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Wang C, Lai T, Ye P, Yan Y, Feutry P, He B, Huang Z, Zhu T, Wang J, Chen X. Novel duplication remnant in the first complete mitogenome of Hemitriakis japanica and the unique phylogenetic position of family Triakidae. Gene 2022; 820:146232. [PMID: 35114282 DOI: 10.1016/j.gene.2022.146232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/22/2021] [Accepted: 01/18/2022] [Indexed: 01/08/2023]
Abstract
In this study, we firstly determined the complete mitogenome of the Japanese topeshark (Hemitriakis japonica), which belong to the family Triakidae and was assessed as Endangered A2d on the IUCN Red List in 2021. The mitogenome is 17,301 bp long, has a high AT content (60.0%), and contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, a control region and specially a 594 bp-long non-coding region between Cytb gene and tRNA-Thr gene. The novel non-coding region share high sequence similarity with segments of the former and latter genes, so it was recognized as a duplication remnant. In addition, the Cytb gene and tRNA-Thr gene tandemly duplicated twice while accompanied by being deleted once at least. This is the first report of mitogenomic gene-arrangement in Triakidae. The phylogenetic trees were constructed using Bayesian inference (BI) and maximum likelihood (ML) methods based on the mitogenomic data of 51 shark species and two outgroups. In summary, basing on a novel type of gene rearrangements in houndshark mitogenome, the possibly rearranged process was analyzed and contributed further insight of shark mitogenomes evolution and phylogeny.
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Affiliation(s)
- Chen Wang
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China
| | - Tinghe Lai
- Guangxi Academy of Oceanography, Nanning 530000, China
| | - Peiyuan Ye
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Yunrong Yan
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524000, China
| | - Pierre Feutry
- CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, Tasmania 7000, Australia
| | - Binyuan He
- Guangxi Academy of Oceanography, Nanning 530000, China
| | | | - Ting Zhu
- Guangxi Academy of Oceanography, Nanning 530000, China
| | - Junjie Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Xiao Chen
- College of Marine Sciences, South China Agriculture University, Guangzhou 510642, China; Guangxi Mangrove Research Center, Beihai 536000, China.
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Huang X, Zhou Z, Lai T, He B, Zhang D. Characterization of the complete mitochondrial genome of blacktip shark Carcharhinus limbatus (Carcharhiniformes: Carcharhinidae). Mitochondrial DNA B Resour 2022; 7:385-386. [PMID: 35187238 PMCID: PMC8856099 DOI: 10.1080/23802359.2021.1914214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In this study, we aimed to determine the complete mitochondrial genome of blacktip shark Carcharhinus limbatus. The mitochondrial genome was 16,705 bp in length, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Phylogenetic analysis was done using the Bayesian inference method, which showed a close relationship between C. limbatus and C. amblyrhynchoides.
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Affiliation(s)
- Xiaolin Huang
- School of Marine Sciences, Ningbo University, Ningbo, China
- Zhejiang Mariculture Research Institute, Wenzhou, China
| | | | - Tinghe Lai
- Guangxi Academy of Oceanography, Nanning, China
| | - Binyuan He
- Guangxi Academy of Oceanography, Nanning, China
| | - Demin Zhang
- School of Marine Sciences, Ningbo University, Ningbo, China
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Gallagher AJ, Shipley ON, Reese B, Singh V. Complete mitochondrial genome of the Caribbean reef shark, Carcharhinus perezi (Carcharhinformes: Carcharhinidae). Mitochondrial DNA B Resour 2021; 6:2662-2664. [PMID: 34435112 PMCID: PMC8381894 DOI: 10.1080/23802359.2021.1964394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The Caribbean reef shark (Carcharhinus perezi; Poey, 1876) is a medium to large-bodied coastal and reef-associated predator found throughout the subtropical and tropical waters of the Atlantic Ocean and Caribbean Sea, although its populations are increasingly threatened by overfishing. We describe the first mitochondrial genome sequence for this species, using Illumina MiSeq sequencing of an individual from The Bahamas. We report the mitogenome sequence of the Caribbean reef shark to be 16,709 bp and composed two rRNA genes, 22 tRNA genes, 13 protein-coding genes, 2 non-coding regions; the D-loop control region and the origin of light-strand replication. We discuss the implications of this new information on future monitoring efforts and conservation measures such as marine protected areas, and urge for greater application of mitochondrial studies of sharks in the Atlantic Ocean.
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Affiliation(s)
- Austin J. Gallagher
- Beneath the Waves, Herndon, VA, USA
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter Cornwall Campus, Penryn, Cornwall, UK
| | - Oliver N. Shipley
- Beneath the Waves, Herndon, VA, USA
- Biology Department, University of New Mexico, Albuquerque, NM, USA
| | - Bo Reese
- Center for Genome Innovation, Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Vijender Singh
- Institute for Systems Genomics, Computational Biology Core, University of Connecticut, Storrs, CT, USA
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Patel E, Bernard AM, Mehlrose M, Harned S, Finnegan KA, Fitzpatrick CK, Lea JS, Shivji MS. The complete mitochondrial genome of a gray reef shark, Carcharhinus amblyrhynchos (Carcharhiniformes: Carcharhinidae), from the Western Indian Ocean. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3498-3499. [PMID: 33458217 PMCID: PMC7782100 DOI: 10.1080/23802359.2020.1827064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We present the mitochondrial genome sequence of a gray reef shark, Carcharhinus amblyrhynchos (Bleeker 1856), a coral reef associated species. This is the first mitogenome for this species from the western Indian Ocean. The mitogenome is 16,705 bp in length, has 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region, and demonstrates a gene arrangement congruent with other shark and most vertebrate species. This mitogenome provides a genomic resource for assisting with population, evolutionary and conservation studies for the gray reef shark, which is increasingly under threat from fisheries.
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Affiliation(s)
- Ela Patel
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, Florida, USA.,Trinity Preparatory School, Florida, USA
| | - Andrea M Bernard
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, Florida, USA
| | - Marissa Mehlrose
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, Florida, USA
| | - Sydney Harned
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, Florida, USA
| | - Kimberly A Finnegan
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, Florida, USA
| | - Cristín K Fitzpatrick
- State Fisheries Genomics Lab, Department of Fisheries and Wildlife, Oregon State University, Oregon, USA
| | - James S Lea
- Save Our Seas Foundation, Geneva, Switzerland.,Department of Zoology, University of Cambridge, Cambridge, UK
| | - Mahmood S Shivji
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, Florida, USA
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Johri S, Chapple TK, Schallert R, Dinsdale EA, Block BA. Complete mitochondrial genome of the whitetip reef shark Triaenodon obesus from the British Indian Ocean Territory Marine Protected Area. Mitochondrial DNA B Resour 2020; 5:2347-2349. [PMID: 33457786 PMCID: PMC7783066 DOI: 10.1080/23802359.2020.1775148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Shaili Johri
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Taylor K. Chapple
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
- Coastal Oregon Marine Experiment Station, Oregon State University, OR, USA
| | - Robert Schallert
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | | | - Barbara A. Block
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
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