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Jain K, Panigrahi M, Nayak SS, Rajawat D, Sharma A, Sahoo SP, Bhushan B, Dutt T. The evolution of contemporary livestock species: Insights from mitochondrial genome. Gene 2024; 927:148728. [PMID: 38944163 DOI: 10.1016/j.gene.2024.148728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/05/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
The domestication of animals marks a pivotal moment in human history, profoundly influencing our demographic and cultural progress. This process has led to significant genetic, behavioral, and physical changes in livestock species compared to their wild ancestors. Understanding the evolutionary history and genetic diversity of livestock species is crucial, and mitochondrial DNA (mtDNA) has emerged as a robust marker for investigating molecular diversity in animals. Its highly conserved gene content across animal species, minimal duplications, absence of introns, and short intergenic regions make mtDNA analysis ideal for such studies. Mitochondrial DNA analysis has uncovered distinct cattle domestication events dating back to 8000 years BC in Southwestern Asia. The sequencing of water buffalo mtDNA in 2004 provided important insights into their domestication history. Caprine mtDNA analysis identified three haplogroups, indicating varied maternal origins. Sheep, domesticated 12,000 years ago, exhibit diverse mtDNA lineages, suggesting multiple domestication events. Ovine mtDNA studies revealed clades A, B, C, and a fourth lineage, group D. The origins of domestic pigs were traced to separate European and Asian events followed by interbreeding. In camels, mtDNA elucidated the phylogeographic structure and genetic differentiation between wild and domesticated species. Horses, domesticated around 3500 BC, show significant mtDNA variability, highlighting their diverse origins. Yaks exhibit unique adaptations for high-altitude environments, with mtDNA analysis providing insights into their adaptation. Chicken mtDNA studies supported a monophyletic origin from Southeast Asia's red jungle fowl, with evidence of multiple origins. This review explores livestock evolution and diversity through mtDNA studies, focusing on cattle, water buffalo, goat, sheep, pig, camel, horse, yak and chicken. It highlights mtDNA's significance in unraveling maternal lineages, genetic diversity, and domestication histories, concluding with insights into its potential application in improving livestock production and reproduction dynamics.
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Affiliation(s)
- Karan Jain
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | | | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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2
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Xu W, Tai J, He K, Xu T, Zhang G, Xu B, Liu H. Complete Mitochondrial Genomes of Nannostomus Pencilfish: Genome Characterization and Phylogenetic Analysis. Animals (Basel) 2024; 14:1598. [PMID: 38891645 PMCID: PMC11171051 DOI: 10.3390/ani14111598] [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: 04/28/2024] [Revised: 05/20/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Although the pencilfish is a globally popular economic fish in the aquarium market, its taxonomic classification could be further refined. In order to understand the taxonomy of species of the genus Nannostomus (Characiformes, Lebiasinidae) and their phylogenetic position within the order Characiformes, in this study, we characterized mitochondrial genomes (mitogenomes) from four Nannostomus species for the first time. The four mitogenomes exhibited the typical circular structure, with overall sizes varying from 16,661 bp to 16,690 bp. They contained 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and 1 control region (CR). Nucleotide composition analysis suggested that the mitochondrial sequences were biased toward A and T. Bayesian inference and maximum likelihood analyses based on PCGs support the family Lebiasinidae classification, described using four Nannostomus species, clustering together with Lebiasina multimaculata from the same family. The results of this study support the current taxonomic classification of the family Lebiasinidae. Phylogenetic analysis also suggested that gene rearrangement would not significantly impact the phylogenetic relationships within the order Characiformes. These results might provide new data regarding the phylogeny and classification of the order Characiformes, thus providing a theoretical basis for the economic development of aquarium fish markets.
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Affiliation(s)
- Wei Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (W.X.); (J.T.); (T.X.); (G.Z.); (B.X.)
| | - Jingzhe Tai
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (W.X.); (J.T.); (T.X.); (G.Z.); (B.X.)
| | - Ke He
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China;
| | - Tangjun Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (W.X.); (J.T.); (T.X.); (G.Z.); (B.X.)
| | - Gaoji Zhang
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (W.X.); (J.T.); (T.X.); (G.Z.); (B.X.)
| | - Boyu Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (W.X.); (J.T.); (T.X.); (G.Z.); (B.X.)
| | - Hongyi Liu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (W.X.); (J.T.); (T.X.); (G.Z.); (B.X.)
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Gao T, Shi Y, Xiao J. Comparative Mitogenomics Reveals Cryptic Species in Sillago ingenuua McKay, 1985 (Perciformes: Sillaginidae). Genes (Basel) 2023; 14:2043. [PMID: 38002986 PMCID: PMC10671150 DOI: 10.3390/genes14112043] [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: 10/04/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
It is unreliable to identify marine fishes only by external morphological features. Species misidentification brings great challenges to fishery research, resource monitoring and ecomanagement. Sillago ingenuua is an important part of commercial marine fishes, and in which, the morphological differences between different groups are not obvious. Here, we compared different geographical groups of S. ingenuua which were collected from Xiamen, Dongshan, Keelung, Songkhla and Java. The results showed that all samples of S. ingenuua were similar in external morphological characteristics and the shape of the swim bladder, but there were two distinctive lineages which were flagged as cryptic species based on DNA barcoding. The comparative mitogenomic results showed that S. ingenuua A and S. ingenuua B were identical in structural organization and gene arrangement. Their nucleotide composition and codon usage were also similar. A phylogenetic analysis was performed based on 13 concatenated PCGs from eight Sillago species. The results showed that the genetic distance between S. ingenuua A and S. ingenuua B was large (D = 0.069), and this genetic distance was large enough to reveal that S. ingenuua A and S. ingenuua B might be different species.
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Affiliation(s)
- Tianxiang Gao
- School of Fishery, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Yijia Shi
- Fisheries College, Jimei University, Xiamen 361021, China;
| | - Jiaguang Xiao
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
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4
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Wang J, Xu W, Liu Y, Bai Y, Liu H. Comparative mitochondrial genomics and phylogenetics for species of the snakehead genus Channa Scopoli, 1777 (Perciformes: Channidae). Gene X 2023; 857:147186. [PMID: 36627090 DOI: 10.1016/j.gene.2023.147186] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/25/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023] Open
Abstract
The family Channidae, members of which are commonly known as snakehead fish, includes 53 Channa species and three Parachanna species. In this study, we characterized mitochondrial genomes (mitogenomes) of five Channa species (C. andrao, C. bleheri, C. ornatipinnis, C. pulchra, and C. stewartii) for the first time. We compared the mitogenomes with the mitogenomes of 11 other Channidae fish. The newly sequenced mitogenomes were 16,714 - 16,895 bp in length and contained 37 typical genes [13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs) and 22 transfer RNA genes (tRNAs)]. Positive AT-skews and negative GC-skews were found in the mitogenomes of Channidae. Most PCGs started with the conventional start codon, ATN; however, the sequence of the stop codon was variable. There was no essential difference in relative synonymous codon usage (RSCU) among the Channidae mitogenomes. The fastest-evolving gene atp8 and slowest-evolving gene cox1 were identified using Ka/Ks and pairwise relative genetic distance (p-distance). The displacement loop (D-loop) regions showed great variability, which affected the size of Channa mitogenomes. One origin of replication on the light strand (OL) region was found between trnN and trnC in the mitogenomes of Channidae. Phylogenetic analysis revealed three new sister pairs (C. andrao + C. bleheri, C. ornatipinnis + C. pulchra, and C. stewartii + C. gachua). Phylogenetic relationships established between the five Channa species based on mitogenomes were also supported by their morphological characteristics and geographical distribution. The novel information we obtained about these mitogenomes will contribute to elucidating the complex relationships among Channa species.
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Affiliation(s)
- Jiachen Wang
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Wei Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Yuyao Liu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Yawen Bai
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Hongyi Liu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
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Low Expression of Mitofusin 1 Gene Leads to Mitochondrial Dysfunction and Embryonic Genome Activation Failure in Ovine-Bovine Inter-Species Cloned Embryos. Int J Mol Sci 2022; 23:ijms231710145. [PMID: 36077543 PMCID: PMC9456037 DOI: 10.3390/ijms231710145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/27/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
Inter-species somatic cell nuclear transfer (iSCNT) is significant in the study of biological problems such as embryonic genome activation and the mitochondrial function of embryos. Here, we used iSCNT as a model to determine whether abnormal embryo genome activation was caused by mitochondrial dysfunction. First, we found the ovine-bovine iSCNT embryos were developmentally blocked at the 8-cell stage. The reactive oxygen species level, mitochondrial membrane potential, and ATP level in ovine-bovine cloned embryos were significantly different from both bovine-bovine and IVF 8-cell stage embryos. RNA sequencing and q-PCR analysis revealed that mitochondrial transport, mitochondrial translational initiation, mitochondrial large ribosomal subunit, and mitochondrial outer membrane genes were abnormally expressed in the ovine-bovine embryos, and the mitochondrial outer membrane and mitochondrial ribosome large subunit genes, mitochondrial fusion gene 1, and ATPase Na+/K+ transporting subunit beta 3 gene were expressed at lower levels in the ovine-bovine cloned embryos. Furthermore, we found that overexpression and knockdown of Mfn1 significantly affected mitochondrial fusion and subsequent biological functions such as production of ATP, mitochondrial membrane potential, reactive oxygen species and gene expressions in cloned embryos. These findings enhance our understanding of the mechanism by which the Mfn1 gene regulates embryonic development and embryonic genome activation events.
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Székvári K, Szabolcsi Z, Kutasy B, Hegedűs G, Virág E. New complete mitogenome datasets and their characterization of the European catfish ( Silurus glanis). Data Brief 2021; 38:107418. [PMID: 34632016 PMCID: PMC8487008 DOI: 10.1016/j.dib.2021.107418] [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: 05/11/2021] [Revised: 08/23/2021] [Accepted: 09/20/2021] [Indexed: 10/31/2022] Open
Abstract
We present new complete mitogenome sequences of Silurus glanis (S. glanis) from 4 samples such as male and female individuals from two countries (Hungary, Czech Republic). The complete mitochondria were determined from genome sequencing by using Illumina MiSeq platform resulting in long, 300 bp. paired-end reads. De novo assembly was performed resulting in one nod (scaffold) covering the total mitochondria in each sample. The mitochondrial genomes were circular, double-stranded molecules of 16,524 bp in length and consisted of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region. These sequences were deposited in the NCBI GeneBank under the accession numbers (MW796040, MW796041, MW796042, MW796043) and compared with the only available S. glanis mitochondrial genome (NC_014261.1) sequenced by unidentified technology and showed 99% similarity. We found in seq1 82, in seq2 82, seq3 83, seq4 82 nucleotide alterations involving 10 protein-coding genes and meaning 29 amino acid substitutions as well.
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Affiliation(s)
- Kinga Székvári
- Festetics Doctoral School, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary.,Department of Plant Science and Biotechnology, Szent István University, i.e. the Predecessor of the Festetics Bioinnovation Group, Keszthely, Hungary
| | - Zoltán Szabolcsi
- Department of Animal Sciences, Georgikon Faculty, Szent István University, Keszthely 8360, Hungary.,Research Centre for Natural Sciences, Institute of Enzimology, Budapest, Hungary
| | - Barbara Kutasy
- Department of Plant Science and Biotechnology, Szent István University, i.e. the Predecessor of the Festetics Bioinnovation Group, Keszthely, Hungary.,Department of Plant Physiology and Plant Ecology, Hungarian University of Agriculture and Life Sciences Georgikon Campus Keszthely, Keszthely, Hungary
| | | | - Eszter Virág
- Department of Plant Science and Biotechnology, Szent István University, i.e. the Predecessor of the Festetics Bioinnovation Group, Keszthely, Hungary.,EduCoMat Ltd., Keszthely, Hungary.,Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Hungary
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7
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Chen YX, Sun CH, Li YK, Fei YL, Xue XM, Hou SL, Zhou YW, Jiang J, Guo HT. Complete mitogenome of Treron sphenurus (Aves, Columbiformes): the first representative from the genus Treron, genomic comparisons and phylogenetic analysis of Columbidae. Anim Biotechnol 2021; 33:1003-1013. [PMID: 33439093 DOI: 10.1080/10495398.2020.1862135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The wedge-tailed green pigeon (Treron sphenurus) has a protective value in the evolution of the family Columbidae. In this study, the complete mitogenome of T. sphenurus from Baise City, China, which represents the first sequenced species of the genus Treron in Tribe Treronini, is reported. This was accomplished using PCR-based methods and a primer-walking sequencing strategy with genus-specific primers. The mitogenome was found to be 18,919 bp in length comprising 37 genes, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region. In terms of structure and composition, many similarities were found between the T. sphenurus and Hemiphaga novaeseelandiae (New Zealand pigeon) mitogenomes. This was further supported by phylogenetic analysis showing that T. sphenurus has a close evolutionary relationship with H. novaeseelandiae. The complete mitogenome of T. sphenurus reported here is expected to provide valuable molecular information for further studies on the phylogeny of the genus Treron and for analyses of the taxonomic status of the family Columbidae.
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Affiliation(s)
- Yun-Xia Chen
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
| | - Cheng-He Sun
- Department of Ecology, Jinan University, Guangzhou, China
| | - Yao-Kai Li
- Department of Ecology, Jinan University, Guangzhou, China
| | - Yi-Ling Fei
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
| | - Xiao-Ming Xue
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
| | - Sen-Lin Hou
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
| | - Yong-Wu Zhou
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
| | - Jing Jiang
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
| | - Hai-Tao Guo
- Nanjing Forest Police College, Nanjing, China.,Key Laboratory of Wildlife Evidence Technology State Forest and Grassland Administration, Nanjing, China
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8
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Kibria MM, Islam N, Billah M, Shawrob KSM, Rumi MH, Siddiki AZ. Complete mitochondrial genome sequence of Catla catla (Hamilton, 1822) from the Halda river of Bangladesh. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3215-3217. [PMID: 33458116 PMCID: PMC7782268 DOI: 10.1080/23802359.2020.1809542] [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: 10/29/2022]
Abstract
Catla (Catla catla) is one of the fastest-growing major carp found in South Asia as well as Bangladesh. Catla catla is the second most popular indigenous carp species in the freshwater aquaculture industry of Bangladesh due to its relatively good taste and high market price. In this study, we disclosed the complete mitochondrial genome sequence of Bangladeshi Catla fish from Halda river located in Chittagong. The circular mitogenome of Catla catla is 16,597 bp in length and nucleotide composition is AT-based (72%), contains 37 genes including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a D-loop (control region).
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Affiliation(s)
- M M Kibria
- Department of Zoology, University of Chittagong, Chittagong, Bangladesh.,Halda River Research Laboratory, University of Chittagong, Chittagong,Bangladesh
| | - N Islam
- Department of Zoology, University of Chittagong, Chittagong, Bangladesh.,Halda River Research Laboratory, University of Chittagong, Chittagong,Bangladesh
| | - M Billah
- Genomics Research Group, Chittagong Veterinary and Animal Sciences University (CVASU), Chittagong, Bangladesh.,College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - K S M Shawrob
- Genomics Research Group, Chittagong Veterinary and Animal Sciences University (CVASU), Chittagong, Bangladesh.,Department of Biotechnology, Inland Norway University of Applied Sciences, Elverum, Norway
| | - M H Rumi
- Genomics Research Group, Chittagong Veterinary and Animal Sciences University (CVASU), Chittagong, Bangladesh
| | - Amam Zonaed Siddiki
- Genomics Research Group, Chittagong Veterinary and Animal Sciences University (CVASU), Chittagong, Bangladesh
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9
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Sun CH, Liu HY, Lu CH. Five new mitogenomes of Phylloscopus (Passeriformes, Phylloscopidae): Sequence, structure, and phylogenetic analyses. Int J Biol Macromol 2020; 146:638-647. [DOI: 10.1016/j.ijbiomac.2019.12.253] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 11/09/2019] [Accepted: 12/28/2019] [Indexed: 11/30/2022]
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10
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Sim HK, Jeon JH, Yu JN, Jin HJ, Hong YK, Jin DH. The complete mitochondrial genome of Liparis ochotensis and a preliminary phylogenetic analysis. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:631-632. [PMID: 33366678 PMCID: PMC7748685 DOI: 10.1080/23802359.2019.1711217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Liparis ochotensis is a snailfish commonly confused with similar fish species because of unclear morphological characteristics. Moreover, molecular genetic studies have not been conducted for snailfish in Korea. Here, we report the complete mitogenome sequence of L. ochotensis, obtained via long PCR using universal primers for the fish mitogenome. The L. ochotensis mitogenome is 17,522 bp long, comprising 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. A neighbour-joining phylogenetic tree based on CO1 sequences depicted a close relationship with Liparis gibbus. The complete mitogenome is a valuable resource to classify and conserve L. ochotensis.
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Affiliation(s)
- Han-Kyeol Sim
- Department of Marine Molecular Bioscience, Gangneung-Wonju National University, Gangneung, Korea
| | - Ju-Hyung Jeon
- Department of Marine Molecular Bioscience, Gangneung-Wonju National University, Gangneung, Korea
| | - Jeong-Nam Yu
- Biodiversity Conservation and Change Division, Freshwater Biodiversity Research Bureau, Nakdonggang National Institute of Biological Resource (NNIBR), Sangju-Si, Korea
| | - Hyung-Joo Jin
- Department of Marine Molecular Bioscience, Gangneung-Wonju National University, Gangneung, Korea
| | - Yong-Ki Hong
- Department of Biotechnology, Pukyong National University, Namgu, Korea
| | - Deuk-Hee Jin
- Department of Marine Molecular Bioscience, Gangneung-Wonju National University, Gangneung, Korea
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11
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Zhang Z, Cheng Q, Ge Y. The complete mitochondrial genome of Rhynchocypris oxycephalus (Teleostei: Cyprinidae) and its phylogenetic implications. Ecol Evol 2019; 9:7819-7837. [PMID: 31346443 PMCID: PMC6635945 DOI: 10.1002/ece3.5369] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 01/18/2023] Open
Abstract
Rhynchocypris oxycephalus (Teleostei: Cyprinidae) is a typical small cold water fish, which is distributed widely and mainly inhabits in East Asia. Here, we sequenced and determined the complete mitochondrial genome of R. oxycephalus and studied its phylogenetic implication. R. oxycephalus mitogenome is 16,609 bp in length (GenBank accession no.: MH885043), and it contains 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and two noncoding regions (the control region and the putative origin of light-strand replication). 12 PCGs started with ATG, while COI used GTG as the start codon. The secondary structure of tRNA-Ser (AGN) lacks the dihydrouracil (DHU) arm. The control region is 943bp in length, with a termination-associated sequence, six conserved sequence blocks (CSB-1, CSB-2, CSB-3, CSB-D, CSB-E, CSB-F), and a repetitive sequence. Phylogenetic analysis was performed with maximum likelihood and Bayesian methods based on the concatenated nucleotide sequence of 13 PCGs and the complete sequence without control region, and the result revealed that the relationship between R. oxycephalus and R. percnurus is closest, while the relationship with R. kumgangensis is farthest. The genus Rhynchocypris is revealed as a polyphyletic group, and R. kumgangensis had distant relationship with other Rhynchocypris species. In addition, COI and ND2 genes are considered as the fittest DNA barcoding gene in genus Rhynchocypris. This work provides additional molecular information for studying R. oxycephalus conservation genetics and evolutionary relationships.
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Affiliation(s)
- Zhichao Zhang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research InstituteChinese Academy of Fishery SciencesShanghaiChina
- Wuxi Fisheries CollegeNanjing Agricultural UniversityWuxiChina
| | - Qiqun Cheng
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research InstituteChinese Academy of Fishery SciencesShanghaiChina
| | - Yushuang Ge
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research InstituteChinese Academy of Fishery SciencesShanghaiChina
- College of Marine SciencesShanghai Ocean UniversityShanghaiChina
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12
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Kalamujić Stroil B, Mušović A, Škrijelj R, Dorić S, Đug S, Pojskić N. Molecular-genetic diversity of the endangered Dalmatian barbelgudgeon, Aulopyge huegelii from the Buško Blato reservoir. Genetica 2019; 147:269-280. [PMID: 31154556 DOI: 10.1007/s10709-019-00069-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 05/28/2019] [Indexed: 10/26/2022]
Abstract
A number of studies investigating different aspects of IUCN endangered species, Aulopyge huegelii Heckel, 1843 (Dalmatian barbelgudgeon) biology have been conducted, but data on molecular genetics are lacking. The goal of this survey was to assess the genetic structure of the A. huegelii population from the Buško Blato reservoir, based on four mitochondrial DNA regions and five microsatellite loci. Excluding cytochrome b, more than one haplotype has been detected in all sequenced mtDNA regions, most of which had not been previously described. A total of seven composite haplotypes were detected. Nucleotide diversity was relatively low for all coding genes but slightly higher for the control region. Microsatellite analysis revealed a relatively high value of major allele frequency, lower values of observed and expected heterozygosity, as well as a moderately reduced number of alleles and genotypes in three of the five observed loci. Although with a clear trend of decline, the level of genetic diversity is still sufficient to ensure the subsistence of the population if the stressors are removed. Otherwise, the loss of heterozygosity will continue, possibly to the point of a complete eradication of the Dalmatian barbelgudgeon from the Buško Blato reservoir.
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Affiliation(s)
- Belma Kalamujić Stroil
- University of Sarajevo-Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8 Kampus, 71000, Sarajevo, Bosnia and Herzegovina.
| | - Aldijana Mušović
- Faculty of Science, University of Sarajevo, Zmaja od Bosne 33-35, 71000, Sarajevo, Bosnia and Herzegovina
| | - Rifat Škrijelj
- Faculty of Science, University of Sarajevo, Zmaja od Bosne 33-35, 71000, Sarajevo, Bosnia and Herzegovina
| | - Semir Dorić
- University of Sarajevo-Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8 Kampus, 71000, Sarajevo, Bosnia and Herzegovina
| | - Samir Đug
- Faculty of Science, University of Sarajevo, Zmaja od Bosne 33-35, 71000, Sarajevo, Bosnia and Herzegovina
| | - Naris Pojskić
- University of Sarajevo-Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8 Kampus, 71000, Sarajevo, Bosnia and Herzegovina
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13
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Ma DM, Fan JJ, Zhu HP, Huang ZH. The complete mitochondrial genome of Cyprinus Carpio Var. Guilin rice flower carp and its phylogeny in Cyprinidae. MITOCHONDRIAL DNA PART B 2019. [DOI: 10.1080/23802359.2019.1591177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Dong-Mei Ma
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture/Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jia-Jia Fan
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture/Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Hua-Ping Zhu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture/Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Zhang-Han Huang
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture/Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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14
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Liu X, Ye X, Liang H, Zhou L, Zhou X, Zou G, Hu G. Mitochondrial genome sequences reveal the evolutionary relationship among different common carp varieties (Cyprinus carpino L.). Meta Gene 2019. [DOI: 10.1016/j.mgene.2018.11.001] [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
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15
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Xue SQ, Li CT, Han Y, Shi LY. Complete mitochondrial genome of Cyprinus carpio triploid. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1586460] [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)
- Shu Qun Xue
- Heilongjiang River Fishery Research Institute, Chinese Academy of Fishery Science, Harbin, China
| | - Chi Tao Li
- Heilongjiang River Fishery Research Institute, Chinese Academy of Fishery Science, Harbin, China
| | - Ying Han
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Lian Yu Shi
- Heilongjiang River Fishery Research Institute, Chinese Academy of Fishery Science, Harbin, China
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16
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Ye X, Lv Y, Wei L, Huang J, Wen Y, Zhang G, Zhang S, Yang Z, Liu K. The complete mitochondrial genome of Jinbian carp Cyprinus carpio (Cypriniformes: Cyprinidae). Mitochondrial DNA B Resour 2018; 3:1096-1097. [PMID: 33474430 PMCID: PMC7800910 DOI: 10.1080/23802359.2018.1495126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 06/18/2018] [Indexed: 11/15/2022] Open
Abstract
Jinbian carp (Cyprinus carpio) is an endemic species in China. The complete mitochondrial genome of Jinbian carp is determined to be 16,581 bp in length and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Its structural organization and gene order are equivalent to other common carp strains. The phylogenetic analyses will contribute to further insights of the taxonomy and phylogeny in Cyprinidae family.
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Affiliation(s)
- Xiangchen Ye
- Aquatic Species Introduction and Breeding Center of Guangxi, Nanning, China
| | - Yejian Lv
- Aquatic Species Introduction and Breeding Center of Guangxi, Nanning, China
| | - Lingjing Wei
- Aquatic Species Introduction and Breeding Center of Guangxi, Nanning, China
| | - Jie Huang
- Extension Station of Fisheries Technology of Liuzhou, Liuzhou, China
| | - Yanhong Wen
- Extension Station of Fisheries Technology of Liuzhou, Liuzhou, China
| | - Guijiao Zhang
- Fisheries Technology Extension Station of Rongshui Miaozu Autonomous County, Liuzhou, China
| | - Sheng Zhang
- Aquatic Species Introduction and Breeding Center of Guangxi, Nanning, China
| | - Zhushan Yang
- Fisheries Technology Extension Station of Rongshui Miaozu Autonomous County, Liuzhou, China
| | - Kang Liu
- Aquatic Species Introduction and Breeding Center of Guangxi, Nanning, China
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17
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Khan MF, Khattak MNK, He D, Rehman AU, Chen Y. Mitochondrial genome sequence and gene organization of Kunar Snow trout ( Schizothorax labiatus ) with phylogenetic consideration. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Alves MJ, Coelho MM, Collares‐Pereira MJ, Dowling TE. MATERNAL ANCESTRY OF THE
RUTILUS ALBURNOIDES
COMPLEX (TELEOSTEI, CYPRINIDAE) AS DETERMINED BY ANALYSIS OF CYTOCHROME
b
SEQUENCES. Evolution 2017; 51:1584-1592. [DOI: 10.1111/j.1558-5646.1997.tb01481.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/1997] [Accepted: 05/30/1997] [Indexed: 11/27/2022]
Affiliation(s)
- M. J. Alves
- Departamento de Zoologia e Antropologia Faculdade de Ciências, Universidade de Lisboa Campo Grande C2 ‐ Piso 3, 1700 Lisboa Portugal
| | - M. M. Coelho
- Departamento de Zoologia e Antropologia Faculdade de Ciências, Universidade de Lisboa Campo Grande C2 ‐ Piso 3, 1700 Lisboa Portugal
| | - M. J. Collares‐Pereira
- Departamento de Zoologia e Antropologia Faculdade de Ciências, Universidade de Lisboa Campo Grande C2 ‐ Piso 3, 1700 Lisboa Portugal
| | - T. E. Dowling
- Department of Biology Arizona State University Tempe Arizona 85287‐1501
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Kappas I, Vittas S, Pantzartzi CN, Drosopoulou E, Scouras ZG. A Time-Calibrated Mitogenome Phylogeny of Catfish (Teleostei: Siluriformes). PLoS One 2016; 11:e0166988. [PMID: 27907107 PMCID: PMC5132296 DOI: 10.1371/journal.pone.0166988] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/07/2016] [Indexed: 11/18/2022] Open
Abstract
A very significant part of the world's freshwater ichthyofauna is represented by ancient, exceptionally diverse and cosmopolitan ray-finned teleosts of the order Siluriformes. Over the years, catfish have been established as an exemplary model for probing historical biogeography at various scales. Yet, several tantalizing gaps still exist in their phylogenetic history, timeline and mode of diversification. Here, we re-examine the phylogeny of catfish by assembling and analyzing almost all publicly available mitogenome data. We constructed an ingroup matrix of 62 full-length mitogenome sequences from 20 catfish families together with four cypriniform outgroups, spanning 15,557 positions in total. Partitioned maximum likelihood analyses and Bayesian relaxed clock dating using fossil age constraints provide some useful and novel insights into the evolutionary history of this group. Loricarioidei are recovered as the first siluriform group to diversify, rendering Neotropics the cradle of the order. The next deepest clade is the South American Diplomystoidei placed as a sister group to all the remaining Siluroidei. The two multifamilial clades of "Big Asia" and "Big Africa" are also recovered, albeit nodal support for the latter is poor. Within "Big Asia", Bagridae are clearly polyphyletic. Other interfamilial relationships, including Clariidae + Heteropneustidae, Doradidae + Auchenipteridae and Ictaluridae + Cranoglanididae are robustly resolved. Our chronogram shows that siluriforms have a Pangaean origin, at least as far back as the Early Cretaceous. The inferred timeline of the basal splits corroborates the "Out-of-South America" hypothesis and accords well with the fossil record. The divergence of Siluroidei most likely postdated the final separation of Africa and South America. An appealing case of phylogenetic affinity elaborated by biogeographic dispersal is exemplified by the Early Paleogene split between the Southeast Asian Cranoglanididae and Ictaluridae, with the latter radiating into North America's freshwater realm by Eocene. The end of Cretaceous probably concludes the major bout of diversification at the family level while with the dawn of the Cenozoic a prolific radiation is evident at the generic level.
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Affiliation(s)
- Ilias Kappas
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Spiros Vittas
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Chrysoula N. Pantzartzi
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Elena Drosopoulou
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Zacharias G. Scouras
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- * E-mail:
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20
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Satoh TP, Miya M, Mabuchi K, Nishida M. Structure and variation of the mitochondrial genome of fishes. BMC Genomics 2016; 17:719. [PMID: 27604148 PMCID: PMC5015259 DOI: 10.1186/s12864-016-3054-y] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/27/2016] [Indexed: 11/10/2022] Open
Abstract
Background The mitochondrial (mt) genome has been used as an effective tool for phylogenetic and population genetic analyses in vertebrates. However, the structure and variability of the vertebrate mt genome are not well understood. A potential strategy for improving our understanding is to conduct a comprehensive comparative study of large mt genome data. The aim of this study was to characterize the structure and variability of the fish mt genome through comparative analysis of large datasets. Results An analysis of the secondary structure of proteins for 250 fish species (248 ray-finned and 2 cartilaginous fishes) illustrated that cytochrome c oxidase subunits (COI, COII, and COIII) and a cytochrome bc1 complex subunit (Cyt b) had substantial amino acid conservation. Among the four proteins, COI was the most conserved, as more than half of all amino acid sites were invariable among the 250 species. Our models identified 43 and 58 stems within 12S rRNA and 16S rRNA, respectively, with larger numbers than proposed previously for vertebrates. The models also identified 149 and 319 invariable sites in 12S rRNA and 16S rRNA, respectively, in all fishes. In particular, the present result verified that a region corresponding to the peptidyl transferase center in prokaryotic 23S rRNA, which is homologous to mt 16S rRNA, is also conserved in fish mt 16S rRNA. Concerning the gene order, we found 35 variations (in 32 families) that deviated from the common gene order in vertebrates. These gene rearrangements were mostly observed in the area spanning the ND5 gene to the control region as well as two tRNA gene cluster regions (IQM and WANCY regions). Although many of such gene rearrangements were unique to a specific taxon, some were shared polyphyletically between distantly related species. Conclusions Through a large-scale comparative analysis of 250 fish species mt genomes, we elucidated various structural aspects of the fish mt genome and the encoded genes. The present results will be important for understanding functions of the mt genome and developing programs for nucleotide sequence analysis. This study demonstrated the significance of extensive comparisons for understanding the structure of the mt genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3054-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Takashi P Satoh
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8654, Japan. .,Collection Center, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba City, Ibaraki, 305-0005, Japan. .,Present address: Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, 459 Shirahama, Nishimuro, Wakayama, 649-2211, Japan.
| | - Masaki Miya
- Natural History Museum and Institute, 955-2 Aoba-cho, Chuo-ku, Chiba City, Chiba, 260-8682, Japan
| | - Kohji Mabuchi
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8654, Japan
| | - Mutsumi Nishida
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8654, Japan. .,Present address: University of the Ryukyus, 1 Senbaru, Nishihara-cho, Okinawa, 908-0213, Japan.
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21
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Shan B, Song N, Han Z, Wang J, Gao T, Yokogawa K. Complete mitochondrial genomes of three sea basses Lateolabrax (Perciformes, Lateolabracidae) species: Genome description and phylogenetic considerations. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Zhang WZ, Xiong XM, Zhang XJ, Wan SM, Guan NN, Nie CH, Zhao BW, Hsiao CD, Wang WM, Gao ZX. Mitochondrial Genome Variation after Hybridization and Differences in the First and Second Generation Hybrids of Bream Fishes. PLoS One 2016; 11:e0158915. [PMID: 27391325 PMCID: PMC4938612 DOI: 10.1371/journal.pone.0158915] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 06/23/2016] [Indexed: 11/28/2022] Open
Abstract
Hybridization plays an important role in fish breeding. Bream fishes contribute a lot to aquaculture in China due to their economically valuable characteristics and the present study included five bream species, Megalobrama amblycephala, Megalobrama skolkovii, Megalobrama pellegrini, Megalobrama terminalis and Parabramis pekinensis. As maternal inheritance of mitochondrial genome (mitogenome) involves species specific regulation, we aimed to investigate in which way the inheritance of mitogenome is affected by hybridization in these fish species. With complete mitogenomes of 7 hybrid groups of bream species being firstly reported in the present study, a comparative analysis of 17 mitogenomes was conducted, including representatives of these 5 bream species, 6 first generation hybrids and 6 second generation hybrids. The results showed that these 17 mitogenomes shared the same gene arrangement, and had similar gene size and base composition. According to the phylogenetic analyses, all mitogenomes of the hybrids were consistent with a maternal inheritance. However, a certain number of variable sites were detected in all F1 hybrid groups compared to their female parents, especially in the group of M. terminalis (♀) × M. amblycephala (♂) (MT×MA), with a total of 86 variable sites between MT×MA and its female parent. Among the mitogenomes genes, the protein-coding gene nd5 displayed the highest variability. The number of variation sites was found to be related to phylogenetic relationship of the parents: the closer they are, the lower amount of variation sites their hybrids have. The second generation hybrids showed less mitogenome variation than that of first generation hybrids. The non-synonymous and synonymous substitution rates (dN/dS) were calculated between all the hybrids with their own female parents and the results indicated that most PCGs were under negative selection.
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Affiliation(s)
- Wei-Zhuo Zhang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, People’s Republic of China
| | - Xue-Mei Xiong
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, People’s Republic of China
| | - Xiu-Jie Zhang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, People’s Republic of China
| | - Shi-Ming Wan
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, People’s Republic of China
| | - Ning-Nan Guan
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, People’s Republic of China
| | - Chun-Hong Nie
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, People’s Republic of China
| | - Bo-Wen Zhao
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, People’s Republic of China
| | - Chung-Der Hsiao
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan
| | - Wei-Min Wang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
| | - Ze-Xia Gao
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, People’s Republic of China
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Huang Q, Ji X, Wang K. The complete mitochondrial genome of dwarf danio, Danio nigrofasciatus. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:2854-5. [DOI: 10.3109/19401736.2015.1053126] [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]
Affiliation(s)
- Quan Huang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Xu Ji
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Kai Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
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Alwan N, Esmaeili HR, Krupp F. Molecular Phylogeny and Zoogeography of the Capoeta damascina Species Complex (Pisces: Teleostei: Cyprinidae). PLoS One 2016; 11:e0156434. [PMID: 27309854 PMCID: PMC4911093 DOI: 10.1371/journal.pone.0156434] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 05/14/2016] [Indexed: 11/19/2022] Open
Abstract
Capoeta damascina was earlier considered by many authors as one of the most common freshwater fish species found throughout the Levant, Mesopotamia, Turkey, and Iran. However, owing to a high variation in morphological characters among and within its various populations, 17 nominal species were described, several of which were regarded as valid by subsequent revising authors. Capoeta damascina proved to be a complex of closely related species, which had been poorly studied. The current study aims at defining C. damascina and the C. damascina species complex. It investigates phylogenetic relationships among the various members of the C. damascina complex, based on mitochondrial and nuclear DNA sequences. Phylogenetic relationships were projected against paleogeographical events to interpret the geographic distribution of the taxa under consideration in relation to the area’s geological history. Samples were obtained from throughout the geographic range and were subjected to genetic analyses, using two molecular markers targeting the mitochondrial cytochrome oxidase I (n = 103) and the two adjacent divergence regions (D1-D2) of the nuclear 28S rRNA genes (n = 65). Six closely related species were recognized within the C. damascina complex, constituting two main lineages: A western lineage represented by C. caelestis, C. damascina, and C. umbla and an eastern lineage represented by C. buhsei, C. coadi, and C. saadii. The results indicate that speciation of these taxa is rather a recent event. Dispersal occurred during the Pleistocene, resulting in present-day distribution patterns. A coherent picture of the phylogenetic relationships and evolutionary history of the C. damascina species complex is drawn, explaining the current patterns of distribution as a result of paleogeographic events and ecological adaptations.
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Affiliation(s)
- Nisreen Alwan
- Senckenberg Research Institute and Museum of Nature, Frankfurt 60325, Germany
- Modern University for Business and Science, School of Health Sciences, P.O. Box 113–7501, Beirut, Lebanon
- * E-mail: ;
| | - Hamid-Reza Esmaeili
- Shiraz University, Department of Biology, College of Sciences, Shiraz 71454, Iran
| | - Friedhelm Krupp
- Senckenberg Research Institute and Museum of Nature, Frankfurt 60325, Germany
- Qatar Natural History Museum, Qatar Museums Authority, P.O. Box 2777, Doha, Qatar
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25
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Yu JN, Noh EY, Bae CH, Lim CE, Kim S. Complete mitogenome sequences of a Korean spine loach, Iksookimia koreensis(Kim, 1975). Mitochondrial DNA A DNA Mapp Seq Anal 2016. [DOI: 10.3109/19401736.2014.982559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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26
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Lo Presti R, Lisa C, Di Stasio L. Molecular genetics in aquaculture. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2009.299] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Yu JN, Kim BJ, Kim C, Yeo JH, Kim S. The complete mitochondrial genome of the black star fat minnow (Rhynchocypris semotilus), an endemic and endangered fish of Korea. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:114-115. [PMID: 26709416 DOI: 10.3109/19401736.2015.1111348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Black star fat minnow (Rhynchocypris semotilus) is an endemic and critically endangered freshwater fish in Korea. Its genome was 16 605 bp long and consisted of 13 protein-coding genes (PCG), two rRNA genes, 22 tRNA genes, and a control region. The gene order and the composition of R. semotilus were similar to that of most other vertebrates. Four overlapping regions in ATP8/ATP6, ATP6/COX3, ND4L/ND4, and ND5/ND6, among the 13 PCGs were found. The control region was located between the tRNA-Pro and tRNA-Phe genes and was determined to be 935 bp in length with the 3' end containing a 12 TA-repeat sequence. Phylogenetic analysis suggested that R. semotilus is most closely related to R. oxycephalus.
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Affiliation(s)
- Jeong-Nam Yu
- a National Institute of Biological Resources, Environmental Research Complex , Incheon , Korea
| | - Byung-Jik Kim
- a National Institute of Biological Resources, Environmental Research Complex , Incheon , Korea
| | - Changmu Kim
- a National Institute of Biological Resources, Environmental Research Complex , Incheon , Korea
| | - Joo-Hong Yeo
- a National Institute of Biological Resources, Environmental Research Complex , Incheon , Korea
| | - Soonok Kim
- a National Institute of Biological Resources, Environmental Research Complex , Incheon , Korea
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Abstract
Mitochondrial DNA has the characteristic of quick evolution, matrilineal inheritance, and simple molecular structure, and it serves as the most used marker for molecular study. As an important role of genomics, studying it can help understand the origins, history, and adaptation of domestication. Because of its wide spread popularity, chicken is one of the important domestic animals, which provides humans with a stable source of protein, including both meat and eggs. This article reviews recent studies of chicken mitochondrial DNA. Mitochondrial D-loop and mitochondrial genomics pinpoint the geographic origins of the domestic chicken which was multiple origins; moreover, the mitochondria gene mutation has an association with high-altitude adaptation and the mitochondria-associated diseases' study in poultry is not performed.
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Affiliation(s)
- Dan Lan
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Ya'an, Sichuan , China
| | - Yaodong Hu
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Ya'an, Sichuan , China
| | - Qing Zhu
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Ya'an, Sichuan , China
| | - Yiping Liu
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Ya'an, Sichuan , China
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Yu JN, Kwak M. The complete mitochondrial genome of Brachymystax lenok tsinlingensis (Salmoninae, Salmonidae) and its intraspecific variation. Gene 2015; 573:246-53. [PMID: 26188159 DOI: 10.1016/j.gene.2015.07.049] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/02/2015] [Accepted: 07/14/2015] [Indexed: 11/19/2022]
Abstract
The Manchurian trout, Brachymystax lenok tsinlingensis, is endangered in Korea, where the southern range limit for this cold-freshwater fish occurs. In this study, the complete mitochondrial genome of Korean B. lenok tsinlingensis was sequenced and its genetic characteristics were identified. The mitogenome of B. lenok tsinlingensis comprises 16,748 base pairs containing 37 genes (13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes) and one major non-coding region (control region), making it similar to the majority of vertebrate mitogenomes. Interestingly, at the base of the stem region of OL in B. lenok tsinlingensis, the conserved motif is replaced by a 5'-ACCGG-3' motif instead of the 5'-GCCGG-3'. We also identified an 81-base-pair tandem-repeat motif in the control region, the length of which is reduced by one nucleotide compared to those in B. lenok and Hucho species. The number of repeat motifs differed between Korean and Chinese B. lenok tsinlingensis, with two and three reiterations, respectively. The control region of B. lenok and its relatives will be used as a genetic marker in evolution/genetic studies and as a PCR-based marker for rapid identification of their lineages.
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Affiliation(s)
- Jeong-Nam Yu
- National Institute of Biological Resources, Environmental Research Complex, Incheon 404-708, Republic of Korea
| | - Myounghai Kwak
- National Institute of Biological Resources, Environmental Research Complex, Incheon 404-708, Republic of Korea.
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Xia A, Zhong L, Chen X, Bian W, Zhang T, Shi Y. Complete mitochondrial genome of spined sleeper Eleotris oxycephala (Perciformes, Eleotridae) and phylogenetic consideration. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.07.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Yu JN, Noh EY, Bae CH, Lim CE, Kim S. Complete mitogenome sequences of a Korean spine loach, Iksookimia koreensis (Kim, 1975). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2065-6. [PMID: 26305162 DOI: 10.3109/19401736.2014.982558] [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: 11/13/2022]
Abstract
Here, we present the complete mitogenome sequences from a Korean spine loach (Iksookimia koreensis Kim 1975), an endemic species of Korea. The total length of mitogenome was 16 563 bp, consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region (D-loop). Except for ND6 and eight tRNA genes, all of the other mitochondrial genes were encoded on the heavy strand. The control region harbored conserved sequence blocks (CSB-D, E, F, CSB-1, CBS-2 and CBS-3) and TA-nucleotide microsatellite repeats in its 3' end. Our complete mitogenomes will be valuable resources for phylogeny, genetics and conservation of the genus Iksookimia.
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Affiliation(s)
- Jeong-Nam Yu
- a National Institute of Biological Resources, Environmental Research Complex , Incheon , Korea
| | - Eun-Young Noh
- a National Institute of Biological Resources, Environmental Research Complex , Incheon , Korea
| | - Chang-Hwan Bae
- a National Institute of Biological Resources, Environmental Research Complex , Incheon , Korea
| | - Chae-Eun Lim
- a National Institute of Biological Resources, Environmental Research Complex , Incheon , Korea
| | - Soonok Kim
- a National Institute of Biological Resources, Environmental Research Complex , Incheon , Korea
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Yu JN, Jun J, Lim CE, Kim S. Sequence and organization of the complete mitogenome of a Siberian stone loach, Barbatula toni (Dybowsky, 1869) (Cypriniformes: Balitoridae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:1798-9. [PMID: 26305807 DOI: 10.3109/19401736.2014.963818] [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: 11/13/2022]
Abstract
In this study, we determined the complete mitogenome sequence of Siberian stone loach, Barbatula toni (Dybowsky, 1869). The total length of mitogenome is 16 623 bp, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region (D-loop). The genome organization and gene order were identical to that of the typical vertebrates. The control region harbors conserved sequence blocks (CSB-D, E, F, CSB-1, CBS-2 and CBS-3) and TA-nucleotide microsatellite repeats in its 3' end. The complete mitogenome may provide important molecular data for further phylogenetic analyses for higher taxa of teleost fishes, especially for the fishes in order Cypriniformes.
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Affiliation(s)
- Jeong-Nam Yu
- a National Institute of Biological Resources, Environmental Research Complex , Incheon , Korea
| | - Jumin Jun
- a National Institute of Biological Resources, Environmental Research Complex , Incheon , Korea
| | - Chae Eun Lim
- a National Institute of Biological Resources, Environmental Research Complex , Incheon , Korea
| | - Soonok Kim
- a National Institute of Biological Resources, Environmental Research Complex , Incheon , Korea
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Tran TN, Niu DH, Nguyen HD, Xie SM, Li JL. Populations genetic structure of the razor clam Sinonovacula constricta from China, Korea and Vietnam. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.07.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Yue X, Shi J, Zou Y, Wang B. The complete mitochondrial genome sequence of Schizothorax lissolabiatus (Cypriniformes: Cyprinidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2450-2. [PMID: 25976234 DOI: 10.3109/19401736.2015.1033693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Schizothorax lissolabiatus is a widely distributed fish species in Lancang River, Yuanjiang River, Pearl River, Nujiang River in China. The complete mitochondrial genome sequence of S. lissolabiatus from Yuanjiang River (the upper Red River) has been sequenced, which is 16,583 bp in length and contains 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and 2 main non-coding regions: origin of light-strand replication and control region. Except for eight tRNA and ND6 genes, most of the genes are encoded on the heavy strand. The length of mitochondrial genome, the order, composition and anticodons of all genes are exactly similar to that of S. dolichonema. The phylogenetic tree suggested S. prenanti, S. dolichonema and S. lissolabiatus may have closer affinities than other fish of the genus Schizothorax.
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Affiliation(s)
- Xingjian Yue
- a Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, School of Life Sciences, Neijiang Normal University , Neijiang , P. R. China
| | - Jinrong Shi
- a Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, School of Life Sciences, Neijiang Normal University , Neijiang , P. R. China
| | - Yuanchao Zou
- a Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, School of Life Sciences, Neijiang Normal University , Neijiang , P. R. China
| | - Bin Wang
- a Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, School of Life Sciences, Neijiang Normal University , Neijiang , P. R. China
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Yu Y, Feng Y, Wang H, Yang Y, Duan Y, Zhou Z, Zhang M. Complete mitochondrial genome of a Wild Amur Moose (Alces alces cameloides). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4061-4062. [PMID: 25629496 DOI: 10.3109/19401736.2014.1003843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, the complete mitochondrial genome (mt DNA) of Amur Moose (Alces alces cameloides) was sequenced, using muscle tissue obtained from a male Amur moose. The total length of the mitochondrial genome is 16,305 bp. The genome structure of Amur moose is similar to other moose and it contains 12S rRNA gene, 16S rRNA gene, 22 tRNA genes, 13 protein-coding genes, and 1 control region.
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Affiliation(s)
- Yanze Yu
- a College of Wildlife Resources, Northeast Forestry University , Harbin , PR China and.,b Heilongjiang Academy of Forestry , Harbin , PR China
| | - Yuan Feng
- a College of Wildlife Resources, Northeast Forestry University , Harbin , PR China and
| | - Hongcheng Wang
- a College of Wildlife Resources, Northeast Forestry University , Harbin , PR China and
| | - Yong Yang
- a College of Wildlife Resources, Northeast Forestry University , Harbin , PR China and
| | - Yubao Duan
- a College of Wildlife Resources, Northeast Forestry University , Harbin , PR China and
| | - Zhengyan Zhou
- a College of Wildlife Resources, Northeast Forestry University , Harbin , PR China and
| | - Minghai Zhang
- a College of Wildlife Resources, Northeast Forestry University , Harbin , PR China and
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36
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Hinsinger DD, Debruyne R, Thomas M, Denys GPJ, Mennesson M, Utage J, Dettai A. Fishing for barcodes in the Torrent: from COI to complete mitogenomes on NGS platforms. ACTA ACUST UNITED AC 2015. [DOI: 10.1515/dna-2015-0019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe adoption of Next-Generation Sequencing (NGS) by the field of DNA barcoding of Metazoa has been hindered by the fit between the classical COI barcode and the Sanger-based sequencing method. Here we describe a framework for the sequencing and multiplexing of mitogenomes on NGS platforms that implements (I) a universal long-range PCR-based amplification technique, (II) a two-level multiplexing approach (i.e. divergence-based and specific tag indexing), and (III) a dedicated demultiplexing and assembling script from an Ion Torrent sequencing platform. We provide a case study of mitogenomes obtained for two vouchered individuals of daces Leuciscus burdigalensis and L. oxyrrhis and show that this workflow enables to recover over 100 mitogenomes per sequencing chip on a PGM sequencer, bringing the individual cost down below 7,50€ per mitogenome (as of current 2015 sequencing costs). The use of several kilobases for identification purposes, as involved in the improved DNA-barcode we propose, stress the need for data reliability, especially through metadata. Based on both scientific and economic considerations, this framework presents a relevant approach for multiplexing samples, adaptable on any desktop NGS platform. It enables to extend from the prevalent barcoding approach by shifting from the single COI to complete mitogenome sequencing
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Eichmiller JJ, Bajer PG, Sorensen PW. The relationship between the distribution of common carp and their environmental DNA in a small lake. PLoS One 2014; 9:e112611. [PMID: 25383965 PMCID: PMC4226586 DOI: 10.1371/journal.pone.0112611] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 10/19/2014] [Indexed: 01/18/2023] Open
Abstract
Although environmental DNA (eDNA) has been used to infer the presence of rare aquatic species, many facets of this technique remain unresolved. In particular, the relationship between eDNA and fish distribution is not known. We examined the relationship between the distribution of fish and their eDNA (detection rate and concentration) in a lake. A quantitative PCR (qPCR) assay for a region within the cytochrome b gene of the common carp (Cyprinus carpio or ‘carp’), an ubiquitous invasive fish, was developed and used to measure eDNA in Lake Staring (MN, USA), in which both the density of carp and their distribution have been closely monitored for several years. Surface water, sub-surface water, and sediment were sampled from 22 locations in the lake, including areas frequently used by carp. In water, areas of high carp use had a higher rate of detection and concentration of eDNA, but there was no effect of fish use on sediment eDNA. The detection rate and concentration of eDNA in surface and sub-surface water were not significantly different (p≥0.5), indicating that eDNA did not accumulate in surface water. The detection rate followed the trend: high-use water > low-use water > sediment. The concentration of eDNA in sediment samples that were above the limit of detection were several orders of magnitude greater than water on a per mass basis, but a poor limit of detection led to low detection rates. The patchy distribution of eDNA in the water of our study lake suggests that the mechanisms that remove eDNA from the water column, such as decay and sedimentation, are rapid. Taken together, these results indicate that effective eDNA sampling methods should be informed by fish distribution, as eDNA concentration was shown to vary dramatically between samples taken less than 100 m apart.
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Affiliation(s)
- Jessica J Eichmiller
- Department of Fisheries, Wildlife, and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, Twin Cities, St. Paul, Minnesota, United States of America
| | - Przemyslaw G Bajer
- Department of Fisheries, Wildlife, and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, Twin Cities, St. Paul, Minnesota, United States of America
| | - Peter W Sorensen
- Department of Fisheries, Wildlife, and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, Twin Cities, St. Paul, Minnesota, United States of America
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38
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Norfatimah M, Teh L, Salleh M, Mat Isa M, SitiAzizah M. Complete mitochondrial genome of Malaysian Mahseer (Tor tambroides). Gene 2014; 548:263-9. [DOI: 10.1016/j.gene.2014.07.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 07/08/2014] [Accepted: 07/14/2014] [Indexed: 10/25/2022]
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Gotesman M, Abd-Elfattah A, Kattlun J, Soliman H, El-Matbouli M. Investigating the interactions of Cyprinid herpesvirus-3 with host proteins in goldfish Carassius auratus. JOURNAL OF FISH DISEASES 2014; 37:835-41. [PMID: 23998394 DOI: 10.1111/jfd.12172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/23/2013] [Accepted: 07/26/2013] [Indexed: 05/18/2023]
Affiliation(s)
- M Gotesman
- Clinical Division of Fish Medicine, University of Veterinary Medicine, Vienna, Austria
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40
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Dai L, Guo B, Chu Z, Wang Y, Wang X, Huang T. Complete mitochondrial genome of Paramisgurnus dabryanus. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1257-9. [PMID: 25090380 DOI: 10.3109/19401736.2014.945545] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, the complete mitochondrial genome of Paramisgurnus dabryanus was obtained by PCR base on 18 pairs of primers. Among the 18 primers, the 14 primers were from the previously published universal primers for Cyprinus carpio L. mitogenome amplification. The remaining 4 primers were designed on the basis of related species mtDNA sequences. The genome is 16,570 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 of Paramisgurnus dabryanus is T 27.3%, C 26.9%, A 28.5%, and G 17.4%. The sequence is a slight A + T bias of 55.8%, which is similar to other fishes. Mitochondrial genome is widely used in phylogenetic analysis, evolutionary genomics, species identification and related research of fish.
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Affiliation(s)
- Luyi Dai
- a Zhejiang Ocean University , Dinghai District , Zhoushan City , P. R. China
| | - Baoying Guo
- a Zhejiang Ocean University , Dinghai District , Zhoushan City , P. R. China
| | - Zhangjie Chu
- a Zhejiang Ocean University , Dinghai District , Zhoushan City , P. R. China
| | - Yong Wang
- a Zhejiang Ocean University , Dinghai District , Zhoushan City , P. R. China
| | - Xiaojun Wang
- a Zhejiang Ocean University , Dinghai District , Zhoushan City , P. R. China
| | - Tao Huang
- a Zhejiang Ocean University , Dinghai District , Zhoushan City , P. R. China
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41
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Hu GF, Liu XJ, Li Z, Liang HW, Hu SN, Zou GW. Complete mitochondrial genome of Xingguo red carp (Cyprinus carpio var. singuonensis) and purse red carp (Cyprinus carpio var. wuyuanensis). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:244-5. [PMID: 24521498 DOI: 10.3109/19401736.2014.883607] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genomes of Xingguo red carp (Cyprinus carpio var. singuonensis) and purse red carp (Cyprinus carpio var. wuyuanensis) were sequenced. Comparison of these two mitochondrial genomes revealed that the mtDNAs of these two common carp varieties were remarkably similar in genome length, gene order and content, and AT content. However, size variation between these two mitochondrial genomes presented here showed 39 site differences in overall length. About 2 site differences were located in rRNAs, 3 in tRNAs, 3 in the control region, 31 in protein-coding genes. Thirty-one variable bases in the protein-coding regions between the two varieties mitochondrial sequences led to three variable amino acids, which were mainly located in the protein ND5 and ND4.
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Affiliation(s)
- Guang-Fu Hu
- a Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences , Wuhan , China and.,b College of Fisheries, Huazhong Agricultural University , Wuhan , China
| | - Xiang-Jiang Liu
- b College of Fisheries, Huazhong Agricultural University , Wuhan , China
| | - Zhong Li
- a Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences , Wuhan , China and
| | - Hong-Wei Liang
- a Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences , Wuhan , China and
| | - Shao-Na Hu
- a Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences , Wuhan , China and
| | - Gui-Wei Zou
- a Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences , Wuhan , China and
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42
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Hu GF, Liu XJ, Zou GW, Li Z, Liang HW, Hu SN. Complete mitochondrial genome of Yangtze River wild common carp (Cyprinus carpio haematopterus) and Russian scattered scale mirror carp (Cyprinus carpio carpio). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:263-4. [PMID: 24521500 DOI: 10.3109/19401736.2014.883617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We sequenced the complete mitogenomes of (Cyprinus carpio haematopterus) and Russian scattered scale mirror carp (Cyprinus carpio carpio). Comparison of these two mitogenomes revealed that the mitogenomes of these two common carp strains were remarkably similar in genome length, gene order and content, and AT content. There were only 55 bp variations in 16,581 nucleotides. About 1 bp variation was located in rRNAs, 2 bp in tRNAs, 9 bp in the control region and 43 bp in protein-coding genes. Furthermore, forty-three variable nucleotides in the protein-coding genes of the two strains led to four variable amino acids, which were located in the ND2, ATPase 6, ND5 and ND6 genes, respectively.
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Affiliation(s)
- Guang Fu Hu
- a Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences , Wuhan , China and.,b College of Fisheries, Huazhong Agricultural University , Wuhan , China
| | - Xiang Jiang Liu
- b College of Fisheries, Huazhong Agricultural University , Wuhan , China
| | - Gui Wei Zou
- a Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences , Wuhan , China and
| | - Zhong Li
- a Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences , Wuhan , China and
| | - Hong-Wei Liang
- a Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences , Wuhan , China and
| | - Shao-Na Hu
- a Yangtze River Fisheries Research Institute, The Chinese Academy of Fisheries Sciences , Wuhan , China and
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Lin M, Zou J, Wang C. Complete mitochondrial genomes of domesticated and wild common carp (Cyprinus carpio L.). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:50-1. [PMID: 24438270 DOI: 10.3109/19401736.2013.869690] [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: 11/13/2022]
Abstract
Glass red common carp (Cyprinus carpio var. wananensis) were occasionally found among wild common carp (Cyprinus carpio) 50 years ago. In this paper, we determined the complete sequences of Glass red common carp and wild common carp mitogenomes. Both mitogenomes exhibited the same length of 16,581 bp, order in 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. The sequence similarity between them reached 99.62% and 100% in 21 tRNA genes (excluding tRNA(Ser)) and 2 protein-coding genes (ATP8 and ND4L), respectively. The two mitogenomes will be useful in elucidating the evolutional relationship of the common carp.
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Affiliation(s)
- Mingxue Lin
- a Key Laboratory of Freshwater Fishery Germplasm Resources , Ministry of Agriculture, Shanghai Ocean University , Shanghai , P.R. China and
| | - Jixing Zou
- b College of Animal Sciences, South China Agricultural University , Guangzhou , P.R. China
| | - Chenghui Wang
- a Key Laboratory of Freshwater Fishery Germplasm Resources , Ministry of Agriculture, Shanghai Ocean University , Shanghai , P.R. China and
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The carp-goldfish nucleocytoplasmic hybrid has mitochondria from the carp as the nuclear donor species. Gene 2013; 536:265-71. [PMID: 24365595 DOI: 10.1016/j.gene.2013.12.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 12/10/2013] [Accepted: 12/11/2013] [Indexed: 11/21/2022]
Abstract
It is widely accepted that mitochondria and its DNA (mtDNA) exhibit strict maternal inheritance, with sperm contributing no or non-detectable mitochondria to the next generation. In fish, nuclear transfer (NT) through the combination of a donor nucleus and an enucleated oocyte can produce fertile nucleocytoplasmic hybrids (NCHs) even between different genera and subfamilies. One of the best studied fish NCHs is CyCa produced by transplanting the nuclei plus cytoplasm from the common carp (Cyprinus carpio var. wuyuanensis) into the oocytes of the wild goldfish (Carassius auratus), which has been propagated by self-mating for three generations. These NCH fish thus provide a unique model to study the origin of mitochondria. Here we report the complete mtDNA sequence of the CyCa hybrid and its parental species carp and goldfish as nuclear donor and cytoplasm host, respectively. Interestingly, the mtDNA of NCH fish CyCa is 99.69% identical to the nuclear donor species carp, and 89.25% identical to the oocyte host species goldfish. Furthermore, an amino acid sequence comparison of 13 mitochondrial proteins reveals that CyCa is 99.68% identical to the carp and 87.68% identical to the goldfish. On an mtDNA-based phylogenetic tree, CyCa is clustered with the carp but separated from the goldfish. A real-time PCR analysis revealed the presence of carp mtDNA but the absence of goldfish mtDNA. These results demonstrate--for the first time to our knowledge--that the mtDNA of a NCH such as CyCa fish may originate from its nuclear donor rather than its oocyte host.
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Xiao Y, Song N, Li J, Xiao Z, Gao T. Significant population genetic structure detected in the small yellow croaker Larimichthys polyactis inferred from mitochondrial control region. MITOCHONDRIAL DNA 2013; 26:409-19. [PMID: 24228686 DOI: 10.3109/19401736.2013.843076] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The population genetic structure of the small yellow croaker (Larimichthys polyactis) between China and Korea was further estimated by broad-scale sampling locations (Gulf of Bohai, Yellow Sea including Korea). One hundred and seventeen individuals from eight localities from coastal waters of China and Korea were analyzed based on mtDNA control region sequences (5' mtDNA CR). A total of 97 polymorphic sites were checked, which defined 136 haplotypes. A pattern with high levels of haplotype diversity (h=0.994 ± 0.002) and nucleotide diversity (л=0.020 ± 0.010) was detected in the examined range, and the genetic diversity of Korea populations was higher than that of China populations. Population genetic structure analyses (MDS, AMOVA, Fst, Barrier) showed that significant genetic differentiation existed between China and Korea populations. The migration analysis indicated asymmetry migration also existed among populations, which was consistent with the result of population genetic structure. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimateic and physiographic evidence, we inferred that the genetic make-up of extant populations of L. polyactis was shaped by Pleistocene environmental impacts on the historical demography of this species. Coalescent analyses (Neutrality tests, Mismatch distribution analysis, Bayesian skyline analyses) showed that the species along coastline of China and Korea has experienced population expansions originated in its most recent history at about 32-196 kya and 166-662 kya before present, respectively.
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Affiliation(s)
- Yongshuang Xiao
- Institute of Evolution & Marine Biodiversity, Ocean University of China , Qingdao , China and
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46
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Assessing the genetic diversity and population structure of Culter alburnus in China based on mitochondrial 16S rRNA and COI gene sequences. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.04.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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47
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Yu JN, Kim BJ, Kim S, Oh K, Lim CE. Complete mitochondrial genome of the rare hypogean gobiid, Luciogobius pallidus, from Korea. MITOCHONDRIAL DNA 2013; 26:118-20. [PMID: 23815332 DOI: 10.3109/19401736.2013.809447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The rare hypogean gobiid, Luciogobius pallidus, inhabits mainly in groundwater, spring, or upper rocky tidal regions in Korea and Japan. In this paper, the complete mitochondrial genome sequence of L. pallidus was firstly determined. The gene composition and order of L. pallidus were similar to most of the other fishes. The total length of the rare hypogean gobiid mitochondrial genome is 16,480 bp, including 13 protein-coding genes, 22 tRNA, 2 rRNA and 1 control region (CR). All genes were encoded on the heavy (H)-strand, with the exceptions of ND6 and eight tRNA genes, as found in other vertebrates. The CR (833 bp in length) is located between the tRNA-Pro and tRNA-Phe genes and contains three central conserved sequence blocks (CSB-D, CSB-E and CSB-F), three conserved sequence blocks (CSB-1, CBS-2 and CBS-3), and its 3' end embeds a poly-T-nucleotide sequence.
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Affiliation(s)
- Jeong-Nam Yu
- National Institute of Biological Resources, Environmental Research Complex , Incheon , Korea
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48
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Bej D, Sahoo L, Das SP, Swain S, Jayasankar P, Das P. Complete mitochondrial genome sequence of Cirrhinus mrigala (Hamilton, 1822). MITOCHONDRIAL DNA 2013; 24:91-93. [PMID: 22994312 DOI: 10.3109/19401736.2012.722998] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The complete mitochondrial genome of Cirrhinus mrigala was determined using the polymerase chain reaction. The mitogenome (16,594 bp) has the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one control region. The overall base composition on the heavy strand was as follows: A: 32.0%, G: 15.5%, C: 28.0%, T: 24.55% and the A+T content: 56.5%. The control region contains a dinucleotide repeat motif, (TA)14, a termination-associated sequence and three conserved sequence blocks. These mitogenome sequence data would play an important role in population genetics and the molecular taxonomy of cultivable cyprinids in India.
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Affiliation(s)
- Dillip Bej
- Fish Genetics and Biotechnology Division, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha 751002, India
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Wang SY, Luo J, Murphy RW, Wu SF, Zhu CL, Gao Y, Zhang YP. Origin of Chinese goldfish and sequential loss of genetic diversity accompanies new breeds. PLoS One 2013; 8:e59571. [PMID: 23527220 PMCID: PMC3602300 DOI: 10.1371/journal.pone.0059571] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 02/19/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Goldfish, Carassius auratus, have experienced strong anthropogenic selection during their evolutionary history, generating a tremendous extent of morphological variation relative to that in native Carassius. To locate the geographic origin of goldfish, we analyzed nucleotide sequences from part of the control region (CR) and the entire cytochrome b (Cytb) mitochondrial DNA genes for 234 goldfish and a large series of native specimens. Four important morphological characteristics used in goldfish taxonomy-body shape, dorsal fin, eye shape, and tailfin-were selected for hypothesis-testing to identify those that better correspond to evolutionary history. PRINCIPAL FINDING Haplotypes of goldfish rooted in two sublineages (C5 and C6), which contained the haplotypes of native C. a. auratus from southern China. Values of F(ST) and N(m) revealed a close relationship between goldfish and native C. a. auratus from the lower Yangtze River. An extraordinary, stepwise loss of genetic diversity was detected from native fish to goldfish and from Grass-goldfish relative to other breeds. Significantly negative results for the tests of Tajima's D and Fu and Li's D* and F* were identified in goldfish, including the Grass breed. The results identified eye-shape as being the least informative character for grouping goldfish with respect to their evolutionary history. Fisher's exact test identified matrilineal constraints on domestication. CONCLUSIONS Chinese goldfish have a matrilineal origin from native southern Chinese C. a. auratus, especially the lineages from the lower Yangtze River. Anthropogenic selection of the native Carassius eliminated aesthetically unappealing goldfish and this action appeared to be responsible for the stepwise decrease in genetic diversity of domesticated goldfish, a process similar to that reported for the domestication of pigs, rice, and maize. The three-breed taxonomy--Grass-goldfish, Egg-goldfish, and Wen-goldfish--better reflected the history of domestication.
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Affiliation(s)
- Shu-Yan Wang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Jing Luo
- Laboratory for Conservation and Utilization of Bio-resources, College of Life Sciences, Yunnan University, Kunming, China
| | - Robert W. Murphy
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Canada
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
| | - Chun-Ling Zhu
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
| | - Yun Gao
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
- * E-mail: (YG); (Y-PZ)
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, China
- Laboratory for Conservation and Utilization of Bio-resources, College of Life Sciences, Yunnan University, Kunming, China
- * E-mail: (YG); (Y-PZ)
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Dong XL, Xu W, Wei YY, Xu QY. The complete mitochondrial genome of Barbus capito (Cypriniformes, Cyprinidae). ACTA ACUST UNITED AC 2013; 24:326-7. [PMID: 23369073 DOI: 10.3109/19401736.2012.760076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The mitogenome of Barbus capito was 16,603 bp long containing 1 D-loop region, 2 rRNA, 22 tRNA, and 13 protein-coding genes. Eight tRNA genes and one protein-coding gene were encoded on light strand, the others on heavy strand. The base composition and gene arrangement of B. capito mitogenome were identical to typical vertebrate.
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Affiliation(s)
- Xiao-Li Dong
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fisheries Science, Harbin, China
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