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Cruz BA, Cappelmann A, Chutjian H, Roman JC, Reid MA, Wright J, Gonzalez AD, Keyman T, Griffith KM, Appiah-Madson HJ, Distel DL, Hayes VE, Drewery J, Pettay DT, Staton JL, Brugler MR. Complete mitochondrial genomes of the black corals Alternatipathesmirabilis Opresko & Molodtsova, 2021 and Parantipatheslarix (Esper, 1788) (Cnidaria, Anthozoa, Hexacorallia, Antipatharia, Schizopathidae). Zookeys 2024; 1196:79-93. [PMID: 38560095 PMCID: PMC10980879 DOI: 10.3897/zookeys.1196.116837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 04/04/2024] Open
Abstract
We describe the complete mitogenomes of the black corals Alternatipathesmirabilis Opresko & Molodtsova, 2021 and Parantipatheslarix (Esper, 1790) (Cnidaria, Anthozoa, Hexacorallia, Antipatharia, Schizopathidae). The analysed specimens include the holotype of Alternatipathesmirabilis, collected from Derickson Seamount (North Pacific Ocean; Gulf of Alaska) at 4,685 m depth and a potential topotype of Parantipatheslarix, collected from Secca dei Candelieri (Mediterranean Sea; Tyrrhenian Sea; Salerno Gulf; Italy) at 131 m depth. We also assemble, annotate and make available nine additional black coral mitogenomes that were included in a recent phylogeny (Quattrini et al. 2023b), but not made easily accessible on GenBank. This is the first study to present and compare two mitogenomes from the same species of black coral (Stauropathesarctica (Lütken, 1871)) and, thus, place minimum boundaries on the expected level of intraspecific variation at the mitogenome level. We also compare interspecific variation at the mitogenome-level across five different specimens of Parantipathes Brook, 1889 (representing at least two different species) from the NE Atlantic and Mediterranean Sea.
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Affiliation(s)
- Brendan A. Cruz
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Anneau Cappelmann
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Hope Chutjian
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Jude C. Roman
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Mason A. Reid
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Jacob Wright
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Aydanni D. Gonzalez
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Taylor Keyman
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Kierstin M. Griffith
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Hannah J. Appiah-Madson
- Ocean Genome Legacy Center, Northeastern University, 430 Nahant Road, Nahant, MA 01908, USANortheastern UniversityNahantUnited States of America
| | - Daniel L. Distel
- Ocean Genome Legacy Center, Northeastern University, 430 Nahant Road, Nahant, MA 01908, USANortheastern UniversityNahantUnited States of America
| | - Vonda E. Hayes
- Department of Fisheries & Oceans Canada, Northwest Atlantic Fisheries Centre, 80 East White Hills Road, St. John’s, Newfoundland & Labrador, A1C 5X1, CanadaNorthwest Atlantic Fisheries CentreNewfoundland & LabradorCanada
| | - Jim Drewery
- Marine Directorate of Scottish Government, Marine Laboratory, 375 Victoria Road, Aberdeen AB11 9DB, Scotland, UKMarine Directorate of Scottish Government, Marine LaboratoryAberdeenUnited Kingdom
| | - D. Tye Pettay
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Joseph L. Staton
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
| | - Mercer R. Brugler
- Department of Natural Sciences, University of South Carolina Beaufort, 1100 Boundary St, Beaufort, SC 29902, USAUniversity of South Carolina BeaufortBeaufortUnited States of America
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USAAmerican Museum of Natural HistoryNew YorkUnited States of America
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC 20560, USANational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
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Shizuru LEK, Montgomery AD, Wagner D, Freel EB, Toonen RJ. The complete mitochondrial genome of a species of Cirrhipathes de Blainville, 1830 from Kaua'i, Hawai'i (Hexacorallia: Antipatharia). Mitochondrial DNA B Resour 2024; 9:223-226. [PMID: 38313464 PMCID: PMC10836483 DOI: 10.1080/23802359.2024.2310130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 01/20/2024] [Indexed: 02/06/2024] Open
Abstract
This study reports the first mitogenome from the antipatharian (black coral) genus Cirrhipathes (GenBank accession number ON653414). The 20,452 bp mitochondrial genome of Cirrhipathes cf. anguina LS-2022 consists of 13 protein-coding genes, two rRNA genes, and two tRNA genes (trnM and trnW). The mitogenome is typical of other antipatharian families, including an A + T biased (64.1%) base composition and cytochrome c oxidase subunit I (COX1) intron with embedded homing endonuclease gene (HEG). A phylogenetic tree based on complete mitogenome sequences of currently available antipatharians indicates Cirrhipathes cf. anguina LS-2022 is sister and closely related to Stichopathes sp. SCBUCN-8849. However, it seems unlikely that intergeneric taxa share 99.97% similarity across their complete mitogenomes, raising questions about the current taxonomy of this group. This study highlights the need for additional vouchered antipatharian species to be sequenced so phylogenetic relationships can be compared with accepted taxonomy.
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Affiliation(s)
- Leah E K Shizuru
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Anthony D Montgomery
- US Fish and Wildlife Service, Pacific Fish and Wildlife Office, Honolulu, HI, USA
| | | | - Evan B Freel
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
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Wang J, Zhang T, Chang S, Li J, Jiang Y. Complete mitochondrial genome and its phylogenetic implications of Rhinogobio nasutus, an endemic species from the Yellow River. Mol Biol Rep 2023; 50:10651-10656. [PMID: 37962705 DOI: 10.1007/s11033-023-08871-x] [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: 06/21/2023] [Accepted: 09/29/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND Rhinogobio nasutus, an endemic species from the Yellow River, is listed under the second class of the National Key Protected Wildlife List in China due to its dramatically decreased population. Despite its important status, the mitochondrial genes and phylogenetic relationships of R. nasutus are unknown. METHODS AND RESULTS The complete mitochondrial genome of R. nasutus was sequenced, assembled, and annotated for the first time. The mitochondrial genome was 16,609 bp in length, consisting of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and 1 non-coding control region. The gene order in the mitochondrial genome of R. nasutus was identical to that of other Rhinogobios species. Analysis of synonymous and non-synonymous nucleotide substitutions showed that the Ka/Ks ratio in all tested protein-coding genes was less than 1, indicating that these genes were evolving under purifying selection. Further phylogenetic analysis showed that R. nasutus was first clustered with R. typus, then grouped with the other two Rhinogobio species, indicating the phylogenetically close relationship between R. nasutus and R. typus. CONCLUSIONS This was the first genomic resource developed for R. nasutus, which could not only improve our understanding of its phylogenetic status, but also serve as a genomic tool for the development of genetic markers that will be used in conservation and evolutionary genetics studies.
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Affiliation(s)
- Jiali Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Tianyang Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China
| | - Songhuan Chang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Jiongtang Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China
| | - Yanliang Jiang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, CAFS Key Laboratory of Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
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