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Liu K, Xie N, Wang Y, Liu X. Extensive mitogenomic heteroplasmy and its implications in the phylogeny of the fish genus Megalobrama. 3 Biotech 2023; 13:115. [PMID: 36915286 PMCID: PMC10006376 DOI: 10.1007/s13205-023-03523-0] [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: 11/13/2022] [Accepted: 02/13/2023] [Indexed: 03/12/2023] Open
Abstract
Megalobrama is China's most economically valuable fish genera. Four species make up this genus: M. amblycephala (MA), M. terminalis (MT), M. pellegrini (MP), and M. hoffmanni (MH). Many researchers have investigated the genetic relationship of Megalobrama based on mitochondrial DNA (mtDNA) and discovered that the branches of the phylogenetic tree for MT and MP are intertwined. We hypothesized that this occurs because mitogenomic heteroplasmy is overlooked when working with mtDNA, which causes MP and MT positions to intersect in phylogenetic trees. To eliminate the influence of nuclear mitochondrial DNA fragments (NUMTs) before analyzing mitogenomic heteroplasmy, we used PLastZ to identify NUMTs, which were then removed from the samples for the subsequent heteroplasmy analysis. Using the heteroplasmy caller icHET, we discovered 126, 339, 135, and 203 heteroplasmic variants in six MA, MT, MP, and MH samples. We reconstructed the Megalobrama fish genus's phylogenetic tree using the RY coding method and rejecting the third position on codons, which improved the performance of the phylogenetic tree by increasing the ratio of treeness to relative component variability from 100.02 ± 1.76 to 688.59 ± 190.56. Despite this, the RY coding method cannot alter the intersection of MP and MT positions in phylogenetic trees. We hypothesize that gene flow between MT and MP leads to intertwining mtDNA-based phylogenetic trees. In conclusion, our findings on the mitogenomic heteroplasmy of Megalobrama provide new insights into mtDNA-based phylogenetic studies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03523-0.
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Affiliation(s)
- Kai Liu
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Nan Xie
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Yuxi Wang
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Liu
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
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Liu K, Xie N, Ma HJ. Next-generation sequencing reveals the mitogenomic heteroplasmy in the topmouth culter (Culter alburnus Basilewsky, 1855). Mol Biol Rep 2021; 49:943-950. [PMID: 34727288 DOI: 10.1007/s11033-021-06913-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/29/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND The mitogenomic heteroplasmy is the presence of multiple haplotypes in the mitochondria, which could cause genetic diseases and is also associated with many critical biological functions. The topmouth culter (Culter alburnus Basilewsky, 1855) is one of the most important freshwater fish in the family of Cyprinidae in China. At present, there are no reports on the topmouth culter's mtDNA heteroplasmy and the existence of which is not known. METHODS AND RESULTS This study aimed to analyze the mitogenomic heteroplasmy in the topmouth culter by the next-generation sequencing of the fins' total DNA. The results confirmed the existence of the heteroplasmy and indicated the presence of the extensive heteroplasmy in the topmouth culter's mitogenome. There were 38 heteroplasmic variations in the protein-coding genes from the three specimens, with 33 non-synonymous substitutions accounting for 86.84% and five synonymous substitutions accounting for 13.16%. Among them, the ND6 had the most heteroplasmic variations but only one synonymous substitution. After removing the putative nuclear mitochondrial DNA fragments, the ratio of primary haplotype in the three specimens was 43.89%, 74.72%, and 32.76%, respectively. The three specimens contained 21, 7, and 21 haplotypes of the mitogenomes, respectively. Due to the extensive heteroplasmy, we reconstructed the phylogenetic tree of the topmouth culter using the RY-coding method, which improved the performance of the phylogenetic tree to some extent. CONCLUSIONS This study reported the mitogenomic heteroplasmy in the topmouth culter and enhanced the knowledge regarding the mitogenomic heteroplasmy in phylogenetic studies. As the topmouth culter is a commercial species, the mitogenomic heteroplasmy is crucial for the fisheries management of the topmouth culter.
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Affiliation(s)
- Kai Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang, China.
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Heng-Jia Ma
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
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Liu K, Feng XY, Ma HJ, Xie N. Comparative mitochondrial genome analysis of the Mongolian redfin, Chanodichthys mongolicus (Xenocyprididae) from China reveals heteroplasmy. Mitochondrial DNA B Resour 2021; 6:2601-2604. [PMID: 34409154 PMCID: PMC8366642 DOI: 10.1080/23802359.2021.1961627] [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: 11/16/2022] Open
Abstract
This study determined the mitochondrial genome (mitogenome) of Chanodichthys mongolicus from China's Qiantang River and analyzed its phylogenetic history in the Subfamily Cultrinae. Next-generation sequencing was used to obtain the mitogenome of C. mongolicus, GenBank Accession Number MZ032228. The mitochondrial genome length of C. mongolicus from China's Qiantang River is 16,622 bp. The genome contains 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and two central noncoding regions (the control region and the origin of light strand replication). Based on BLAST comparisons, the sequence identity of C. mongolicus MZ032228 from China's Qiantang River was 99.84% to that of Ancherythroculter wangi MG783573 from China's Nei River, 99.75% to C. mongolicus AP009060 from Russia's Black River. The phylogenetic analysis is consistent with BLAST comparisons in confirming that A. wangi MG783573 and C. mongolicus MZ032228 show a high genetic similarity. This study also confirms mitochondrial DNA heteroplasmy in C. mongolicus for the first time and documents 35 heterogeneous loci that were detected.
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Affiliation(s)
- Kai Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Xiao-yu Feng
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Heng-Jia Ma
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
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Mustafa SI, Schwarzacher T, Heslop-Harrison JS. Complete mitogenomes from Kurdistani sheep: abundant centromeric nuclear copies representing diverse ancestors. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:1180-1193. [DOI: 10.1080/24701394.2018.1431226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Sarbast Ihsan Mustafa
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Department of Animal Production, University of Duhok, Duhok, Iraq
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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Cheng X, Xu C, DeGiorgio M. Fast and robust detection of ancestral selective sweeps. Mol Ecol 2017; 26:6871-6891. [DOI: 10.1111/mec.14416] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/16/2017] [Accepted: 10/23/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Xiaoheng Cheng
- Huck Institutes of Life Sciences; Pennsylvania State University; University Park PA USA
- Department of Biology; Pennsylvania State University; University Park PA USA
| | - Cheng Xu
- Huck Institutes of Life Sciences; Pennsylvania State University; University Park PA USA
| | - Michael DeGiorgio
- Department of Biology; Pennsylvania State University; University Park PA USA
- Department of Statistics; Pennsylvania State University; University Park PA USA
- Institute for CyberScience; Pennsylvania State University; University Park PA USA
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He X, Chen X, Zhang W, Pu Y, Song S, Han J, Dong K, Zhao Q, Guan W, Ma Y, Jiang L. High occurrence of length heteroplasmy in domestic Bactrian camel (Camelus bactrianus). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:851-854. [PMID: 27937010 DOI: 10.1080/24701394.2016.1197219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Heteroplasmy is the presence of more than one mitochondrial DNA (mtDNA) variant within a cell, tissue, or individual. In this study, sequence variation was investigated in the control region (CR) of mitochondrial DNA (mtDNA) from 135 individuals belonging to five primary domestic Bactrian camel breeds in China and Mongolia. Due to variation of the repeat unit G(T/C)(AC)n, length heteroplasmy was detected within each camel by direct sequencing and fragment analysis. A high occurrence of mtDNA heteroplasmy, up to 100 percentages was observed in five camel populations. Our study provides the first evidence of extensive length heteroplasmy in Bactrian camels.
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Affiliation(s)
- Xiaohong He
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Xiaofei Chen
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Wenbin Zhang
- c Bactrian Camels Institute of Alxa League , Inner Mongolia Autonomous Region , China
| | - Yabin Pu
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Shen Song
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Jianlin Han
- b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,d International Livestock Research Institute (ILRI) , Nairobi , Kenya
| | - Kunzhe Dong
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Qianjun Zhao
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Weijun Guan
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Yuehui Ma
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Lin Jiang
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
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E GX, Zhao YJ, Huang YF. Sheep mitochondrial heteroplasmy arises from tandem motifs and unspecific PCR amplification. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:91-95. [PMID: 27841052 DOI: 10.1080/24701394.2016.1242582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The mitochondrial DNA control region (D-loop) is a widely used molecular marker in evolutionary and phylogeographic research. However, the occurrence of heteroplasmy of the D-loop region within individuals has rarely been investigated. In this study, a total of 85 Chinese sheep were used to amplify a partial D-loop region, and 15 heteroplasmic animals (17.64%) were identified. A comparative analysis of the PCR amplification and cloning of the D-loop sequences from the heteroplasmic samples revealed most of the sequencing profile from the heteroplasmic regions started at the beginning of a 75-bp random repeat motif. In addition, a total of 22 nonsyngeneic sequences with a D-loop were found in 61 of the clones obtained from the 4 random heteroplasmic and 3 homozygote animals, and their genomic locations were compared for homology. In summary, the D-Loop sequencing profiles appear to be heteroplasmic and could arise from tandem repeat motifs and unspecific replication during PCR amplification; however, they are not likely due to the presence of multiple mitochondrial genomes within an individual.
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Affiliation(s)
- Guang-Xin E
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Yong-Ju Zhao
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Yong-Fu Huang
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
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Guangxin E, Yong-Ju Z, Ri-Su N, Yue-Hui M, Jia-Hua Z, Li-Peng C, Xiao-Yu Q, Zhong-Quan Z, Ya-Wang S, Xin W, Yong-Fu H. Meta-analysis evidence of maternal lineages in Chinese Tibetan sheep using mtDNA D-loop panel. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:579-583. [PMID: 27159711 DOI: 10.3109/24701394.2016.1143469] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Tibetan sheep is an indigenous breed living in the entire Tibetan Plateau, and its origin and phylogenic relationships are still uncertain and controversial. In this study, we analyzed partial mtDNA D-loop sequences of 156 Chinese Tibetan sheep individuals from 12 distributed geographic ecotype populations. Phylogenetic analysis indicated that three maternal lineages (haplogroups A, B and C) were found in this breed and that Ovis vignei and Ovis ammon have possibly contributed to the original Tibetan sheep. The absence of haplogroups D and E in Tibetan sheep suggests that this breed did not originate in the Middle East, China.
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Affiliation(s)
- E Guangxin
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Zhao Yong-Ju
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Na Ri-Su
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Ma Yue-Hui
- b Institute of Animal Science , Chinese Academy of Agricultural Sciences (CAAS) , Beijing , China
| | - Zhang Jia-Hua
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Chen Li-Peng
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Qiu Xiao-Yu
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Zhao Zhong-Quan
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Sun Ya-Wang
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Wu Xin
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Huang Yong-Fu
- a College of Animal Science and Technology Chongqing Key Laboratory of Forage & Herbivore Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
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