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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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Peng L, Hua W, Chen Y, Wang W, Xue Z. Comparative analysis of the population diversity of black rockfish (Sebastes schlegelii) in northern China. Mol Biol Rep 2023; 50:10015-10024. [PMID: 37902911 DOI: 10.1007/s11033-023-08821-7] [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: 08/15/2023] [Accepted: 09/12/2023] [Indexed: 11/01/2023]
Abstract
The nearshore marine fish known as black rockfish (Sebastes schlegelii) is found in the Yellow Sea, Bohai Sea, and East China Sea. The population structure and genetic diversity of S. schlegelii are vulnerable to the effects of artificial stocking, environmental pollution, overfishing, and climate change, so relevant studies are urgently needed. This study used comparative mtDNA loop (D-loop) analysis to examine the genetic diversity and natural population structure of 98 individuals from the northern Chinese cities of Qingdao, Jinzhou, and Dalian. A total of 22 haplotypes were identified in the three groups of samples, with the most common haplotypes being Hap-2, Hap-3, Hap-4, Hap-5, and Hap-6. The results of genetic diversity based on the D-LOOP sequence showed that the genetic diversity of S. schlegelii in the study area showed high Hd and low π type, indicating that the genetic diversity of S. schlegelii was low. Analyses of molecular variance (AMOVA) showed that the percentage of among population variation was - 0.29%, and the percentage of within population variation was 100.29%, indicating that the genetic variation was mainly from within the population. Between the three locations, the genetic differentiation index (Fst) was - 0.0113 ~ 0.0061, and there was no genetic differentiation among the populations. The results of gene flow (Nm) coefficients showed that the average Nm among the three populations was infinite (Nm = inf > > 4) and the three populations formed a stochastic unit. The results of the neutrality test (Tajima's D, Fu's Fs) and the frequency of nucleotide mismatch distribution demonstrated that the three geographic populations of S. schlegelii did not undergo a large population expansion in recent history. Based on the above conclusions, the S. schlegelii as a whole should be protected in situ.
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Affiliation(s)
- Lei Peng
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China
- College of Aquatic and Life Science, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China
| | - Wenyuan Hua
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China
- College of Aquatic and Life Science, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China
| | - Yan Chen
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China
- College of Aquatic and Life Science, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China
| | - Wei Wang
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China.
- College of Aquatic and Life Science, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China.
| | - Zhuang Xue
- Key Laboratory of Applied Biology and Aquaculture of Northern Fishes in Liaoning Province, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China.
- College of Aquatic and Life Science, Dalian Ocean University, No. 52 Heishijiao Street, Dalian, 116023, China.
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Comparative mitochondrial genomics of tetras: insights into phylogenetic relationships in Characidae. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01195-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Skorupski J. Characterisation of the Complete Mitochondrial Genome of Critically Endangered Mustela lutreola (Carnivora: Mustelidae) and Its Phylogenetic and Conservation Implications. Genes (Basel) 2022; 13:genes13010125. [PMID: 35052465 PMCID: PMC8774856 DOI: 10.3390/genes13010125] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/28/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023] Open
Abstract
In this paper, a complete mitochondrial genome of the critically endangered European mink Mustela lutreola L., 1761 is reported. The mitogenome was 16,504 bp in length and encoded the typical 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes, and harboured a putative control region. The A+T content of the entire genome was 60.06% (A > T > C > G), and the AT-skew and GC-skew were 0.093 and −0.308, respectively. The encoding-strand identity of genes and their order were consistent with a collinear gene order characteristic for vertebrate mitogenomes. The start codons of all protein-coding genes were the typical ATN. In eight cases, they were ended by complete stop codons, while five had incomplete termination codons (TA or T). All tRNAs had a typical cloverleaf secondary structure, except tRNASer(AGC) and tRNALys, which lacked the DHU stem and had reduced DHU loop, respectively. Both rRNAs were capable of folding into complex secondary structures, containing unmatched base pairs. Eighty-one single nucleotide variants (substitutions and indels) were identified. Comparative interspecies analyses confirmed the close phylogenetic relationship of the European mink to the so-called ferret group, clustering the European polecat, the steppe polecat and the black-footed ferret. The obtained results are expected to provide useful molecular data, informing and supporting effective conservation measures to save M. lutreola.
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Affiliation(s)
- Jakub Skorupski
- Institute of Marine and Environmental Sciences, University of Szczecin, Adama Mickiewicza 16 St., 70-383 Szczecin, Poland; ; Tel.: +48-91-444-16-85
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
- The European Mink Centre, 71-415 Szczecin, Poland
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Xu W, Lin S, Liu H. Mitochondrial genomes of five Hyphessobrycon tetras and their phylogenetic implications. Ecol Evol 2021; 11:12754-12764. [PMID: 34594536 PMCID: PMC8462149 DOI: 10.1002/ece3.8019] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 11/10/2022] Open
Abstract
To date, the taxonomic status and phylogenetic affinities within Hyphessobrycon, even among other genera in Characidae, remain unclear. Here, we determined five new mitochondrial genomes (mitogenomes) of Hyphessobrycon species (H. elachys, H. flammeus, H. pulchripinnis, H. roseus, and H. sweglesi). The mitogenomes were all classical circular structures, with lengths ranging from 16,008 to 17,224 bp. The type of constitutive genes and direction of the coding strand that appeared in the mitogenomes were identical to those of other species in Characidae. The highest value of the Ka/Ks ratio within 13 protein-coding genes (PCGs) was found in ND2 with 0.83, suggesting that they were subject to purifying selection in the Hyphessobrycon genus. Comparison of the control region sequences among seven Hyphessobrycon fish revealed that repeat units differ in length and copy number across different species, which led to sharp differences in mitogenome sizes. Phylogenetic trees based on the 13 PCGs did not support taxonomic relationships, as the Hyphessobrycon fish mixed with those from other genera. These data were combined to explore higher level relationships within Characidae and could aid in the understanding of the evolution of this group.
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Affiliation(s)
- Wei Xu
- College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
| | - Shupeng Lin
- College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
| | - Hongyi Liu
- College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
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Unusual mtDNA Control Region Length Heteroplasmy in the COS-7 Cell Line. Genes (Basel) 2020; 11:genes11060607. [PMID: 32486194 PMCID: PMC7348793 DOI: 10.3390/genes11060607] [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: 05/08/2020] [Revised: 05/22/2020] [Accepted: 05/29/2020] [Indexed: 11/29/2022] Open
Abstract
The COS-7 cell line is a workhorse of virology research. To expand this cell line’s utility and to enable studies on mitochondrial DNA (mtDNA) transcription and replication, we determined the complete nucleotide sequence of its mitochondrial genome by Sanger sequencing. In contrast to other available mtDNA sequences from Chlorocebus aethiops, the mtDNA of the COS-7 cell line was found to contain a variable number of perfect copies of a 108 bp unit tandemly repeated in the control region. We established that COS-7 cells are heteroplasmic with at least two variants being present: with four and five repeat units. The analysis of the mitochondrial genome sequences from other primates revealed that tandem repeats are absent from examined mtDNA control regions of humans and great apes, but appear in lower primates, where they are present in a homoplasmic state. To our knowledge, this is the first report of mtDNA length heteroplasmy in primates.
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Wetjen M, Cortey M, Vera M, Schmidt T, Schulz R, García-Marín JL. Occurrence of length polymorphism and heteroplasmy in brown trout. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2016.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Wang X, Liu N, Zhang H, Yang XJ, Huang Y, Lei F. Extreme variation in patterns of tandem repeats in mitochondrial control region of yellow-browed tits (Sylviparus modestus, Paridae). Sci Rep 2015; 5:13227. [PMID: 26288099 PMCID: PMC4541255 DOI: 10.1038/srep13227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 07/21/2015] [Indexed: 11/09/2022] Open
Abstract
To investigate the evolutionary pattern and origins of tandem repeats in the mitochondrial control region of the yellow-browed tit (Sylviparus modestus), the control region and another four mitochondrial loci from fifteen individuals were analyzed. A 117-bp tandem repeat unit that repeated once, twice or three times in different individuals was found, and a rarely reported arrangement for this tandem repeats region that a 5' imperfect copy at its downstream and a 3' imperfect copy at its upstream was observed. The haplotype network, phylogenetic trees, and ancestral state reconstruction of the combined dataset of five loci suggested multiple origins of the same repeat number. The turnover model via slipped-strand mispairing was introduced to interpret the results, because mispairing occurred so frequently that multiple origins of certain repeat number were observed. Insertion via recombination should be a better explanation for the origin of this tandem repeat unit, considering characteristics of the combined sequence of the 3' and 5' imperfect copy, including identification of its homolog in other passerines and its predicted secondary structure.
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Affiliation(s)
- Xiaoyang Wang
- Co-Innovation Center for Qinba regions' sustainable development, College of Life Sciences, Shaanxi Normal University, No. 199, South Chang'an Road, Xi'an 710062, China
| | - Nian Liu
- Co-Innovation Center for Qinba regions' sustainable development, College of Life Sciences, Shaanxi Normal University, No. 199, South Chang'an Road, Xi'an 710062, China
| | - Hongli Zhang
- College of Life Science, Datong University, Xingyun Street, Datong 037009, China
| | - Xiao-Jun Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32, Jiaochang East Road, Kunming 650223, China
| | - Yuan Huang
- Co-Innovation Center for Qinba regions' sustainable development, College of Life Sciences, Shaanxi Normal University, No. 199, South Chang'an Road, Xi'an 710062, China
| | - Fumin Lei
- 1] Co-Innovation Center for Qinba regions' sustainable development, College of Life Sciences, Shaanxi Normal University, No. 199, South Chang'an Road, Xi'an 710062, China [2] Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
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