Chen IP, Tang CY, Chiou CY, Hsu JH, Wei NV, Wallace CC, Muir P, Wu H, Chen CA. Comparative analyses of coding and noncoding DNA regions indicate that Acropora (Anthozoa: Scleractina) possesses a similar evolutionary tempo of nuclear vs. mitochondrial genomes as in plants. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2009; 11:141-152. [PMID: 18670809 DOI: 10.1007/s10126-008-9129-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Accepted: 06/20/2008] [Indexed: 05/26/2023]
Abstract
Evidence suggests that the mitochondrial (mt)DNA of anthozoans is evolving at a slower tempo than their nuclear DNA; however, parallel surveys of nuclear and mitochondrial variations and calibrated rates of both synonymous and nonsynonymous substitutions across taxa are needed in order to support this scenario. We examined species of the scleractinian coral genus Acropora, including previously unstudied species, for molecular variations in protein-coding genes and noncoding regions of both nuclear and mt genomes. DNA sequences of a calmodulin (CaM)-encoding gene region containing three exons, two introns and a 411-bp mt intergenic spacer (IGS) spanning the cytochrome b (cytb) and NADH 2 genes, were obtained from 49 Acropora species. The molecular evolutionary rates of coding and noncoding regions in nuclear and mt genomes were compared in conjunction with published data, including mt cytochrome b, the control region, and nuclear Pax-C introns. Direct sequencing of the mtIGS revealed an average interspecific variation comparable to that seen in published data for mt cytb. The average interspecific variation of the nuclear genome was two to five times greater than that of the mt genome. Based on the calibration of the closure of Panama Isthmus (3.0 mya) and closure of the Tethy Seaway (12 mya), synonymous substitution rates ranged from 0.367% to 1.467% Ma(-1) for nuclear CaM, which is about 4.8 times faster than those of mt cytb (0.076-0.303% Ma(-1)). This is similar to the findings in plant genomes that the nuclear genome is evolving at least five times faster than those of mitochondrial counterparts.
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Affiliation(s)
- I-Ping Chen
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan
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Chen C, Chiou CY, Dai CF, Chen CA. Unique mitogenomic features in the scleractinian family pocilloporidae (scleractinia: astrocoeniina). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2008; 10:538-553. [PMID: 18478295 DOI: 10.1007/s10126-008-9093-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2007] [Revised: 02/28/2008] [Accepted: 03/02/2008] [Indexed: 05/26/2023]
Abstract
The complete DNA sequences of three mitochondrial (mt) genomes were obtained from the scleractinian corals, Stylophora pistillata, Pocillopora damicornis, and Madracis mirabilis, and were compared to the published mt genomes to elucidate phylogenetically unique features of the family Pocilloporidae. The entire mt genomes of pocilloporid corals ranged from 16,951 to 17,425 bp with the A+T contents of their sense strands ranging from 68.4% to 70.2%. The gene order of protein-coding genes was identical to those of other scleractinian corals. The novel atp8 gene, first described in confamilial Seriatopora corals, was also confirmed using reverse transcription-polymerase chain reaction (RT-PCR), Northern blot, and sequence analyses in other genera of the Pocilloporidae. The intergenic spacer between atp6 and nad4, containing distinct repeated elements, conserved sequence blocks and domains, and functional structures, possesses typical characteristics of a putative control region for the four coral genera. A duplicated trnW, detected in the region close to the cox1 gene and which shares the highly conserved primary and secondary structures of its original counterpart, was discovered in both Seriatopora and Stylophora. These molecular characteristics are unique and provide the phylogenetic information for future evaluation of the status of the family Pocilloporidae in the evolutionary history of scleractinian corals.
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Affiliation(s)
- Chienhsun Chen
- Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
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Gissi C, Iannelli F, Pesole G. Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species. Heredity (Edinb) 2008; 101:301-20. [PMID: 18612321 DOI: 10.1038/hdy.2008.62] [Citation(s) in RCA: 419] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The mitochondrial genome (mtDNA) of Metazoa is a good model system for evolutionary genomic studies and the availability of more than 1000 sequences provides an almost unique opportunity to decode the mechanisms of genome evolution over a large phylogenetic range. In this paper, we review several structural features of the metazoan mtDNA, such as gene content, genome size, genome architecture and the new parameter of gene strand asymmetry in a phylogenetic framework. The data reviewed here show that: (1) the plasticity of Metazoa mtDNA is higher than previously thought and mainly due to variation in number and location of tRNA genes; (2) an exceptional trend towards stabilization of genomic features occurred in deuterostomes and was exacerbated in vertebrates, where gene content, genome architecture and gene strand asymmetry are almost invariant. Only tunicates exhibit a very high degree of genome variability comparable to that found outside deuterostomes. In order to analyse the genomic evolutionary process at short evolutionary distances, we have also compared mtDNAs of species belonging to the same genus: the variability observed in congeneric species significantly recapitulates the evolutionary dynamics observed at higher taxonomic ranks, especially for taxa showing high levels of genome plasticity and/or fast nucleotide substitution rates. Thus, the analysis of congeneric species promises to be a valuable approach for the assessment of the mtDNA evolutionary trend in poorly or not yet sampled metazoan groups.
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Affiliation(s)
- C Gissi
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università di Milano, Milano, Italy.
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The Mitochondrial Genome of a Deep-Sea Bamboo Coral (Cnidaria, Anthozoa, Octocorallia, Isididae): Genome Structure and Putative Origins of Replication Are Not Conserved Among Octocorals. J Mol Evol 2008; 67:125-36. [DOI: 10.1007/s00239-008-9116-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Revised: 03/14/2008] [Accepted: 04/23/2008] [Indexed: 10/22/2022]
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