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Ma J, Dong X, Xu K, Zeng J, Wang Z, Li J. The Characterization of the Mitochondrial Genome of Fulgoraria rupestris and Phylogenetic Considerations within the Neogastropoda. Genes (Basel) 2024; 15:1076. [PMID: 39202435 PMCID: PMC11353978 DOI: 10.3390/genes15081076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 09/03/2024] Open
Abstract
Fulgoraria rupestris is a predatory marine gastropod belonging to Neogastropoda and possessing considerable taxonomic significance. However, research on this species remains limited. We acquired the complete mitochondrial genome of F. rupestris through second-generation sequencing and conducted an analysis of its genome structural features. The mitochondrial genome of F. rupestris spans a total length of 16,223 bp and encompasses 37 genes (13 protein-coding genes (PCGs), 22 transfer RNAs, and 2 ribosomal RNAs). Notably, most tRNAs exhibit the typical cloverleaf structure, but there is an absence of the Dihydrouridine (DHU) arm in the trnS1 and trnS2 genes. The A + T content is 68.67%, indicating a pronounced AT bias. Additionally, we conducted a selection pressure analysis on the mitochondrial genomes of four species within Volutidae, revealing that all PCGs are subjected to purifying selection. In comparison to other species within Neogastropoda, F. rupestris shares an identical gene arrangement. Additionally, based on mitochondrial genome sequences of the 13 PCGs from 50 species within Neogastropoda, we constructed a phylogenetic tree. The phylogenetic tree indicates F. rupestris forms a clade with species within the family Volutidae (Cymbium olla, Neptuneopsis gilchristi, and Melo melo). This study serves as a valuable reference for future research on F. rupestris, offering insights for the upcoming phylogenetic and taxonomic classification within Neogastropoda. Furthermore, the findings provide valuable information for the development of genetic resources in this context.
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Affiliation(s)
- Jiale Ma
- Marine and Fisheries Institute of Zhejiang Ocean University, Zhoushan 316022, China; (J.M.); (J.Z.); (Z.W.)
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China;
- Zhejiang Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Xiangli Dong
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Kaida Xu
- Marine and Fisheries Institute of Zhejiang Ocean University, Zhoushan 316022, China; (J.M.); (J.Z.); (Z.W.)
- Zhejiang Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Jiaying Zeng
- Marine and Fisheries Institute of Zhejiang Ocean University, Zhoushan 316022, China; (J.M.); (J.Z.); (Z.W.)
- Zhejiang Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Zhongming Wang
- Marine and Fisheries Institute of Zhejiang Ocean University, Zhoushan 316022, China; (J.M.); (J.Z.); (Z.W.)
- Zhejiang Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China;
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Sun Y, Chen J, Liang X, Li J, Ye Y, Xu K. Sequence comparison of the mitochondrial genomes of Plesionika species (Caridea: Pandalidae), gene rearrangement and phylogenetic relationships of Caridea. PeerJ 2024; 12:e17314. [PMID: 38799064 PMCID: PMC11127644 DOI: 10.7717/peerj.17314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/08/2024] [Indexed: 05/29/2024] Open
Abstract
Background Despite the Caridean shrimps' vast species richness and ecological diversity, controversies persist in their molecular classification. Within Caridea, the Pandalidae family exemplifies significant taxonomic diversity. As of June 25, 2023, GenBank hosts only nine complete mitochondrial genomes (mitogenomes) for this family. The Plesionika genus within Pandalidae is recognized as polyphyletic. To improve our understanding of the mitogenome evolution and phylogenetic relationships of Caridea, this study introduces three novel mitogenome sequences from the Plesionika genus: P. ortmanni, P. izumiae and P. lophotes. Methods The complete mitochondrial genomes of three Plesionika species were sequenced utilizing Illumina's next-generation sequencing (NGS) technology. After assembling and annotating the mitogenomes, we conducted structural analyses to examine circular maps, sequence structure characteristics, base composition, amino acid content, and synonymous codon usage frequency. Additionally, phylogenetic analysis was performed by integrating existing mitogenome sequences of true shrimp available in GenBank. Results The complete mitogenomes of the three Plesionika species encompass 37 canonical genes, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). The lengths of these mitogenomes are as follows: 15,908 bp for P. ortmanni, 16,074 bp for P. izumiae and 15,933 bp for P. lophotes. Our analyses extended to their genomic features and structural functions, detailing base composition, gene arrangement, and codon usage. Additionally, we performed selection pressure analysis on the PCGs of all Pandalidae species available in Genbank, indicating evolutionary purification selection acted on the PCGs across Pandalidae species. Compared with the ancestral Caridea, translocation of two tRNA genes, i.e., trnP or trnT, were found in the two newly sequenced Plesionika species-P. izumiae and P. lophotes. We constructed a phylogenetic tree of Caridea using the sequences of 13 PCGs in mitogenomes. The results revealed that family Pandalidae exhibited robust monophyly, while genus Plesionika appeared to be a polyphyletic group. Conclusions Gene rearrangements within the Pandalidae family were observed for the first time. Furthermore, a significant correlation was discovered between phylogenetics of the Caridea clade and arrangement of mitochondrial genes. Our findings offer a detailed exploration of Plesionika mitogenomes, laying a crucial groundwork for subsequent investigations into genetic diversity, phylogenetic evolution, and selective breeding within this genus.
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Affiliation(s)
- Yuman Sun
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Jian Chen
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Xinjie Liang
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang Province, China
| | - Kaida Xu
- Zhejiang Marine Fishery Research Institute, Zhoushan, Zhejiang Province, China
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs, Zhoushan, Zhejiang Province, China
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Schnitzler CE, Chang ES, Waletich J, Quiroga-Artigas G, Wong WY, Nguyen AD, Barreira SN, Doonan LB, Gonzalez P, Koren S, Gahan JM, Sanders SM, Bradshaw B, DuBuc TQ, Febrimarsa, de Jong D, Nawrocki EP, Larson A, Klasfeld S, Gornik SG, Moreland RT, Wolfsberg TG, Phillippy AM, Mullikin JC, Simakov O, Cartwright P, Nicotra M, Frank U, Baxevanis AD. The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals. Genome Res 2024; 34:498-513. [PMID: 38508693 PMCID: PMC11067881 DOI: 10.1101/gr.278382.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
Hydractinia is a colonial marine hydroid that shows remarkable biological properties, including the capacity to regenerate its entire body throughout its lifetime, a process made possible by its adult migratory stem cells, known as i-cells. Here, we provide an in-depth characterization of the genomic structure and gene content of two Hydractinia species, Hydractinia symbiolongicarpus and Hydractinia echinata, placing them in a comparative evolutionary framework with other cnidarian genomes. We also generated and annotated a single-cell transcriptomic atlas for adult male H. symbiolongicarpus and identified cell-type markers for all major cell types, including key i-cell markers. Orthology analyses based on the markers revealed that Hydractinia's i-cells are highly enriched in genes that are widely shared amongst animals, a striking finding given that Hydractinia has a higher proportion of phylum-specific genes than any of the other 41 animals in our orthology analysis. These results indicate that Hydractinia's stem cells and early progenitor cells may use a toolkit shared with all animals, making it a promising model organism for future exploration of stem cell biology and regenerative medicine. The genomic and transcriptomic resources for Hydractinia presented here will enable further studies of their regenerative capacity, colonial morphology, and ability to distinguish self from nonself.
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Affiliation(s)
- Christine E Schnitzler
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, USA
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | - E Sally Chang
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Justin Waletich
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, USA
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | - Gonzalo Quiroga-Artigas
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, USA
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier CEDEX 05, France
| | - Wai Yee Wong
- Department for Neurosciences and Developmental Biology, University of Vienna, 1030 Vienna, Austria
| | - Anh-Dao Nguyen
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sofia N Barreira
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Liam B Doonan
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway H91 W2TY, Ireland
| | - Paul Gonzalez
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sergey Koren
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - James M Gahan
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway H91 W2TY, Ireland
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Steven M Sanders
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Brian Bradshaw
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway H91 W2TY, Ireland
| | - Timothy Q DuBuc
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway H91 W2TY, Ireland
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania 19081, USA
| | - Febrimarsa
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway H91 W2TY, Ireland
- Pharmaceutical Biology Laboratory, Faculty of Pharmacy, Universitas Muhammadiyah Surakarta, Jawa Tengah 57169, Indonesia
| | - Danielle de Jong
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, USA
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | - Eric P Nawrocki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Alexandra Larson
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, USA
| | - Samantha Klasfeld
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sebastian G Gornik
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway H91 W2TY, Ireland
- Center for Organismal Studies, University of Heidelberg, 69117 Heidelberg, Germany
| | - R Travis Moreland
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Tyra G Wolfsberg
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Adam M Phillippy
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - James C Mullikin
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
- NIH Intramural Sequencing Center, Rockville, Maryland 20852, USA
| | - Oleg Simakov
- Department for Neurosciences and Developmental Biology, University of Vienna, 1030 Vienna, Austria
| | - Paulyn Cartwright
- Department of Evolution and Ecology, University of Kansas, Lawrence, Kansas 66045, USA
| | - Matthew Nicotra
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Uri Frank
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway H91 W2TY, Ireland
| | - Andreas D Baxevanis
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
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Xu M, Li J, Guo B, Xu K, Ye Y, Yan X. Insights into the Deep Phylogeny and Novel Gene Rearrangement of Mytiloidea from Complete Mitochondrial Genome. Biochem Genet 2023; 61:1704-1726. [PMID: 36745306 DOI: 10.1007/s10528-023-10338-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 01/17/2023] [Indexed: 02/07/2023]
Abstract
The extant marine mussels which belong to the Mytiloidea are widespread species inhabiting mostly coastal waters, with some distributed in the deep sea. To clarify the classification systems and phylogenetic relationships range from genus to family level within Mytiloidea, new sequence was used in a phylogenetic analysis including all the available Mytiloidea mitochondrial genomes. In this study, the complete mitochondrial genome of Vignadula atrata is 15,624 bp in length and contains 12 protein-coding genes (PCGs, atp8 is absent), two ribosomal RNA genes, and 22 transfer RNA genes. Phylogenetic analysis based on 12 PCGs showed that it has a close relationship to Bathymodiolus. The analysis of gene rearrangements in the Pteriomorphia showed that the arrangements are highly variable across species, novel gene rearrangements were found within Mytiloidea. The V. atrata mitogenome was provided in detail, with notes on the sequence and a key to the species of Vignadula. This study provides a perspective on the taxonomic histories of the marine mussels and refines the unclear relationship between the origin and evolution of species in Mytiloidea within Bivalvia.
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Affiliation(s)
- Minhui Xu
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Baoying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Kaida Xu
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhejiang Ocean University, Zhoushan, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Xiaojun Yan
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.
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5
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Schnitzler CE, Chang ES, Waletich J, Quiroga-Artigas G, Wong WY, Nguyen AD, Barreira SN, Doonan L, Gonzalez P, Koren S, Gahan JM, Sanders SM, Bradshaw B, DuBuc TQ, Febrimarsa, de Jong D, Nawrocki EP, Larson A, Klasfeld S, Gornik SG, Moreland RT, Wolfsberg TG, Phillippy AM, Mullikin JC, Simakov O, Cartwright P, Nicotra M, Frank U, Baxevanis AD. The genome of the colonial hydroid Hydractinia reveals their stem cells utilize a toolkit of evolutionarily shared genes with all animals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554815. [PMID: 37786714 PMCID: PMC10541594 DOI: 10.1101/2023.08.25.554815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Hydractinia is a colonial marine hydroid that exhibits remarkable biological properties, including the capacity to regenerate its entire body throughout its lifetime, a process made possible by its adult migratory stem cells, known as i-cells. Here, we provide an in-depth characterization of the genomic structure and gene content of two Hydractinia species, H. symbiolongicarpus and H. echinata, placing them in a comparative evolutionary framework with other cnidarian genomes. We also generated and annotated a single-cell transcriptomic atlas for adult male H. symbiolongicarpus and identified cell type markers for all major cell types, including key i-cell markers. Orthology analyses based on the markers revealed that Hydractinia's i-cells are highly enriched in genes that are widely shared amongst animals, a striking finding given that Hydractinia has a higher proportion of phylum-specific genes than any of the other 41 animals in our orthology analysis. These results indicate that Hydractinia's stem cells and early progenitor cells may use a toolkit shared with all animals, making it a promising model organism for future exploration of stem cell biology and regenerative medicine. The genomic and transcriptomic resources for Hydractinia presented here will enable further studies of their regenerative capacity, colonial morphology, and ability to distinguish self from non-self.
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Affiliation(s)
- Christine E Schnitzler
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - E Sally Chang
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Justin Waletich
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Gonzalo Quiroga-Artigas
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier CEDEX 05, France
| | - Wai Yee Wong
- Department of Molecular Evolution and Development, Faculty of Life Science, University of Vienna, A-1090 Vienna, Austria
| | - Anh-Dao Nguyen
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sofia N Barreira
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Liam Doonan
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Paul Gonzalez
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sergey Koren
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James M Gahan
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Steven M Sanders
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Brian Bradshaw
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Timothy Q DuBuc
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
- Swarthmore College, Swarthmore, PA 19081, USA
| | - Febrimarsa
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Danielle de Jong
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Eric P Nawrocki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra Larson
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Samantha Klasfeld
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sebastian G Gornik
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
- Centre for Organismal Studies, University of Heidelberg, Germany
| | - R Travis Moreland
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tyra G Wolfsberg
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam M Phillippy
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James C Mullikin
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- NIH Intramural Sequencing Center, Rockville, MD 20852, USA
| | - Oleg Simakov
- Department of Molecular Evolution and Development, Faculty of Life Science, University of Vienna, A-1090 Vienna, Austria
| | - Paulyn Cartwright
- Department of Evolution and Ecology, University of Kansas, Lawrence, KS 66045, USA
| | - Matthew Nicotra
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Uri Frank
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Andreas D Baxevanis
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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6
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Sun Y, Chen J, Ye Y, Xu K, Li J. Comparison of Mitochondrial Genome Sequences between Two Palaemon Species of the Family Palaemonidae (Decapoda: Caridea): Gene Rearrangement and Phylogenetic Implications. Genes (Basel) 2023; 14:1499. [PMID: 37510403 PMCID: PMC10379425 DOI: 10.3390/genes14071499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
To further understand the origin and evolution of Palaemonidae (Decapoda: Caridea), we determined the mitochondrial genome sequence of Palaemon macrodactylus and Palaemon tenuidactylus. The entire mitochondrial genome sequences of these two Palaemon species encompassed 37 typical genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs), and a control region (CR). The lengths of their mitochondrial genomes were 15,744 bp (P. macrodactylus) and 15,735 bp (P. tenuidactylus), respectively. We analyzed their genomic features and structural functions. In comparison with the ancestral Decapoda, these two newly sequenced Palaemon species exhibited a translocation event, where the gene order was trnK-trnD instead of trnD-trnK. Based on phylogenetic analysis constructed from 13 PCGs, the 12 families from Caridea can be divided into four major clades. Furthermore, it was revealed that Alpheidae and Palaemonidae formed sister groups, supporting the monophyly of various families within Caridea. These findings highlight the significant gene rearrangements within Palaemonidae and provide valuable evidence for the phylogenetic relationships within Caridea.
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Affiliation(s)
- Yuman Sun
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Jian Chen
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Kaida Xu
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
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Xiao J, Tian P, Guo F, Yu S, Wang W, Wang X, Niu W. Characterization of the complete mitochondrial genome of Diploastrea heliopora and phylogeny of the scleractinia species which have group I introns in their COI genes. Saudi J Biol Sci 2021; 28:7054-7060. [PMID: 34867006 PMCID: PMC8626255 DOI: 10.1016/j.sjbs.2021.07.086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/04/2022] Open
Abstract
Mitochondrial genome DNA is a powerful marker for resolving phylogenetic relationships among scleractinian corals. Here, we decode the complete mitochondrial genome of Diploastrea heliopora (Lamarck, 1816) for the first time. The general features are 18 363 bp in length, and conventionally, with 13 protein coding genes, two ribosomal RNAs, and two transfer RNAs. Gene arrangement and distribution are similar to other scleractinian corals. Moreover, the COI gene of D. heliopora is broken up into two parts by a complex group I intron. This intron is 1076 bases in length and contains helical structures (P1-P10, except P2) and four conserved regions (P, Q, R, and S). The mitochondrial genome of D. heliopora has asymmetric base composition (13.03% C, 20.29% G, 25.91% A, and 40.77% for T). Based on concatenated protein coding genes, ML and BI trees show similar phylogenetic relationship: D. heliopora clustered closely with Sclerophyllia maxima and Echinophyllia aspera into the robust branch. The data and conclusion in this study are reference for further phylogenetic studies of corals.
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Affiliation(s)
- Jiaguang Xiao
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Peng Tian
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Feng Guo
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Shuangen Yu
- Fisheries College, Ocean University of China, Qingdao 266003, China
| | - Wei Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xiaolei Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Wentao Niu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
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8
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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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9
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Stampar SN, Broe MB, Macrander J, Reitzel AM, Brugler MR, Daly M. Linear Mitochondrial Genome in Anthozoa (Cnidaria): A Case Study in Ceriantharia. Sci Rep 2019; 9:6094. [PMID: 30988357 PMCID: PMC6465557 DOI: 10.1038/s41598-019-42621-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/04/2019] [Indexed: 01/10/2023] Open
Abstract
Sequences and structural attributes of mitochondrial genomes have played a critical role in the clarification of relationships among Cnidaria, a key phylum of early-diverging animals. Among the major lineages of Cnidaria, Ceriantharia (“tube anemones”) remains one of the most enigmatic in terms of its phylogenetic position. We sequenced the mitochondrial genomes of two ceriantharians to see whether the complete organellar genome would provide more support for the phylogenetic placement of Ceriantharia. For both Isarachnanthus nocturnus and Pachycerianthus magnus, the mitochondrial gene sequences could not be assembled into a single circular genome. Instead, our analyses suggest that both species have mitochondrial genomes consisting of multiple linear fragments. Linear mitogenomes are characteristic of members of Medusozoa, one of the major lineages of Cnidaria, but are unreported for Anthozoa, which includes the Ceriantharia. The inferred number of fragments and variation in gene order between species is much greater within Ceriantharia than among the lineages of Medusozoa. We identify origins of replication for each of the five putative chromosomes of the Isarachnanthus nocturnus mitogenome and for each of the eight putative chromosomes of the Pachycerianthus magnus mitogenome. At 80,923 bp, I. nocturnus now holds the record for the largest animal mitochondrial genome reported to date. The novelty of the mitogenomic structure in Ceriantharia highlights the distinctiveness of this lineage but, because it appears to be both unique to and diverse within Ceriantharia, it is uninformative about the phylogenetic position of Ceriantharia relative to other Anthozoa. The presence of tRNAMet and tRNATrp in both ceriantharian mitogenomes supports a closer relationship between Ceriantharia and Hexacorallia than between Ceriantharia and any other cnidarian lineage, but phylogenetic analysis of the genes contained in the mitogenomes suggests that Ceriantharia is sister to a clade containing Octocorallia + Hexacorallia indicating a possible suppression of tRNATrp in Octocorallia.
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Affiliation(s)
- Sérgio N Stampar
- Departamento de Ciências Biológicas, Faculdade de Ciências e Letras, UNESP - Universidade Estadual Paulista, Assis, SP, Brazil.
| | - Michael B Broe
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Jason Macrander
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA.,Department of Biology, Florida Southern College, Lakeland, FL, USA
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Mercer R Brugler
- Biological Sciences Department, NYC College of Technology, City University of New York, 285 Jay Street, Brooklyn, New York, 11201, USA.,Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, New York, 10024, USA
| | - Marymegan Daly
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
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10
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Wai A, Shen C, Carta A, Dansen A, Crous PW, Hausner G. Intron-encoded ribosomal proteins and N-acetyltransferases within the mitochondrial genomes of fungi: here today, gone tomorrow? Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:573-584. [DOI: 10.1080/24701394.2019.1580272] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Alvan Wai
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Chen Shen
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Andrell Carta
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Alexandra Dansen
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Pedro W. Crous
- The Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, The Netherlands
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
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11
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Chi SI, Urbarova I, Johansen SD. Expression of homing endonuclease gene and insertion-like element in sea anemone mitochondrial genomes: Lesson learned from Anemonia viridis. Gene 2018; 652:78-86. [PMID: 29366757 DOI: 10.1016/j.gene.2018.01.067] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/19/2017] [Accepted: 01/19/2018] [Indexed: 11/16/2022]
Abstract
The mitochondrial genomes of sea anemones are dynamic in structure. Invasion by genetic elements, such as self-catalytic group I introns or insertion-like sequences, contribute to sea anemone mitochondrial genome expansion and complexity. By using next generation sequencing we investigated the complete mtDNAs and corresponding transcriptomes of the temperate sea anemone Anemonia viridis and its closer tropical relative Anemonia majano. Two versions of fused homing endonuclease gene (HEG) organization were observed among the Actiniidae sea anemones; in-frame gene fusion and pseudo-gene fusion. We provided support for the pseudo-gene fusion organization in Anemonia species, resulting in a repressed HEG from the COI-884 group I intron. orfA, a putative protein-coding gene with insertion-like features, was present in both Anemonia species. Interestingly, orfA and COI expression were significantly up-regulated upon long-term environmental stress corresponding to low seawater pH conditions. This study provides new insights to the dynamics of sea anemone mitochondrial genome structure and function.
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Affiliation(s)
- Sylvia Ighem Chi
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Ilona Urbarova
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Steinar D Johansen
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway; Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
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12
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Yahalomi D, Haddas-Sasson M, Rubinstein ND, Feldstein T, Diamant A, Huchon D. The Multipartite Mitochondrial Genome of Enteromyxum leei (Myxozoa): Eight Fast-Evolving Megacircles. Mol Biol Evol 2017; 34:1551-1556. [PMID: 28333349 DOI: 10.1093/molbev/msx072] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Myxozoans are a large group of poorly characterized cnidarian parasites. To gain further insight into their evolution, we sequenced the mitochondrial (mt) genome of Enteromyxum leei and reevaluate the mt genome structure of Kudoa iwatai. Although the typical animal mt genome is a compact, 13-25 kb, circular chromosome, the mt genome of E. leei was found to be fragmented into eight circular chromosomes of ∼23 kb, making it the largest described animal mt genome. Each chromosome was found to harbor a large noncoding region (∼15 kb), nearly identical between chromosomes. The protein coding genes show an unusually high rate of sequence evolution and possess little similarity to their cnidarian homologs. Only five protein coding genes could be identified and no tRNA genes. Surprisingly, the mt genome of K. iwatai was also found to be composed of two chromosomes. These observations confirm the remarkable plasticity of myxozoan mt genomes.
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Affiliation(s)
- Dayana Yahalomi
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Michal Haddas-Sasson
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Nimrod D Rubinstein
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Feldstein
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,The Steinhardt Museum of Natural History and Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv, Israel
| | - Arik Diamant
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat, Israel
| | - Dorothée Huchon
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,The Steinhardt Museum of Natural History and Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv, Israel
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13
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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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14
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Abstract
BACKGROUND Mitogenome diversity is staggering among early branching animals with respect to size, gene density, content and order, and number of tRNA genes, especially in cnidarians. This last point is of special interest as tRNA cleavage drives the maturation of mitochondrial mRNAs and is a primary mechanism for mt-RNA processing in animals. Mitochondrial RNA processing in non-bilaterian metazoans, some of which possess a single tRNA gene in their mitogenomes, is essentially unstudied despite its importance in understanding the evolution of mitochondrial transcription in animals. RESULTS We characterized the mature mitochondrial mRNA transcripts in a species of the octocoral genus Sinularia (Alcyoniidae: Octocorallia), and defined precise boundaries of transcription units using different molecular methods. Most mt-mRNAs were polycistronic units containing two or three genes and 5' and/or 3' untranslated regions of varied length. The octocoral specific, mtDNA-encoded mismatch repair gene, the mtMutS, was found to undergo alternative polyadenylation, and exhibited differential expression of alternate transcripts suggesting a unique regulatory mechanism for this gene. In addition, a long noncoding RNA complementary to the ATP6 gene (lncATP6) potentially involved in antisense regulation was detected. CONCLUSIONS Mt-mRNA processing in octocorals possessing a single mt-tRNA is complex. Considering the variety of mitogenome arrangements known in cnidarians, and in general among non-bilaterian metazoans, our findings provide a first glimpse into the complex mtDNA transcription, mt-mRNA processing, and regulation among early branching animals and represent a first step towards understanding its functional and evolutionary implications.
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15
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Zhang B, Zhang Y, Wang X, Zhang H, Lin Q. The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep-sea environment. Ecol Evol 2017; 7:4951-4962. [PMID: 28690821 PMCID: PMC5496520 DOI: 10.1002/ece3.3067] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/13/2017] [Accepted: 04/24/2017] [Indexed: 01/14/2023] Open
Abstract
The deep sea is one of the most extensive ecosystems on earth. Organisms living there survive in an extremely harsh environment, and their mitochondrial energy metabolism might be a result of evolution. As one of the most important organelles, mitochondria generate energy through energy metabolism and play an important role in almost all biological activities. In this study, the mitogenome of a deep‐sea sea anemone (Bolocera sp.) was sequenced and characterized. Like other metazoans, it contained 13 energy pathway protein‐coding genes and two ribosomal RNAs. However, it also exhibited some unique features: just two transfer RNA genes, two group I introns, two transposon‐like noncanonical open reading frames (ORFs), and a control region‐like (CR‐like) element. All of the mitochondrial genes were coded by the same strand (the H‐strand). The genetic order and orientation were identical to those of most sequenced actiniarians. Phylogenetic analyses showed that this species was closely related to Bolocera tuediae. Positive selection analysis showed that three residues (31 L and 42 N in ATP6, 570 S in ND5) of Bolocera sp. were positively selected sites. By comparing these features with those of shallow sea anemone species, we deduced that these novel gene features may influence the activity of mitochondrial genes. This study may provide some clues regarding the adaptation of Bolocera sp. to the deep‐sea environment.
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Affiliation(s)
- Bo Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yan‐Hong Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hui‐Xian Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
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16
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Tissue- and Condition-Specific Isoforms of Mammalian Cytochrome c Oxidase Subunits: From Function to Human Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:1534056. [PMID: 28593021 PMCID: PMC5448071 DOI: 10.1155/2017/1534056] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/29/2017] [Indexed: 01/05/2023]
Abstract
Cytochrome c oxidase (COX) is the terminal enzyme of the electron transport chain and catalyzes the transfer of electrons from cytochrome c to oxygen. COX consists of 14 subunits, three and eleven encoded, respectively, by the mitochondrial and nuclear DNA. Tissue- and condition-specific isoforms have only been reported for COX but not for the other oxidative phosphorylation complexes, suggesting a fundamental requirement to fine-tune and regulate the essentially irreversible reaction catalyzed by COX. This article briefly discusses the assembly of COX in mammals and then reviews the functions of the six nuclear-encoded COX subunits that are expressed as isoforms in specialized tissues including those of the liver, heart and skeletal muscle, lung, and testes: COX IV-1, COX IV-2, NDUFA4, NDUFA4L2, COX VIaL, COX VIaH, COX VIb-1, COX VIb-2, COX VIIaH, COX VIIaL, COX VIIaR, COX VIIIH/L, and COX VIII-3. We propose a model in which the isoforms mediate the interconnected regulation of COX by (1) adjusting basal enzyme activity to mitochondrial capacity of a given tissue; (2) allosteric regulation to adjust energy production to need; (3) altering proton pumping efficiency under certain conditions, contributing to thermogenesis; (4) providing a platform for tissue-specific signaling; (5) stabilizing the COX dimer; and (6) modulating supercomplex formation.
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17
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Loss and Gain of Group I Introns in the Mitochondrial Cox1 Gene of the Scleractinia (Cnidaria; Anthozoa). Zool Stud 2017; 56:e9. [PMID: 31966208 DOI: 10.6620/zs.2017.56-09] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/12/2017] [Indexed: 01/21/2023]
Abstract
Yaoyang Chuang, Marcelo Kitahara, Hironobu Fukami, Dianne Tracey, David J. Miller, and Chaolun Allen Chen (2017) Group I introns encoding a homing endonuclease gene (HEG) that is potentially capable of sponsoring mobility are present in the cytochrome oxidase subunit 1 (cox1) gene of some Hexacorallia, including a number of scleractinians assigned to the "robust" coral clade. In an e ort to infer the evolutionary history of this cox1 group I intron, DNA sequences were determined for 12 representative "basal" and "complex" corals and for 11 members of the Corallimorpharia, a sister order of the Scleractinia. Comparisons of insertion sites, secondary structures, and amino acid sequences of the HEG implied a common origin for cox1 introns of corallimorpharians, and basal and complex corals, but cox1 introns of robust corals were highly divergent, most likely reflecting independent acquisition. Phylogenetic analyses with a calibrated molecular clock suggested that cox1 introns of scleractinians and corallimorpharians have persisted at the same insertion site as that in the common ancestor 552 million years ago (mya). This ancestral intron was probably lost in complex corals around 213 to 190 mya at the junction between the Trassic and Jurassic. The coral cox1 gene remained intronless until new introns, probably from sponges or fungi, reinvaded different positions of the cox1 gene in robust corals around 135 mya in the Cretaceous, and then it subsequently began to lose them around 65.5 mya in some robust coral lineages coincident with the later Maastrichtian extinction at the Cretaceous-Tertiary boundary.
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18
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Szafranski P. Evolutionarily recent, insertional fission of mitochondrial cox2 into complementary genes in bilaterian Metazoa. BMC Genomics 2017; 18:269. [PMID: 28359330 PMCID: PMC5374615 DOI: 10.1186/s12864-017-3626-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 03/14/2017] [Indexed: 11/21/2022] Open
Abstract
Background Mitochondrial genomes (mtDNA) of multicellular animals (Metazoa) with bilateral symmetry (Bilateria) are compact and usually carry 13 protein-coding genes for subunits of three respiratory complexes and ATP synthase. However, occasionally reported exceptions to this typical mtDNA organization prompted speculation that, as in protists and plants, some bilaterian mitogenomes may continue to lose their canonical genes, or may even acquire new genes. To shed more light on this phenomenon, a PCR-based screen was conducted to assess fast-evolving mtDNAs of apocritan Hymenoptera (Arthropoda, Insecta) for genomic rearrangements that might be associated with the modification of mitochondrial gene content. Results Sequencing of segmental inversions, identified in the screen, revealed that the cytochrome oxidase subunit II gene (cox2) of Campsomeris (Dielis) (Scoliidae) was split into two genes coding for COXIIA and COXIIB. The COXII-derived complementary polypeptides apparently form a heterodimer, have reduced hydrophobicity compared with the majority of mitogenome-encoded COX subunits, and one of them, COXIIB, features increased content of Cys residues. Analogous cox2 fragmentation is known only in two clades of protists (chlorophycean algae and alveolates), where it has been associated with piecewise relocation of this gene into the nucleus. In Campsomeris mtDNA, cox2a and cox2b loci are separated by a 3-kb large cluster of several antiparallel overlapping ORFs, one of which, qnu, seems to encode a nuclease that may have played a role in cox2 fission. Conclusions Although discontinuous mitochondrial protein genes encoding fragmented, complementary polypeptides are known in protists and some plants, split cox2 of Campsomeris is the first case of such a gene arrangement found in animals. The reported data also indicate that bilaterian animal mitogenomes may be carrying lineage-specific genes more often than previously thought, and suggest a homing endonuclease-based mechanism for insertional mitochondrial gene fission. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3626-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, ABBR, R851C, Houston, TX, 77030, USA.
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19
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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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20
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Patra AK, Kwon YM, Kang SG, Fujiwara Y, Kim SJ. The complete mitochondrial genome sequence of the tubeworm Lamellibrachia satsuma and structural conservation in the mitochondrial genome control regions of Order Sabellida. Mar Genomics 2016; 26:63-71. [PMID: 26776396 DOI: 10.1016/j.margen.2015.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 12/30/2015] [Accepted: 12/30/2015] [Indexed: 11/18/2022]
Abstract
The control region of the mitochondrial genomes shows high variation in conserved sequence organizations, which follow distinct evolutionary patterns in different species or taxa. In this study, we sequenced the complete mitochondrial genome of Lamellibrachia satsuma from the cold-seep region of Kagoshima Bay, as a part of whole genome study and extensively studied the structural features and patterns of the control region sequences. We obtained 15,037 bp of mitochondrial genome using Illumina sequencing and identified the non-coding AT-rich region or control region (354 bp, AT=83.9%) located between trnH and trnR. We found 7 conserved sequence blocks (CSB), scattered throughout the control region of L. satsuma and other taxa of Annelida. The poly-TA stretches, which commonly form the stem of multiple stem-loop structures, are most conserved in the CSB-I and CSB-II regions. The mitochondrial genome of L. satsuma encodes a unique repetitive sequence in the control region, which forms a unique secondary structure in comparison to Lamellibrachia luymesi. Phylogenetic analyses of all protein-coding genes indicate that L. satsuma forms a monophyletic clade with L. luymesi along with other tubeworms found in cold-seep regions (genera: Lamellibrachia, Escarpia, and Seepiophila). In general, the control region sequences of Annelida could be aligned with certainty within each genus, and to some extent within the family, but with a higher rate of variation in conserved regions.
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Affiliation(s)
- Ajit Kumar Patra
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea; Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon 305-333, Republic of Korea.
| | - Yong Min Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea.
| | - Sung Gyun Kang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea; Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon 305-333, Republic of Korea.
| | - Yoshihiro Fujiwara
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka 237-0061, Japan.
| | - Sang-Jin Kim
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea; Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon 305-333, Republic of Korea; National Marine Biodiversity Institute of Korea, Seocheon 325-902, Republic of Korea.
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21
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SINKOVICS JOSEPHG. The cnidarian origin of the proto-oncogenes NF-κB/STAT and WNT-like oncogenic pathway drives the ctenophores (Review). Int J Oncol 2015; 47:1211-29. [PMID: 26239915 PMCID: PMC4583530 DOI: 10.3892/ijo.2015.3102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 06/26/2015] [Indexed: 01/09/2023] Open
Abstract
The cell survival pathways of the diploblastic early multicellular eukaryotic hosts contain and operate the molecular machinery resembling those of malignantly transformed individual cells of highly advanced multicellular hosts (including Homo). In the present review, the STAT/NF-κB pathway of the cnidarian Nematostella vectensis is compared with that of human tumors (malignant lymphomas, including Reed-Sternberg cells) pointing out similarities, including possible viral initiation in both cases. In the ctenophore genome and proteome, β-catenin gains intranuclear advantages due to a physiologically weak destructive complex in the cytoplasm, and lack of natural inhibitors (the dickkopfs). Thus, a scenario similar to what tumor cells initiate and achieve is presented through several constitutive loss-of-function type mutations in the destructive complex and in the elimination of inhibitors. Vice versa, malignantly transformed individual cells of advanced multicellular hosts assume pheno-genotypic resemblance to cells of unicellular or early multicellular hosts, and presumably to their ancient predecessors, by returning to the semblance of immortality and to the resumption of the state of high degree of resistance to physicochemical insults. Human leukemogenic and oncogenic pathways are presented for comparisons. The supreme bioengineers RNA/DNA complex encoded both the malignantly transformed immortal cell and the human cerebral cortex. The former generates molecules for the immortality of cellular life in the Universe. The latter invents the inhibitors of the process in order to gain control over it.
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Affiliation(s)
- JOSEPH G. SINKOVICS
- St. Joseph Hospital's Cancer Institute Affiliated with the H.L. Moffitt Comprehensive Cancer Center; Department of Molecular Medicine, The University of South Florida Morsani College of Medicine, Tampa, FL, USA
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22
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Brandão MM, Spoladore L, Faria LCB, Rocha ASL, Silva-Filho MC, Palazzo R. Ancient DNA sequence revealed by error-correcting codes. Sci Rep 2015; 5:12051. [PMID: 26159228 PMCID: PMC4498232 DOI: 10.1038/srep12051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 06/16/2015] [Indexed: 11/09/2022] Open
Abstract
A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code.
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Affiliation(s)
- Marcelo M Brandão
- 1] Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil [2] Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, 13400-918, Piracicaba, SP, Brazil
| | - Larissa Spoladore
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, 13400-918, Piracicaba, SP, Brazil
| | - Luzinete C B Faria
- Departamento de Telemática, Faculdade de Engenharia Elétrica e de Computação, Universidade Estadual de Campinas, 13081-970, Campinas, SP, Brazil
| | - Andréa S L Rocha
- Departamento de Telemática, Faculdade de Engenharia Elétrica e de Computação, Universidade Estadual de Campinas, 13081-970, Campinas, SP, Brazil
| | - Marcio C Silva-Filho
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, 13400-918, Piracicaba, SP, Brazil
| | - Reginaldo Palazzo
- Departamento de Telemática, Faculdade de Engenharia Elétrica e de Computação, Universidade Estadual de Campinas, 13081-970, Campinas, SP, Brazil
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23
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Foox J, Brugler M, Siddall ME, Rodríguez E. Multiplexed pyrosequencing of nine sea anemone (Cnidaria: Anthozoa: Hexacorallia: Actiniaria) mitochondrial genomes. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2826-32. [PMID: 26104159 DOI: 10.3109/19401736.2015.1053114] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Six complete and three partial actiniarian mitochondrial genomes were amplified in two semi-circles using long-range PCR and pyrosequenced in a single run on a 454 GS Junior, doubling the number of complete mitogenomes available within the order. Typical metazoan mtDNA features included circularity, 13 protein-coding genes, 2 ribosomal RNA genes, and length ranging from 17,498 to 19,727 bp. Several typical anthozoan mitochondrial genome features were also observed including the presence of only two transfer RNA genes, elevated A + T richness ranging from 54.9 to 62.4%, large intergenic regions, and group 1 introns interrupting NADH dehydrogenase subunit 5 and cytochrome c oxidase subunit I, the latter of which possesses a homing endonuclease gene. Within the sea anemone Alicia sansibarensis, we report the first mitochondrial gene order rearrangement within the Actiniaria, as well as putative novel non-canonical protein-coding genes. Phylogenetic analyses of all 13 protein-coding and 2 ribosomal genes largely corroborated current hypotheses of sea anemone interrelatedness, with a few lower-level differences.
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Affiliation(s)
- Jonathan Foox
- a Richard Gilder Graduate School, American Museum of Natural History , New York , NY , USA
| | - Mercer Brugler
- b Sackler Institute for Comparative Genomics, Division of Invertebrate Zoology, American Museum of Natural History , New York , NY , USA , and.,c Biological Sciences Department, NYC College of Technology (CUNY) , Brooklyn , NY , USA
| | - Mark Edward Siddall
- a Richard Gilder Graduate School, American Museum of Natural History , New York , NY , USA .,b Sackler Institute for Comparative Genomics, Division of Invertebrate Zoology, American Museum of Natural History , New York , NY , USA , and
| | - Estefanía Rodríguez
- a Richard Gilder Graduate School, American Museum of Natural History , New York , NY , USA .,b Sackler Institute for Comparative Genomics, Division of Invertebrate Zoology, American Museum of Natural History , New York , NY , USA , and
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24
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Wei-Ye L, Fang SH, Wang YQ. Complete mitochondrial genome of Epigonichthys cultellus (Cephalochordata: Branchiostomatidae). Zoolog Sci 2015; 31:766-72. [PMID: 25366160 DOI: 10.2108/zs130213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The systematic position of the amphioxus species with dextral gonads distributed in the southeast Pacific and Indian Oceans has remained to be clarified due to the adoption of different names by different researchers. Mitochondrial (mt) DNA is generally considered to be a powerful molecular marker in taxonomic studies. For a reliable systematics of the amphioxi collected from the South China Sea, we sequenced the complete mtDNA from a single specimen and compared it with those of the other eight amphioxus species. The present mtDNA genome contains 13 protein-coding genes, 22 tRNA genes, and two rRNA genes, with the same gene order as those in Branchiostoma and Epigonichthys, which, however, is different from that in Asymmetron. Based on our morphological data (including measurements of some characters) and the features of the mt genome, together with the distribution records of the dextral-gonad amphioxi, we conclude that the present mtDNA sequence most likely represents that of E. cultellus.
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Affiliation(s)
- Li Wei-Ye
- 1 School of Life Sciences, Xiamen University, Xiamen 361102, China
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25
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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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26
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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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27
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Xu T, Tang D, Jin X. A surprising arrangement pattern and phylogenetic consideration: the complete mitochondrial genome of Belanger's croaker Johnius belangerii (Percoidei: Sciaenidae). ACTA ACUST UNITED AC 2013; 26:655-7. [PMID: 24156716 DOI: 10.3109/19401736.2013.843077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Johnius belangerii has been determined for the first time in this article. It was 19,154 base pairs in length, and is composed of 37 genes (13 protein-coding genes, 22 tRNA genes and 2 ribosomal RNA genes). Totally, 5 notable non-coding regions were observed, and a non-coding of 1091 bp was identified as control region based on its location and AT richness. An 800 bp tandem repeat sequence was identified in the fifth non-coding region. We investigated the mitochondrial gene arrangement pattern and found that that the tRNA(Val), 12SrRNA, 16SrRNA and tRNA(Phe) genes of J. belangerii mitogenome were orderly placed at the beginning of heavy strand. This order is different from other croakers. Combine with the phylogenetic reconstruction and genes arrangement pattern of J. belangerii mitochondrial genome, we consider J. belangerii is the most ancient genus within family Sciaenidae.
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Affiliation(s)
- Tianjun Xu
- Laboratory for Marine Living Resources and Molecular Engineering, College of Marine Science, Zhejiang Ocean University , Zhoushan, Zhejiang Province , P.R. China
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28
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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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29
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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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30
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Song S, Jiang F, Yuan J, Guo W, Miao Y. Exceptionally high cumulative percentage of NUMTs originating from linear mitochondrial DNA molecules in the Hydra magnipapillata genome. BMC Genomics 2013; 14:447. [PMID: 23826818 PMCID: PMC3716686 DOI: 10.1186/1471-2164-14-447] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 07/03/2013] [Indexed: 11/10/2022] Open
Abstract
Background In contrast to most animal genomes, mitochondrial genomes in species belonging to the phylum Cnidaria show distinct variations in genome structure, including the mtDNA structure (linear or circular) and the presence or absence of introns in protein-coding genes. Therefore, the analysis of nuclear insertions of mitochondrial sequences (NUMTs) in cnidarians allows us to compare the NUMT content in animals with different mitochondrial genome structures. Results NUMT identification in the Hydra magnipapillata, Nematostella vectensis and Acropora digitifera genomes showed that the NUMT density in the H. magnipapillata genome clearly exceeds that in other two cnidarians with circular mitochondrial genomes. We found that H. magnipapillata is an exceptional ancestral metazoan with a high NUMT cumulative percentage but a large genome, and its mitochondrial genome linearisation might be responsible for the NUMT enrichment. We also detected the co-transposition of exonic and intronic fragments within NUMTs in N. vectensis and provided direct evidence that mitochondrial sequences can be transposed into the nuclear genome through DNA-mediated fragment transfer. In addition, NUMT expression analyses showed that NUMTs are co-expressed with adjacent protein-coding genes, suggesting the relevance of their biological function. Conclusions Taken together, our results provide valuable information for understanding the impact of mitochondrial genome structure on the interaction of mitochondrial molecules and nuclear genomes.
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Affiliation(s)
- Shen Song
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan 650201, China
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31
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Beagley CT, Wolstenholme DR. Characterization and localization of mitochondrial DNA-encoded tRNAs and nuclear DNA-encoded tRNAs in the sea anemone Metridium senile. Curr Genet 2013; 59:139-52. [PMID: 23801360 DOI: 10.1007/s00294-013-0395-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 06/12/2013] [Accepted: 06/15/2013] [Indexed: 10/26/2022]
Abstract
The mitochondrial (mt) genome of the sea anemone Metridium senile contains genes for only two transfer RNAs (tRNAs), tRNAf-Met and tRNATrp. Experiments were conducted to seek evidence for the occurrence of functional tRNAs corresponding to these genes and for the participation of nuclear DNA-encoded tRNAs in mt-protein synthesis. RNA sequences corresponding to the two mt-tRNA genes were located in mitochondria and it was shown that 3'-CC (and possibly A, but no other nucleotide) is added post-transcriptionally to the 3' end of at least 50 % of mt-tRNAf-Met molecules and to a small fraction of the mt-tRNATrp molecules. Using specific oligonucleotide primers based on expected nuclear DNA-encoded tRNAs in a series of RACE experiments, we located the nuclear genes for tRNAGln, tRNAIle, tRNAi-Met, tRNAVal and tRNAThr. Data from Northern blot analyses indicated that mtDNA-encoded tRNAf-Met is limited to mitochondria but that nuclear DNA-encoded tRNAVal and tRNAi-Met are present in the cytoplasm and in mitochondria. These data provide direct evidence that in M. senile, mature, functional tRNAs are transcribed from the mtDNA-encoded tRNAf-Met and tRNATrp genes, and are consistent with the interpretation that both nuclear DNA-encoded tRNAVal and tRNAi-Met are utilized in mitochondrial and cytosolic protein synthesis.
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Affiliation(s)
- C Timothy Beagley
- Department of Biology, University of Utah, Salt Lake City, UT 84121, USA.
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32
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Kayal E, Roure B, Philippe H, Collins AG, Lavrov DV. Cnidarian phylogenetic relationships as revealed by mitogenomics. BMC Evol Biol 2013; 13:5. [PMID: 23302374 PMCID: PMC3598815 DOI: 10.1186/1471-2148-13-5] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 12/21/2012] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Cnidaria (corals, sea anemones, hydroids, jellyfish) is a phylum of relatively simple aquatic animals characterized by the presence of the cnidocyst: a cell containing a giant capsular organelle with an eversible tubule (cnida). Species within Cnidaria have life cycles that involve one or both of the two distinct body forms, a typically benthic polyp, which may or may not be colonial, and a typically pelagic mostly solitary medusa. The currently accepted taxonomic scheme subdivides Cnidaria into two main assemblages: Anthozoa (Hexacorallia + Octocorallia) - cnidarians with a reproductive polyp and the absence of a medusa stage - and Medusozoa (Cubozoa, Hydrozoa, Scyphozoa, Staurozoa) - cnidarians that usually possess a reproductive medusa stage. Hypothesized relationships among these taxa greatly impact interpretations of cnidarian character evolution. RESULTS We expanded the sampling of cnidarian mitochondrial genomes, particularly from Medusozoa, to reevaluate phylogenetic relationships within Cnidaria. Our phylogenetic analyses based on a mitochogenomic dataset support many prior hypotheses, including monophyly of Hexacorallia, Octocorallia, Medusozoa, Cubozoa, Staurozoa, Hydrozoa, Carybdeida, Chirodropida, and Hydroidolina, but reject the monophyly of Anthozoa, indicating that the Octocorallia + Medusozoa relationship is not the result of sampling bias, as proposed earlier. Further, our analyses contradict Scyphozoa [Discomedusae + Coronatae], Acraspeda [Cubozoa + Scyphozoa], as well as the hypothesis that Staurozoa is the sister group to all the other medusozoans. CONCLUSIONS Cnidarian mitochondrial genomic data contain phylogenetic signal informative for understanding the evolutionary history of this phylum. Mitogenome-based phylogenies, which reject the monophyly of Anthozoa, provide further evidence for the polyp-first hypothesis. By rejecting the traditional Acraspeda and Scyphozoa hypotheses, these analyses suggest that the shared morphological characters in these groups are plesiomorphies, originated in the branch leading to Medusozoa. The expansion of mitogenomic data along with improvements in phylogenetic inference methods and use of additional nuclear markers will further enhance our understanding of the phylogenetic relationships and character evolution within Cnidaria.
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Affiliation(s)
- Ehsan Kayal
- Dept. Ecology, Evolution, and Organismal Biology, Iowa State University, 50011, Ames, Iowa, USA
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 20013-7012, Washington, DC, USA
| | - Béatrice Roure
- Dept. Biochimie, Fac. Médecine, Université de Montral, Pavillon Roger-Gaudry, C.P. 6128, Succ. Centre-Ville, H3C 3J7, Montral, QC, Canada
| | - Hervé Philippe
- Dept. Biochimie, Fac. Médecine, Université de Montral, Pavillon Roger-Gaudry, C.P. 6128, Succ. Centre-Ville, H3C 3J7, Montral, QC, Canada
| | - Allen G Collins
- National Systematics Laboratory of NOAA’s Fisheries Service, National Museum of Natural History, MRC-153, Smithsonian Institution, PO Box 37012, 20013-7012, Washington, DC, USA
| | - Dennis V Lavrov
- Dept. Ecology, Evolution, and Organismal Biology, Iowa State University, 50011, Ames, Iowa, USA
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Fukami H, Omori M, Hatta M. Phylogenetic relationships in the coral family acroporidae, reassessed by inference from mitochondrial genes. Zoolog Sci 2012; 17:689-96. [PMID: 18517306 DOI: 10.2108/zsj.17.689] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/1999] [Accepted: 01/22/2000] [Indexed: 11/17/2022]
Abstract
Phylogenetic relationships within the dominant reef coral family Acroporidae were inferred from the mitochondrial genes cytochrome b and ATPase 6. The rate of nucleotide substitution in the genes gave proper resolution to deduce genetic relationships between the genera in this family. The molecular phylogeny divided this family into three major lineages: the genera Astreopora, Montipora and Acropora. The genus Anacropora was included in the same clade as the genus Montipora, suggesting its recent speciation from Montipora. The subgenus Isopora was significantly distant from the subgenus Acropora. Taken together with morphological and reproductive differences, we propose that these two subgenera be classified as independent genera. The divergence times deduced from the genetic distances were consistent with the fossil record for the major genera. The results also suggest that the extant reef corals speciated and expanded very recently, probably after the Miocene, from single lineage which survived repeated extinction by climate changes during the Cenozoic era.
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Brockman SA, McFadden CS. The mitochondrial genome of Paraminabea aldersladei (Cnidaria: Anthozoa: Octocorallia) supports intramolecular recombination as the primary mechanism of gene rearrangement in octocoral mitochondrial genomes. Genome Biol Evol 2012; 4:994-1006. [PMID: 22975720 PMCID: PMC3468961 DOI: 10.1093/gbe/evs074] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Sequencing of the complete mitochondrial genome of the soft coral Paraminabea aldersladei (Alcyoniidae) revealed a unique gene order, the fifth mt gene arrangement now known within the cnidarian subclass Octocorallia. At 19,886 bp, the mt genome of P. aldersladei is the second largest known for octocorals; its gene content and nucleotide composition are, however, identical to most other octocorals, and the additional length is due to the presence of two large, noncoding intergenic regions. Relative to the presumed ancestral octocoral gene order, in P. aldersladei a block of three protein-coding genes (nad6–nad3–nad4l) has been translocated and inverted. Mapping the distribution of mt gene arrangements onto a taxonomically comprehensive phylogeny of Octocorallia suggests that all of the known octocoral gene orders have evolved by successive inversions of one or more evolutionarily conserved blocks of protein-coding genes. This mode of genome evolution is unique among Metazoa, and contrasts strongly with that observed in Hexacorallia, in which extreme gene shuffling has occurred among taxonomic orders. Two of the four conserved gene blocks found in Octocorallia are, however, also conserved in the linear mt genomes of Medusozoa and in one group of Demospongiae. We speculate that the rate and mechanism of gene rearrangement in octocorals may be influenced by the presence in their mt genomes of mtMutS, a putatively active DNA mismatch repair protein that may also play a role in mediating intramolecular recombination.
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35
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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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Kayal E, Bentlage B, Collins AG, Kayal M, Pirro S, Lavrov DV. Evolution of linear mitochondrial genomes in medusozoan cnidarians. Genome Biol Evol 2011; 4:1-12. [PMID: 22113796 PMCID: PMC3267393 DOI: 10.1093/gbe/evr123] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In nearly all animals, mitochondrial DNA (mtDNA) consists of a single circular molecule that encodes several subunits of the protein complexes involved in oxidative phosphorylation as well as part of the machinery for their expression. By contrast, mtDNA in species belonging to Medusozoa (one of the two major lineages in the phylum Cnidaria) comprises one to several linear molecules. Many questions remain on the ubiquity of linear mtDNA in medusozoans and the mechanisms responsible for its evolution, replication, and transcription. To address some of these questions, we determined the sequences of nearly complete linear mtDNA from 24 species representing all four medusozoan classes: Cubozoa, Hydrozoa, Scyphozoa, and Staurozoa. All newly determined medusozoan mitochondrial genomes harbor the 17 genes typical for cnidarians and map as linear molecules with a high degree of gene order conservation relative to the anthozoans. In addition, two open reading frames (ORFs), polB and ORF314, are identified in cubozoan, schyphozoan, staurozoan, and trachyline hydrozoan mtDNA. polB belongs to the B-type DNA polymerase gene family, while the product of ORF314 may act as a terminal protein that binds telomeres. We posit that these two ORFs are remnants of a linear plasmid that invaded the mitochondrial genomes of the last common ancestor of Medusozoa and are responsible for its linearity. Hydroidolinan hydrozoans have lost the two ORFs and instead have duplicated cox1 at each end of their mitochondrial chromosome(s). Fragmentation of mtDNA occurred independently in Cubozoa and Hydridae (Hydrozoa, Hydroidolina). Our broad sampling allows us to reconstruct the evolutionary history of linear mtDNA in medusozoans.
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Affiliation(s)
- Ehsan Kayal
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, USA.
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Watanabe K, Yokobori SI. tRNA Modification and Genetic Code Variations in Animal Mitochondria. J Nucleic Acids 2011; 2011:623095. [PMID: 22007289 PMCID: PMC3191813 DOI: 10.4061/2011/623095] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 07/04/2011] [Indexed: 12/03/2022] Open
Abstract
In animal mitochondria, six codons have been known as nonuniversal genetic codes, which vary in the course of animal evolution. They are UGA (termination codon in the universal genetic code changes to Trp codon in all animal mitochondria), AUA (Ile to Met in most metazoan mitochondria), AAA (Lys to Asn in echinoderm and some platyhelminth mitochondria), AGA/AGG (Arg to Ser in most invertebrate, Arg to Gly in tunicate, and Arg to termination in vertebrate mitochondria), and UAA (termination to Tyr in a planaria and a nematode mitochondria, but conclusive evidence is lacking in this case). We have elucidated that the anticodons of tRNAs deciphering these nonuniversal codons (tRNATrp for UGA, tRNAMet for AUA, tRNAAsn for AAA, and tRNASer and tRNAGly for AGA/AGG) are all modified; tRNATrp has 5-carboxymethylaminomethyluridine or 5-taurinomethyluridine, tRNAMet has 5-formylcytidine or 5-taurinomethyluridine, tRNASer has 7-methylguanosine and tRNAGly has 5-taurinomethyluridine in their anticodon wobble position, and tRNAAsn has pseudouridine in the anticodon second position. This review aims to clarify the structural relationship between these nonuniversal codons and the corresponding tRNA anticodons including modified nucleosides and to speculate on the possible mechanisms for explaining the evolutional changes of these nonuniversal codons in the course of animal evolution.
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Affiliation(s)
- Kimitsuna Watanabe
- Department of Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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Bilewitch JP, Degnan SM. A unique horizontal gene transfer event has provided the octocoral mitochondrial genome with an active mismatch repair gene that has potential for an unusual self-contained function. BMC Evol Biol 2011; 11:228. [PMID: 21801381 PMCID: PMC3166940 DOI: 10.1186/1471-2148-11-228] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 07/29/2011] [Indexed: 11/22/2022] Open
Abstract
Background The mitochondrial genome of the Octocorallia has several characteristics atypical for metazoans, including a novel gene suggested to function in DNA repair. This mtMutS gene is favored for octocoral molecular systematics, due to its high information content. Several hypotheses concerning the origins of mtMutS have been proposed, and remain equivocal, although current weight of support is for a horizontal gene transfer from either an epsilonproteobacterium or a large DNA virus. Here we present new and compelling evidence on the evolutionary origin of mtMutS, and provide the very first data on its activity, functional capacity and stability within the octocoral mitochondrial genome. Results The mtMutS gene has the expected conserved amino acids, protein domains and predicted tertiary protein structure. Phylogenetic analysis indicates that mtMutS is not a member of the MSH family and therefore not of eukaryotic origin. MtMutS clusters closely with representatives of the MutS7 lineage; further support for this relationship derives from the sharing of a C-terminal endonuclease domain that confers a self-contained mismatch repair function. Gene expression analyses confirm that mtMutS is actively transcribed in octocorals. Rates of mitochondrial gene evolution in mtMutS-containing octocorals are lower than in their hexacoral sister-group, which lacks the gene, although paradoxically the mtMutS gene itself has higher rates of mutation than other octocoral mitochondrial genes. Conclusions The octocoral mtMutS gene is active and codes for a protein with all the necessary components for DNA mismatch repair. A lower rate of mitochondrial evolution, and the presence of a nicking endonuclease domain, both indirectly support a theory of self-sufficient DNA mismatch repair within the octocoral mitochondrion. The ancestral affinity of mtMutS to non-eukaryotic MutS7 provides compelling support for an origin by horizontal gene transfer. The immediate vector of transmission into octocorals can be attributed to either an epsilonproteobacterium in an endosymbiotic association or to a viral infection, although DNA viruses are not currently known to infect both bacteria and eukaryotes, nor mitochondria in particular. In consolidating the first known case of HGT into an animal mitochondrial genome, these findings suggest the need for reconsideration of the means by which metazoan mitochondrial genomes evolve.
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Affiliation(s)
- Jaret P Bilewitch
- School of Biological Sciences, University of Queensland, St, Lucia, Brisbane, Queensland, Australia
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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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Cheng R, Zheng X, Lin X, Yang J, Li Q. Determination of the complete mitochondrial DNA sequence of Octopus minor. Mol Biol Rep 2011; 39:3461-70. [PMID: 21710247 DOI: 10.1007/s11033-011-1118-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 06/20/2011] [Indexed: 01/31/2023]
Abstract
In this study, we have determined the complete nucleotide sequence of the mitochondrial genome of Octopus minor. It is 15,974 nucleotide pairs and encodes 13 proteins, two ribosomal RNAs and 22 tRNAs of the mitochondrion's own protein synthesizing system. Seven of thirteen proteins are encoded by the H-strand, while the other six proteins, as well as the two ribosomal RNAs are encoded by the L-strand. The nucleotide composition of the proteins showed a nucleotide bias against G encoded by the H-strand, while they showed a nucleotide bias against A and C encoded by the L-strand. Two of the 13 protein coding genes of O. minor began with the unorthodox translation initiation codon ATA and all others use the standard ATG. In addition, six of thirteen mt proteins of O. minor have unambiguous termination codons. There are four cases where tRNA genes appear to overlap. The long noncoding region (LNCR) of O. minor was 930 nucleotides and no repeated sequences were found in this LNCR. The gene arrangements of O. minor showed remarkable similarity to that of O. ocellatus and O. vulgaris. Phylogenetic analysis demonstrated that O. minor appears as sister taxan to the monophyletic group combined by O. ocellatus and O. vulgaris, suggesting a relative distant genetic relationship between O. minor and the other two octopus species.
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Affiliation(s)
- Rubin Cheng
- Fisheries College, Ocean University of China, Qingdao, 266003, China
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41
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Birrell JA, Hirst J. Truncation of subunit ND2 disrupts the threefold symmetry of the antiporter-like subunits in complex I from higher metazoans. FEBS Lett 2010; 584:4247-52. [PMID: 20846527 DOI: 10.1016/j.febslet.2010.09.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Accepted: 09/09/2010] [Indexed: 11/27/2022]
Abstract
Three of the conserved, membrane-bound subunits in NADH:ubiquinone oxidoreductase (complex I) are related to one another, and to Mrp sodium-proton antiporters. Recent structural analysis of two prokaryotic complexes I revealed that the three subunits each contain fourteen transmembrane helices that overlay in structural alignments: the translocation of three protons may be coordinated by a lateral helix connecting them together (Efremov, R.G., Baradaran, R. and Sazanov, L.A. (2010). The architecture of respiratory complex I. Nature 465, 441-447). Here, we show that in higher metazoans the threefold symmetry is broken by the loss of three helices from subunit ND2; possible implications for the mechanism of proton translocation are discussed.
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Affiliation(s)
- James A Birrell
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Cambridge, UK
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42
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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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Erpenbeck D, Voigt O, Wörheide G, Lavrov DV. The mitochondrial genomes of sponges provide evidence for multiple invasions by Repetitive Hairpin-forming Elements (RHE). BMC Genomics 2009; 10:591. [PMID: 20003196 PMCID: PMC2800124 DOI: 10.1186/1471-2164-10-591] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Accepted: 12/09/2009] [Indexed: 01/14/2023] Open
Abstract
Background The mitochondrial (mt) genomes of sponges possess a variety of features, which appear to be intermediate between those of Eumetazoa and non-metazoan opisthokonts. Among these features is the presence of long intergenic regions, which are common in other eukaryotes, but generally absent in Eumetazoa. Here we analyse poriferan mitochondrial intergenic regions, paying particular attention to repetitive sequences within them. In this context we introduce the mitochondrial genome of Ircinia strobilina (Lamarck, 1816; Demospongiae: Dictyoceratida) and compare it with mtDNA of other sponges. Results Mt genomes of dictyoceratid sponges are identical in gene order and content but display major differences in size and organization of intergenic regions. An even higher degree of diversity in the structure of intergenic regions was found among different orders of demosponges. One interesting observation made from such comparisons was of what appears to be recurrent invasions of sponge mitochondrial genomes by repetitive hairpin-forming elements, which cause large genome size differences even among closely related taxa. These repetitive hairpin-forming elements are structurally and compositionally divergent and display a scattered distribution throughout various groups of demosponges. Conclusion Large intergenic regions of poriferan mt genomes are targets for insertions of repetitive hairpin- forming elements, similar to the ones found in non-metazoan opisthokonts. Such elements were likely present in some lineages early in animal mitochondrial genome evolution but were subsequently lost during the reduction of intergenic regions, which occurred in the Eumetazoa lineage after the split of Porifera. Porifera acquired their elements in several independent events. Patterns of their intra-genomic dispersal can be seen in the mt genome of Vaceletia sp.
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Affiliation(s)
- Dirk Erpenbeck
- Department of Earth- and Environmental Sciences, Palaeontology & Geobiology and GeoBioCenter LMU, Ludwig-Maximilians Universität München, Richard-Wagner-Str, 10, 80333 München, Germany.
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Rand DM. 'Why genomes in pieces?' revisited: sucking lice do their own thing in mtDNA circle game. Genome Res 2009; 19:700-2. [PMID: 19411594 DOI: 10.1101/gr.091132.109] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- David M Rand
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA.
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SINNIGER F, PAWLOWSKI J. The partial mitochondrial genome of Leiopathes glaberrima (Hexacorallia: Antipatharia) and the first report of the presence of an intron in COI in black corals. ACTA ACUST UNITED AC 2009. [DOI: 10.3755/galaxea.11.21] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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46
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Abascal F, Zardoya R, Posada D. Genetic code prediction for metazoan mitochondria with GenDecoder. Methods Mol Biol 2009; 537:233-242. [PMID: 19378147 DOI: 10.1007/978-1-59745-251-9_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
There is a standard genetic code that is used by most organisms, but exceptions exist in which particular codons are translated with a different meaning, i.e., as a different amino acid. The characterization of the genetic code of an organism is hence a key step for properly analyzing and translating its protein-coding genes. Such characterization is particularly important in the case of metazoan mitochondrial genomes for two reasons: first, many variant codes occur in them and second, mitochondrial data is frequently used for evolutionary studies. Variant codes are usually found by comparative sequence analyses. Given a protein alignment, if a particular codon for a given species occurs at positions in which a particular amino acid is frequently found in other species, then the most likely hypothesis is that the codon is translated as that particular amino acid in that species. Previously, we have shown that this method can be very reliable provided that enough taxa and positions are included in the comparisons and have implemented it in the web-ser GenDecoder (http://darwin.uvigo.es/software/gendecoder.html). In this chapter we describe the rationale of the method used by GenDecoder and its usage through worked examples, highlighting the potential problems that can arise during the analysis.
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Affiliation(s)
- Federico Abascal
- Departamento de Genética, Bioquímica e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Spain
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Fukami H, Chen CA, Budd AF, Collins A, Wallace C, Chuang YY, Chen C, Dai CF, Iwao K, Sheppard C, Knowlton N. Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria). PLoS One 2008; 3:e3222. [PMID: 18795098 PMCID: PMC2528942 DOI: 10.1371/journal.pone.0003222] [Citation(s) in RCA: 165] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Accepted: 06/30/2008] [Indexed: 01/27/2023] Open
Abstract
Modern hard corals (Class Hexacorallia; Order Scleractinia) are widely studied because of their fundamental role in reef building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders, families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia) might be imbedded within the stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families) and various outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b), with analyses of nuclear genes (ß-tubulin, ribosomal DNA) of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly divergent “robust” and “complex” clades. However, the recent suggestion that corallimorpharians are true corals that have lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also often by morphological characters which had been ignored or never noted previously. The concordance of molecular characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as the potential to trace the evolutionary history of this ecologically important group using fossils.
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Affiliation(s)
- Hironobu Fukami
- Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, Shirahama, Wakayama, Japan
| | - Chaolun Allen Chen
- Biodiversity Research Centre, Academia Sinica, Nangang, Taipei, Taiwan
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Ann F. Budd
- Department of Geoscience, University of Iowa, Iowa City, Iowa, United States of America
| | - Allen Collins
- National Systematics Laboratory, NOAA Fisheries Service, National Museum of Natural History, MRC 153, Smithsonian Institution, Washington, D. C., United States of America
| | | | - Yao-Yang Chuang
- Biodiversity Research Centre, Academia Sinica, Nangang, Taipei, Taiwan
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Chienhsun Chen
- Biodiversity Research Centre, Academia Sinica, Nangang, Taipei, Taiwan
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Chang-Feng Dai
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Kenji Iwao
- Akajima Marine Science Laboratory, Zamami-son, Okinawa, Japan
| | - Charles Sheppard
- Department of Biological Sciences, University of Warwick, Coventry, United Kingdom
| | - Nancy Knowlton
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, MRC 163, Washington, D. C., United States of America
- * E-mail:
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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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49
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Voigt O, Erpenbeck D, Wörheide G. A fragmented metazoan organellar genome: the two mitochondrial chromosomes of Hydra magnipapillata. BMC Genomics 2008; 9:350. [PMID: 18655725 PMCID: PMC2518934 DOI: 10.1186/1471-2164-9-350] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Accepted: 07/26/2008] [Indexed: 01/30/2023] Open
Abstract
Background Animal mitochondrial (mt) genomes are characteristically circular molecules of ~16–20 kb. Medusozoa (Cnidaria excluding Anthozoa) are exceptional in that their mt genomes are linear and sometimes subdivided into two to presumably four different molecules. In the genus Hydra, the mt genome comprises one or two mt chromosomes. Here, we present the whole mt genome sequence from the hydrozoan Hydra magnipapillata, comprising the first sequence of a fragmented metazoan mt genome encoded on two linear mt chromosomes (mt1 and mt2). Results The H. magnipapillata mt chromosomes contain the typical metazoan set of 13 genes for respiratory proteins, the two rRNA genes and two tRNA genes. All genes are unidirectionally oriented on mt1 and mt2, and several genes overlap. The gene arrangement suggests that the two mt chromosomes originated from one linear molecule that separated between nd5 and rns. Strong correlations between the AT content of rRNA genes (rns and rnl) and the AT content of protein-coding genes among 24 cnidarian genomes imply that base composition is mainly determined by mt genome-wide constraints. We show that identical inverted terminal repeats (ITR) occur on both chromosomes; these ITR contain a partial copy or part of the 3' end of cox1 (54 bp). Additionally, both mt chromosomes possess identical oriented sequences (IOS) at the 5' and 3' ends (5' and 3' IOS) adjacent to the ITR. The 5' IOS contains trnM and non-coding sequences (119 bp), whereas the 3' IOS comprises a larger part (mt2) with a larger partial copy of cox1 (243 bp). Conclusion ITR are also documented in the two other available medusozoan mt genomes (Aurelia aurita and Hydra oligactis). In H. magnipapillata, the arrangement of ITR and 5' IOS and 3' IOS suggest that these regions are crucial for mt DNA replication and/or transcription initiation. An analogous organization occurs in a highly fragmented ichthyosporean mt genome. With our data, we can reject a model of mt replication that has previously been proposed for Hydra. This raises new questions regarding replication mechanisms probably employed by all medusozoans, and also has general implications for the expected organization of fragmented linear mt chromosomes of other taxa.
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Affiliation(s)
- Oliver Voigt
- Courant Research Center Geobiology, Georg-August-Universität Göttingen, Goldschmidtstr, 3, 37077 Göttingen, Germany.
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50
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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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