1
|
Qi Z, Shi J, Yu Y, Yin G, Zhou X, Yu Y. Paternal Mitochondrial DNA Leakage in Natural Populations of Large-Scale Loach, Paramisgurnus dabryanus. BIOLOGY 2024; 13:604. [PMID: 39194542 DOI: 10.3390/biology13080604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/02/2024] [Accepted: 08/08/2024] [Indexed: 08/29/2024]
Abstract
Animal mitochondrial DNA is usually considered to comply with strict maternal inheritance, and only one mitochondrial DNA haplotype exists in an individual. However, mitochondrial heteroplasmy, the occurrence of more than one mitochondrial haplotype, has recently been reported in some animals, such as mice, mussels, and birds. This study conducted extensive field surveys to obtain representative samples to investigate the existence of paternal inheritance of mitochondrial DNA (mtDNA) in natural fish populations. Evidence of paternal mitochondrial DNA leakage of P. dabryanus was discovered using high-throughput sequencing and bioinformatics methods. Two distinct mitochondrial haplotypes (16,569 bp for haplotype I and 16,646 bp for haplotype II) were observed, differing by 18.83% in nucleotide sequence. Phylogenetic analysis suggests divergence between these haplotypes and potential interspecific hybridization with M. anguillicaudatus, leading to paternal leakage. In natural populations of P. dabryanus along the Yangtze River, both haplotypes are present, with Type I being dominant (75% copy number). Expression analysis shows that Type I has higher expression levels of ND3 and ND6 genes compared to Type II, suggesting Type I's primary role. This discovery of a species with two mitochondrial types provides a model for studying paternal leakage heterogeneity and insights into mitochondrial genome evolution and inheritance.
Collapse
Affiliation(s)
- Zixin Qi
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaoxu Shi
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Agronomy and Life Science Department, Zhaotong University, Zhaotong 657000, China
| | - Yue Yu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangmei Yin
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoyun Zhou
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongyao Yu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| |
Collapse
|
2
|
Chu D, Zhang H, Li X, Jiang H, Lv J, Shao C, Mu L, Wang X, Wang Y, Deng Z. Molecular characteristics of mitochondrial DNA and phylogenetic analysis of the hybrid loach of Misgurnus anguillicaudatus (female) and M. bipartitus (male). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1566788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Dechang Chu
- School of agriculture and bioengineering, Heze University, Heze, China
| | - Hongmei Zhang
- School of agriculture and bioengineering, Heze University, Heze, China
| | - Xiaodong Li
- School of Chemistry and Bioengineering, Hechi University, Yizhou, China
| | - Huimin Jiang
- School of agriculture and bioengineering, Heze University, Heze, China
| | - Jixin Lv
- School of agriculture and bioengineering, Heze University, Heze, China
| | - Chenchen Shao
- School of agriculture and bioengineering, Heze University, Heze, China
| | - Linying Mu
- School of agriculture and bioengineering, Heze University, Heze, China
| | - Xiaoyu Wang
- School of agriculture and bioengineering, Heze University, Heze, China
| | - Yanan Wang
- School of agriculture and bioengineering, Heze University, Heze, China
| | - Zhenxu Deng
- School of agriculture and bioengineering, Heze University, Heze, China
| |
Collapse
|
3
|
Zhang G, Yang X, Shao C, Wang Y, Wang X, Mu L, Lv J, Wang J. Complete mitochondrial genome of the hybrid loach of Paramisgurnus dabryanus ssp. (female) and Misgurnus bipartitus (male). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1610098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Guosong Zhang
- Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| | - Xi Yang
- E-commerce Office, Heze Information Engineering School, Heze, Shandong, China
| | - Chenchen Shao
- Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| | - Yanan Wang
- Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| | - Xiaoyu Wang
- Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| | - Linying Mu
- Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| | - Jixin Lv
- Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| | - Juan Wang
- Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| |
Collapse
|
4
|
Zhang G, Zhu D, Li X, Liang X, Cai K, Zhang H, Zhang G. Complete mitochondrial genome of natural diploid loaches Misgurnus anguillicaudatus from the Taihu Lake. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:566-567. [PMID: 33474243 PMCID: PMC7799572 DOI: 10.1080/23802359.2018.1467227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Misgurnus anguillicaudatus is a highly valued, aquaculture-relevant food fish in East Asian countries. Because of overfishing and environmental pollution, the number of wild Taihu loach has been sharply decreased in these years. In this study, the complete mitochondrial genome of Taihu loach was obtained by PCR. The genome is 16,646 bp in length, including 2 ribosomal RNA genes. Thirteen proteins-coding genes, 22 transfer RNA genes, and a non-coding control region, the gene composition and order of which was similar to most reported from other vertebrates. Sequence analysis showed that the overall base composition is 29.8% for A, 28.2% for T, 25.7% for C, and 16.3% for G. The phylogenetic tree showed that Misgurnus family got together for one branch, which includes Taihu M. anguillicaudatus, and the other loaches had their own branches. Also the mitochondrial genome sequence of M. anguillicaudatus were aligned by BLAST, compared with Cobitinae the sequence similarity could reach >94%, and the similarity to Misgurnus was >99%.
Collapse
Affiliation(s)
- Guosong Zhang
- School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| | - Daoyu Zhu
- School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| | - Xiaodong Li
- Chemistry and Bioengineering School, Hechi University, Yizhou, Guangxi, China
| | - Xia Liang
- School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| | - Kejun Cai
- Department of Life Science, Huzhou University, Huzhou, Zhejiang, China
| | - Haili Zhang
- School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| | - Guisheng Zhang
- School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| |
Collapse
|
5
|
Zhang G, Sun X, Zhang G, Liang X, Cai K, Zhang H, Zhu D. Molecular characteristics of mitochondrial DNA and phylogenetic analysis of the hybrid loach of Misgurnus anguillicaudatus (female) and Paramisgurnus dabryanus ssp. (male). MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:545-546. [PMID: 33490520 PMCID: PMC7800276 DOI: 10.1080/23802359.2018.1467226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The hybrid loach of Misgurnus anguillicaudatus (female) and Paramisgurnus dabryanus ssp. (male) has the desirable trait of growth performance. Recently, farming scale of this hybrid has been gradually increased in Asia, suggesting a promise of a new variety for loach. In this study, the complete mitochondrial genome of the hybrid loach was obtained by PCR. The genome is 16,646 bp in length, including two ribosomal RNA genes. Thirteen proteins-coding genes, 22 transfer RNA genes, and a non-coding control region, the gene composition and order of were similar to most reported from other vertebrates. Sequence analysis showed that the overall base composition is 29.8% for A, 28.3% for T, 25.6% for C, and 16.3% for G. The phylogenetic tree showed that Misgurnus family got together for one branch, which includes this hybrid loach, and the other loaches had their own branches. Also the mitochondrial genome sequences of the hybrid loach were aligned by BLAST, compared with Cobitidae the sequence similarity could reach >95%, and the similarity to Misgurnus was >99%. The hybrid loach follows the matrilineal inheritance.
Collapse
Affiliation(s)
- Guosong Zhang
- School of Agriculture and Bioengineering, Heze University, Heze, China
| | - Xizhai Sun
- School of Agriculture and Bioengineering, Heze University, Heze, China
| | - Guisheng Zhang
- School of Agriculture and Bioengineering, Heze University, Heze, China
| | - Xia Liang
- School of Agriculture and Bioengineering, Heze University, Heze, China
| | - Kejun Cai
- Department of Life Science, Huzhou University, Huzhou, China
| | - Haili Zhang
- School of Agriculture and Bioengineering, Heze University, Heze, China
| | - Daoyu Zhu
- School of Agriculture and Bioengineering, Heze University, Heze, China
| |
Collapse
|
6
|
Liang X, Zhu D, Li X, Cai K, Zhang H, Zhang G. Complete mitochondrial genome of Taiwanese loach, Paramisgurnus dabryanus ssp. (Cobitinae). Mitochondrial DNA B Resour 2018; 3:340-341. [PMID: 33474162 PMCID: PMC7800862 DOI: 10.1080/23802359.2018.1450665] [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: 02/10/2018] [Accepted: 03/06/2018] [Indexed: 11/04/2022] Open
Abstract
Taiwanese loach was bred in Formosa and then widely cultivated in China. Because of overfishing and environmental pollution, the number of wild Taiwanese loach has been sharply decreased in these years. Also the taxonomic status of Taiwanese loach is still unclear. In this study, the complete mitochondrial genome of Taiwanese loach was obtained by PCR. The genome is 16,569 bp in length, including 2 ribosomal RNA genes, 13 proteins-coding genes, 22 transfer RNA genes, and a non-coding control region, the gene composition and order of which was similar to most reported from other vertebrates. Sequence analysis showed that the overall base composition is 29.5% for A, 27.5% for T, 26.4% for C, and 16.6% for G. The sequence is a slight A + T bias of 57.0%. By analyzing phylogenetic analysis and BLAST, the similarity to Paramisgurnus was >99%, we dare to speculate that the Taiwanese loach cultivated in China was a subspecies of P. dabryanus. Mitogenome information from this study could be a useful basis for conservation and phylogenetics of Taiwanese loach, P. dabryanus ssp.
Collapse
Affiliation(s)
- Xia Liang
- Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| | - Daoyu Zhu
- Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| | - Xiaodong Li
- School of Chemistry and Bioengineering, Hechi University, Yizhou, Guangxi, China
| | - Kejun Cai
- Department of Life Science, Huzhou University, Huzhou, Zhejiang, China
| | - Haili Zhang
- Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| | - Guosong Zhang
- Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| |
Collapse
|
7
|
Liang X, Zhu D, Li X, Cai K, Zhang H, Zhang G. Complete mitochondrial genome of the hybrid loach of Paramisgurnus dabryanus ssp. (female) and Misgurnus anguillicaudatus (male). Mitochondrial DNA B Resour 2018; 3:336-337. [PMID: 33490506 PMCID: PMC7800976 DOI: 10.1080/23802359.2018.1450654] [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: 02/05/2018] [Accepted: 03/06/2018] [Indexed: 10/26/2022] Open
Abstract
The hybrid loach of P. dabryanus ssp. (female) and M. anguillicaudatus (male) has the desirable trait of growth performance. There is no report of the complete genome of this hybrid. In this study, the complete mitochondrial genome of this hybrid loach was obtained, and the genome is 16,569 bp in length, including two ribosomal RNA genes. Thirteen proteins-coding genes, 22 transfer RNA genes, and a non-coding control region, the gene composition and order of which was similar to most reported from other vertebrates. Sequence analysis showed that the overall base composition is 29.5% for A, 27.5% for T, 26.4% for C, and 16.6% for G. The sequence is a slight A + T bias of 57.0%. The phylogenetic tree showed that the hybrid loach to be one of Paramisgurnus, and the relationships of M. anguillicaudatus were closer. Also the mitochondrial genome sequence of loach were aligned by BLAST, compared with Cobitinae the sequence similarity could reach >90%, and the similarity to Paramisgurnus was >99%. Mitogenome information from this study could be a useful basis for conservation and phylogenetics of this hybrid loach.
Collapse
Affiliation(s)
- Xia Liang
- Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| | - Daoyu Zhu
- Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| | - Xiaodong Li
- School of Chemistry and Bioengineering, Hechi University, Yizhou, Guangxi, China
| | - Kejun Cai
- Department of Life Science, Huzhou University, Huzhou, Zhejiang, China
| | - Haili Zhang
- Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| | - Guosong Zhang
- Key Laboratory for Physiology Biochemistry and Application, School of Agriculture and Bioengineering, Heze University, Heze, Shandong, China
| |
Collapse
|
8
|
Zhu M, Liu F. Mitochondrial genome sequence of Paramisgurnus dabryanus from the Yellow River estuary: implication for Cobitidae phylogeny. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3039-40. [PMID: 26162049 DOI: 10.3109/19401736.2015.1063124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Paramisgurnus dabryanus Sauvage (Cobitidae, Cypriniformes) is a native large-scale loach widely distributed in main inland freshwater systems of China. The complete mitochondrial genome sequence of P. dabryanus from the Yellow River (YR) estuary was characterized in the present study. The circular mitogenome is 16 570 bp in size and contains two ribosomal RNA genes, 22 transfer RNA genes, and 13 protein-coding genes. The overall A + T content is 56.64% in the range of other Cobitidae studied. The mitogenome of P. dabryanus YR has an overall nucleotide sequence identity of 96.9% with that from Zhejiang, and 89.2% with that from Hubei. All the Misgurnus and Paramisgurnus species were clustered into two Misgurnus/Paramisgurnus complex clades with high bootstrap values based on the whole mitogenome sequences. The mitochondrial phylogenomic analysis indicates that the relationships in Cobitidae are inconsistent with the current classification system and taxonomic revision is required on the basis of molecular phylogeny and morphology.
Collapse
Affiliation(s)
- Ming Zhu
- a College of Marine Science and Key Laboratory of Marine Biotechnology of Jiangsu Province, Huaihai Institute of Technology , Lianyungang , PR China .,b Lianyungang Long-Yangtze Biotech Company , Lianyungang , PR China , and
| | - Feng Liu
- c Key Laboratory of Experimental Marine Biology , Institute of Oceanology, Chinese Academy of Sciences , Qingdao , PR China
| |
Collapse
|