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Zhang Q, Li F, Dong Y, Cai X, Gu Y, Wang Z, Shen Z. Phylogenetic analysis of Cyprinus acutidorsalis (Wang, 1979) from the Hainan population using complete mitochondrial genome. Mitochondrial DNA B Resour 2024; 9:841-844. [PMID: 38919809 PMCID: PMC11198120 DOI: 10.1080/23802359.2024.2323004] [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: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 06/27/2024] Open
Abstract
Cyprinus acutidorsalis (Wang, 1979) is an endemic fish in China that is sparsely distributed in the Hainan provinces and Guangxi Zhuang Autonomous Region (GZAR). In this study, the complete mitochondrial genome of C. acutidorsalis from the Hainan population from the Wanquan River was sequenced, and its phylogenetic relationship was analyzed. The circular mtDNA was 16,581 bp in length, and the overall base composition was A (32.0%), C (27.5%), T (24.8%), and G (15.70%), with a slight bias toward A + T. The complete mitogenome encoded 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. Phylogenetic analysis indicated that the most closely related fish to C. acutidorsalis from the Hainan population was C. acutidorsalis from the Guangxi population. These findings offer basic molecular data and a better understanding of the phylogenetic relationships among the Cyprinus species.
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Affiliation(s)
- Qingfeng Zhang
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Research Center for Freshwater Bioresource and Eco-environment Protection in Hainan Province, Haikou, China
| | - Fangyuan Li
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Research Center for Freshwater Bioresource and Eco-environment Protection in Hainan Province, Haikou, China
| | - Yang Dong
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Research Center for Freshwater Bioresource and Eco-environment Protection in Hainan Province, Haikou, China
| | - Xingwei Cai
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Research Center for Freshwater Bioresource and Eco-environment Protection in Hainan Province, Haikou, China
| | - Yuan Gu
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Research Center for Freshwater Bioresource and Eco-environment Protection in Hainan Province, Haikou, China
| | - Zhenjiang Wang
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Research Center for Freshwater Bioresource and Eco-environment Protection in Hainan Province, Haikou, China
| | - Zhixin Shen
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
- Research Center for Freshwater Bioresource and Eco-environment Protection in Hainan Province, Haikou, China
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Siddika MA, Ahmed KA, Alam MS, Bushra J, Begum RA. Complete mitogenome and intra-family comparative mitogenomics showed distinct position of Pama Croaker Otolithoides pama. Sci Rep 2024; 14:13820. [PMID: 38879694 PMCID: PMC11180200 DOI: 10.1038/s41598-024-64791-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 06/13/2024] [Indexed: 06/19/2024] Open
Abstract
The Pama Croaker, Otolithoides pama, is an economically important fish species in Bangladesh. Intra-family similarities in morphology and typical barcode sequences of cox1 create ambiguities in its identification. Therefore, morphology and the complete mitochondrial genome of O. pama, and comparative mitogenomics within the family Sciaenidae have been studied. Extracted genomic DNA was subjected to Illumina-based short read sequencing for De-Novo mitogenome assembly. The complete mitogenome of O. pama (Accession: OQ784575.1) was 16,513 bp, with strong AC biasness and strand asymmetry. Relative synonymous codon usage (RSCU) among 13 protein-coding genes (PCGs) of O. pama was also analyzed. The studied mitogenomes including O. pama exhibited consistent sizes and gene orders, except for the genus Johnius which possessed notably longer mitogenomes with unique gene rearrangements. Different genetic distance metrics across 30 species of Sciaenidae family demonstrated 12S rRNA and the control region (CR) as the most conserved and variable regions, respectively, while most of the PCGs undergone a purifying selection. Different phylogenetic trees were congruent with one another, where O. pama was distinctly placed. This study would contribute to distinguishing closely related fish species of Sciaenidae family and can be instrumental in conserving the genetic diversity of O. pama.
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Affiliation(s)
- Most Ayesha Siddika
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh
| | | | - Mohammad Shamimul Alam
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh.
| | - Jannatul Bushra
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Rowshan Ara Begum
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh
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Xu X, Guan W, Niu B, Guo D, Xie QP, Zhan W, Yi S, Lou B. Chromosome-Level Assembly of the Chinese Hooksnout Carp (Opsariichthys bidens) Genome Using PacBio Sequencing and Hi-C Technology. Front Genet 2022; 12:788547. [PMID: 35126459 PMCID: PMC8807397 DOI: 10.3389/fgene.2021.788547] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 12/23/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
- Xiaojun Xu
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Wenzhi Guan
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Baolong Niu
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Dandan Guo
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qing-Ping Xie
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Wei Zhan
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Shaokui Yi
- School of Life Sciences, Huzhou University, Huzhou, China
- *Correspondence: Shaokui Yi, ; Bao Lou,
| | - Bao Lou
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Shaokui Yi, ; Bao Lou,
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Li W, Qiu N, Du H. Complete mitochondrial genome of Rhodeuscyanorostris (Teleostei, Cyprinidae): characterization and phylogenetic analysis. Zookeys 2022; 1081:111-125. [PMID: 35087298 PMCID: PMC8776718 DOI: 10.3897/zookeys.1081.77043] [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: 10/25/2021] [Accepted: 12/14/2021] [Indexed: 11/12/2022] Open
Abstract
Rhodeuscyanorostris Li, Liao & Arai, 2020 is a freshwater fish that is endemic to China and restricted to Chengdu City in Sichuan Province. This study is the first to sequence and characterize the complete mitochondrial genome of R.cyanorostris. The mitogenome of R.cyanorostris is 16580 bp in length, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region (D-loop). The base composition of the sequence is 28.5% A, 27.6% C, 26.4% T, and 17.5% G, with a bias toward A+T. The genome structure, nucleotide composition, and codon usage of the mitogenome of R.cyanorostris are consistent with those of other species of Rhodeus. To verify the molecular phylogeny of the genus Rhodeus, we provide new insights to better understand the taxonomic status of R.cyanorostris. The phylogenetic trees present four major clades based on 19 mitogenomic sequences from 16 Rhodeus species. Rhodeuscyanorostris exhibits the closest phylogenetic relationship with R.pseudosericeus, R.amarus, and R.sericeus. This study discloses the complete mitochondrial genome sequence of R.cyanorostris for the first time and provides the most comprehensive phylogenetic reconstruction of the genus Rhodeus based on whole mitochondrial genome sequences. The information obtained in this study will provide new insights for conservation, phylogenetic analysis, and evolutionary biology research.
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Affiliation(s)
- Wenjing Li
- YANGTZE Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing 100038, ChinaYANGTZE Eco-Environment Engineering Research CenterBeijingChina
| | - Ning Qiu
- Key Laboratory of Environmental Protection Technology on Water Transport, Ministry of Transport, Tianjin research institute for water transport engineering, M.O.T., Tianjin 300456, ChinaMinistry of Transport, Tianjin research institute for water transport engineeringTianjinChina
| | - Hejun Du
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, Hubei 443100, ChinaChinese Sturgeon Research InstituteYichangChina
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Zhang Z, Li S, Zhang J, Song W, Yang J, Mu J. The complete mitochondrial genome of an endangered minnow Aphyocypris lini (Cypriniformes: Xenocyprididae): genome characterization and phylogenetic consideration. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00811-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Sam KK, Lau NS, Shu-Chien AC, Muchlisin ZA, Nugroho RA. Complete Mitochondrial Genomes of Paedocypris micromegethes and Paedocypris carbunculus Reveal Conserved Gene Order and Phylogenetic Relationships of Miniaturized Cyprinids. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.662501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Wang IC, Lin HD, Liang CM, Huang CC, Wang RD, Yang JQ, Wang WK. Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis. Zookeys 2020; 1005:57-72. [PMID: 33390755 PMCID: PMC7765746 DOI: 10.3897/zookeys.1005.57592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/25/2020] [Indexed: 11/25/2022] Open
Abstract
The cyprinid genus Onychostoma Günther, 1896 consists of 24 valid species distributed in Southeast Asia, including Taiwan, Hainan, mainland China and the Indochina region. In the present study, we determined the complete mitochondrial genome of O. lepturum, which is 16,598 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a typical control region (D-loop). To verify the molecular phylogeny of the subfamily Acrossocheilinae, we provide new insights to better understand the taxonomic status of Acrossocheilus, Onychostoma and Folifer brevifilis. The phylogenetic trees presented three major clades based on the 13 protein-coding genes from 28 Acrossocheilinae species. Clades I and II represent the Onychostoma and Acrossocheilus groups, respectively. Species of Acrossocheilus, Onychostoma and F. brevifilis are included in Clade III, which is considered as an ancestral group. This work provides genomic variation information and improves our understanding of the Acrossocheilinae mitogenome, which will be most valuable in providing new insights for phylogenetic analysis and population genetics research.
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Affiliation(s)
- I-Chen Wang
- Department of Environmental Engineering and Science, Feng Chia University, Taichung 407, TaiwanFeng Chia UniversityTaichungTaiwan
| | - Hung-Du Lin
- Department of Environmental Engineering and Science, Feng Chia University, Taichung 407, TaiwanFeng Chia UniversityTaichungTaiwan
| | - Chih-Ming Liang
- Department of Environmental Engineering and Science, Feng Chia University, Taichung 407, TaiwanFeng Chia UniversityTaichungTaiwan
| | - Chi-Chun Huang
- Taiwan Endemic Species Research Institute, Nantou 552, TaiwanTaiwan Endemic Species Research InstituteNantouTaiwan
| | - Rong-Da Wang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, ChinaShanghai Ocean UniversityShanghaiChina
| | - Jin-Quan Yang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, ChinaShanghai Ocean UniversityShanghaiChina
| | - Wei-Kuang Wang
- Department of Environmental Engineering and Science, Feng Chia University, Taichung 407, TaiwanFeng Chia UniversityTaichungTaiwan
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Complete mitochondrial genome of the freshwater fish Acrossocheilus longipinnis (Teleostei: Cyprinidae): genome characterization and phylogenetic analysis. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00440-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Interspecific Mating Behavior Between Introduced Zacco platypus and Native Opsariichthys evolans in Taiwan. Zool Stud 2020; 59:e6. [PMID: 32760452 DOI: 10.6620/zs.2020.59-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/22/2020] [Indexed: 11/18/2022]
Abstract
Introduced freshwater fishes considerably influence the ecology and populations of native species. Previous research has revealed that introduced Zacco platypus may hybridize with chubs that are sister but distinct genera. However, we have little knowledge of Z. platypus' mate choice or its impact on Taiwanese chubs. Therefore, this study identified the interspecific mating behavior between introduced Z. platypus and native Opsariichthys evolans and evaluated the former's invasive impact on cohabitants. Our observations showed that interspecific mating pairs do occur between Z. platypus male(s) and O. evolans female(s). Fifty-three percent of spawning events were interspecific mating and only 43% were between native O. evolans mating pairs. This study showed that Z. platypus male satellites might prefer to engage with Z. platypus, while O. evolans might engage by chance. However, introduced males of Z. platypus may be unable to recognize conspecific females. Meanwhile, introduced females of Z. platypus also have a mate choice preference for males of Z. platypus. Therefore, Z. platypus male hybridization might significantly reduce the successful mating ratio of O. evolans, leading to a dramatic reduction in native O. evolans offspring in the future.
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Garcia de la serrana D, Wreggelsworth K, Johnston IA. Duplication of a Single myhz1.1 Gene Facilitated the Ability of Goldfish ( Carassius auratus) to Alter Fast Muscle Contractile Properties With Seasonal Temperature Change. Front Physiol 2018; 9:1724. [PMID: 30568597 PMCID: PMC6290348 DOI: 10.3389/fphys.2018.01724] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 11/15/2018] [Indexed: 12/25/2022] Open
Abstract
Seasonal temperature changes markedly effect the swimming performance of some cyprinid fish acutely tested at different temperatures, involving a restructuring of skeletal muscle phenotype including changes in contractile properties and myosin heavy chain expression. We analyzed the transcriptome of fast myotomal muscle from goldfish (Carassius auratus L.) acclimated to either 8 or 25°C for 4 weeks (12 h light: 12 h dark) and identified 10 myosin heavy chains (myh) and 13 myosin light chain (myl) transcripts. Goldfish orthologs were classified based on zebrafish nomenclature as myhz1.1α, myhz1.1β, myhz1.1γ, myha, myhb, embryo_myh1, myh9b, smyh2, symh3, and myh11 (myosin heavy chains) and myl1a, myl1b, myl2, myl9a, myl9b, myl3, myl13, myl6, myl12.1a, myl12.1b, myl12.2a, myl12.2b, and myl10 (myosin light chains). The most abundantly expressed transcripts myhz1.1α, myhz1.1β, myhz1.1γ, myha, myl1a, myl1b, myl2, and myl3) were further investigated in fast skeletal muscle of goldfish acclimated to either 4, 8, 15, or 30°C for 12 weeks (12 h light:12 h dark). Total copy number for the myosin heavy chains showed a distinct optimum at 15°C (P < 0.01). Together myhz1.1α and myhz1.1β comprised 90 to 97% of myhc transcripts below 15°C, but only 62% at 30°C. Whereas myhz1.1α and myhz1.1β were equally abundant at 4 and 8°C, myhz1.1β transcripts were 17 and 12 times higher than myhz1.1α at 15 and 30°C, respectively, (P < 0.01). Myhz1.1γ expression was at least nine-fold higher at 30°C than at cooler temperatures (P < 0.01). In contrast, the expression of myha and myosin light chains showed no consistent pattern with acclimation temperature. A phylogenetic analysis indicated that the previously reported ability of goldfish and common carp to alter contractile properties and myofibrillar ATPase activity with temperature acclimation was related to the duplication of a single myhz1.1 fast muscle myosin heavy chain found in basal cyprinids such as the zebrafish (Danio rerio).
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Affiliation(s)
- Daniel Garcia de la serrana
- School of Biology, Scottish Oceans Institute, University of St. Andrews, St Andrews, United Kingdom
- Serra Húnter Fellow, Cell Biology Physiology and Immunology Department, School of Biology, Universitat de Barcelona, Barcelona, Spain
| | - Kristin Wreggelsworth
- School of Biology, Scottish Oceans Institute, University of St. Andrews, St Andrews, United Kingdom
| | - Ian A. Johnston
- School of Biology, Scottish Oceans Institute, University of St. Andrews, St Andrews, United Kingdom
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