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Jiang T, He J, Li J, Zhao L, Niu H, Bu Y. Analysis of the complete mitochondrial genome sequence of Hipposideros pratti. Mitochondrial DNA B Resour 2024; 9:902-906. [PMID: 39055531 PMCID: PMC11271134 DOI: 10.1080/23802359.2024.2381806] [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: 04/26/2024] [Accepted: 07/12/2024] [Indexed: 07/27/2024] Open
Abstract
In order to explore the characteristics of the mitochondrial genome sequence of Pratt's leaf-nosed bat (Hipposideros pratti Thomas 1891) and understand their phylogenetic status in Chiroptera, this study determined the mitochondrial genome sequences of H. pratti from five regions in China using high-throughput sequencing technology, sequence assembly, and genome annotation. The results showed that these sequences contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 non-coding region, all exhibiting a significant AT bias. Based on the phylogenetic tree constructed using 13 protein-coding genes from 15 Chiroptera species, the study found that H. pratti from the five regions clustered together, and then clustered with H. lylei into a single clade. Meanwhile, H. pratti from Jiangxi, Fujian, and Guangdong regions of China showed closer genetic relationships, while H. pratti from Yunnan and Henan regions of China exhibited closer genetic relationships. This study not only supplemented the mitochondrial genome database of H. pratti but also laid a foundation for genetic variation, molecular classification, and evolutionary studies of H. pratti.
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Affiliation(s)
- Tiantian Jiang
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Jingying He
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Jing Li
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Liming Zhao
- Henan Fisheries Technology Extension Center, Zhengzhou, Henan, China
| | - Hongxing Niu
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Yanzhen Bu
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
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Characterization of the Complete Mitochondrial Genome of the Spotted Catfish Arius maculatus (Thunberg, 1792) and Its Phylogenetic Implications. Genes (Basel) 2022; 13:genes13112128. [DOI: 10.3390/genes13112128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/01/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
The spotted catfish, Arius maculatus (Siluriformes), is an important economical aquaculture species inhabiting the Indian Ocean, as well as the western Pacific Ocean. The bioinformatics data in previous studies about the phylogenetic reconstruction of Siluriformes were insufficient and incomplete. In the present study, we presented a newly sequenced A. maculatus mitochondrial genome (mtDNA). The A. maculatus mtDNA was 16,710 bp in length and contained two ribosomal RNA (rRNA) genes, thirteen protein-coding genes (PCGs), twenty-two transfer RNA (tRNA) genes, and one D-loop region. The composition and order of these above genes were similar to those found in most other vertebrates. The relative synonymous codon usage (RSCU) of the 13 PCGs in A. maculatus mtDNA was consistent with that of PCGs in other published Siluriformes mtDNA. Furthermore, the average non-synonymous/synonymous mutation ratio (Ka/Ks) analysis, based on the 13 PCGs of the four Ariidae species, showed a strong purifying selection. Additionally, phylogenetic analysis, according to 13 concatenated PCG nucleotide and amino acid datasets, showed that A. maculatus and Netuma thalassina (Netuma), Occidentarius platypogon (Occidentarius), and Bagre panamensis (Bagre) were clustered as sister clade. The complete mtDNA of A. maculatus provides a helpful dataset for research on the population structure and genetic diversity of Ariidae species.
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Mu W. The complete mitochondrial genome of Saccostrea malabonensis (Ostreida: Ostreidae): characterization and phylogenetic position. MITOCHONDRIAL DNA PART B 2022; 7:1945-1947. [DOI: 10.1080/23802359.2022.2139160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Wendan Mu
- Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
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4
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Yuan Y, Geng G, Liu Q. The complete mitochondrial genome of De Brazza's monkey ( Cercopithecus neglectus). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:680-683. [PMID: 33763548 PMCID: PMC7928065 DOI: 10.1080/23802359.2021.1881929] [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: 11/29/2022]
Abstract
The complete mitochondrial genome of Cercopithecus neglectus was described. The mitogenome is 16,490 bp in length and consists 13 protein-coding genes (PCGs), 22 transfer-RNA genes, two ribosomal-RNA genes, and one non-coding region. All the 13 PCGs were 11,398 bp in length with most common start codon of ATG and termination codon of TAA. The overall GC content was 42.5%. The result of phylogenetic analysis showed that the relationship of C. neglectus was close to C. mona, C. pogonias, C. wolfi and C. denti.
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Affiliation(s)
- Yaohua Yuan
- Endangered Species Conservation and Research Centre, Shanghai Zoological Park, Shanghai, China
| | - Guangyao Geng
- Endangered Species Conservation and Research Centre, Shanghai Zoological Park, Shanghai, China
| | - Qunxiu Liu
- Endangered Species Conservation and Research Centre, Shanghai Zoological Park, Shanghai, China
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Zhang K, Sun J, Xu T, Qiu JW, Qian PY. Phylogenetic Relationships and Adaptation in Deep-Sea Mussels: Insights from Mitochondrial Genomes. Int J Mol Sci 2021; 22:ijms22041900. [PMID: 33672964 PMCID: PMC7918742 DOI: 10.3390/ijms22041900] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 01/31/2021] [Accepted: 02/08/2021] [Indexed: 11/16/2022] Open
Abstract
Mitochondrial genomes (mitogenomes) are an excellent source of information for phylogenetic and evolutionary studies, but their application in marine invertebrates is limited. In the present study, we utilized mitogenomes to elucidate the phylogeny and environmental adaptation in deep-sea mussels (Mytilidae: Bathymodiolinae). We sequenced and assembled seven bathymodioline mitogenomes. A phylogenetic analysis integrating the seven newly assembled and six previously reported bathymodioline mitogenomes revealed that these bathymodiolines are divided into three well-supported clades represented by five Gigantidas species, six Bathymodiolus species, and two "Bathymodiolus" species, respectively. A Common interval Rearrangement Explorer (CREx) analysis revealed a gene order rearrangement in bathymodiolines that is distinct from that in other shallow-water mytilids. The CREx analysis also suggested that reversal, transposition, and tandem duplications with subsequent random gene loss (TDRL) may have been responsible for the evolution of mitochondrial gene orders in bathymodiolines. Moreover, a comparison of the mitogenomes of shallow-water and deep-sea mussels revealed that the latter lineage has experienced relaxed purifying selection, but 16 residues of the atp6, nad4, nad2, cob, nad5, and cox2 genes have underwent positive selection. Overall, this study provides new insights into the phylogenetic relationships and mitogenomic adaptations of deep-sea mussels.
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Affiliation(s)
- Kai Zhang
- Department of Ocean Science, Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong 93117, China; (K.Z.); (J.S.); (T.X.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510225, China
| | - Jin Sun
- Department of Ocean Science, Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong 93117, China; (K.Z.); (J.S.); (T.X.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510225, China
| | - Ting Xu
- Department of Ocean Science, Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong 93117, China; (K.Z.); (J.S.); (T.X.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510225, China
- Department of Biology, Hong Kong Baptist University, Hong Kong 93117, China
| | - Jian-Wen Qiu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510225, China
- Department of Biology, Hong Kong Baptist University, Hong Kong 93117, China
- Correspondence: (J.-W.Q.); (P.-Y.Q.)
| | - Pei-Yuan Qian
- Department of Ocean Science, Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong 93117, China; (K.Z.); (J.S.); (T.X.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510225, China
- Correspondence: (J.-W.Q.); (P.-Y.Q.)
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Yang F, Zhou C, Tran NT, Sun Z, Wu J, Ge H, Lu Z, Zhong C, Zhu Z, Yang Q, Lin Q. Comparison of the complete mitochondrial genome of Phyllophorus liuwutiensis (Echinodermata: Holothuroidea: Phyllophoridae) to that of other sea cucumbers. FEBS Open Bio 2020; 10:1587-1600. [PMID: 32573974 PMCID: PMC7396427 DOI: 10.1002/2211-5463.12914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 05/31/2020] [Accepted: 06/17/2020] [Indexed: 12/25/2022] Open
Abstract
Sea cucumber species are abundant (>1400 species) and widely distributed globally. mtDNA sequencing is frequently used to identify the phylogenetic and evolutionary relationships among species. However, there are no reports on the mitochondrial genome of Phyllophorus liuwutiensis. Here, we performed mtDNA sequencing of P. liuwutiensis to examine its phylogenetic relationships with other echinoderms. Its mitochondrial genome (15 969 bp) contains 37 coding genes, including 13 protein‐coding genes, 22 tRNA genes and 2 rRNA genes. Except for one protein‐coding gene (nad6) and five tRNA genes encoded on the negative strand, all other genes were encoded on the positive strand. The mitochondrial bases of P. liuwutiensis were composed of 29.55% T, 22.16% C, 35.64% A and 12.64% G. The putative control region was 703 bp in length. Seven overlapping regions (1–10 bp) were found. The noncoding region between the genes ranged from 1 to 130 bp in length. One putative control region has been found in the P. liuwutiensis mitogenome. All of the tRNA genes were predicted to fold into a cloverleaf structure. In addition, we compared the gene arrangements of six echinoderms, revealing that the gene order of P. liuwutiensis was a new arrangement.
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Affiliation(s)
- Fuyuan Yang
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China.,College of Fisheries and Life Science, Shanghai Ocean University, China
| | - Chen Zhou
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Ngoc Tuan Tran
- Institute of Marine Sciences, Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, China
| | - Zaiqiao Sun
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Jianshao Wu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Hui Ge
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Zhen Lu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Chenhui Zhong
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Zhihuang Zhu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Qiuhua Yang
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Qi Lin
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China.,College of Fisheries and Life Science, Shanghai Ocean University, China
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Du J, Tian JS, Lu ZC, Zhang SJ, Song XR, Liu GY, Han JB. Identification of the complete mitochondrial genome of the king penguin Aptenodytes patagonicus (Sphenisciformes: Spheniscidae: Aptenodytes). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2191-2192. [PMID: 33365469 PMCID: PMC7687631 DOI: 10.1080/23802359.2019.1623121] [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: 11/23/2022]
Abstract
The complete mitochondrial genome of the king penguin Aptenodytes patagonicus was firstly determined. The mitogenome is 17,477 bp in length and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The total nucleotide composition is 31.0% A, 22.2% T, 33.1% C, and 13.8% G, with a total A + T content of 53.2%. The phylogenetic analysis demonstrates a close relationship between A. patagonicus and A. forsteri. These results provide fundamental information for further phylogeny and genetic studies on Aptenodytes genus.
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Affiliation(s)
- Jing Du
- Dalian Key Laboratory of Conservation Biology for Endangered Marine mammals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, China
| | - Jia-Shen Tian
- Dalian Key Laboratory of Conservation Biology for Endangered Marine mammals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, China
| | - Zhi-Chuang Lu
- Dalian Key Laboratory of Conservation Biology for Endangered Marine mammals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, China
| | - Sheng-Jiu Zhang
- Dalian Sun Asia Tourism Holding Co., Ltd, Dalian, Liaoning, China
| | - Xin-Ran Song
- Dalian Sun Asia Tourism Holding Co., Ltd, Dalian, Liaoning, China
| | - Gui-Ying Liu
- Dalian Key Laboratory of Conservation Biology for Endangered Marine mammals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, China
| | - Jia-Bo Han
- Dalian Key Laboratory of Conservation Biology for Endangered Marine mammals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, China
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8
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Li JY, Zeng C, Yan GY, He LS. Characterization of the mitochondrial genome of an ancient amphipod Halice sp. MT-2017 (Pardaliscidae) from 10,908 m in the Mariana Trench. Sci Rep 2019; 9:2610. [PMID: 30796230 PMCID: PMC6385184 DOI: 10.1038/s41598-019-38735-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 12/11/2018] [Indexed: 01/02/2023] Open
Abstract
Small amphipods (Halice sp. MT-2017) with body length <1 cm were collected from the Challenger Deep (~10,920 m below sea level). The divergence time of their lineage was approximately 109 Mya, making this group ancient compared to others under study. The mitochondrial genome of Halice sp. shared the usual gene components of metazoans, comprising 13 protein coding genes (PCGs), 22 transfer RNAs (tRNAs), and 2 ribosomal RNAs (rRNAs). The arrangement of these genes, however, differed greatly from that of other amphipods. Of the 15 genes that were rearranged with respect to the pancrustacean gene pattern, 12 genes (2 PCGs, 2 rRNAs, and 8 tRNAs) were both translocated and strand-reversed. In contrast, the mitochondrial genomes in other amphipods never show so many reordered genes, and in most instances, only tRNAs were involved in strand-reversion-coupled translocation. Other characteristics, including reversed strand nucleotide composition bias, relatively higher composition of non-polar amino acids, and lower evolutionary rate, were also identified. Interestingly, the latter two features were shared with another hadal amphipod, Hirondellea gigas, suggesting their possible associations with the adaptation to deep-sea extreme habitats. Overall, our data provided a useful resource for future studies on the evolutionary and adaptive mechanisms of hadal faunas.
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Affiliation(s)
- Jun-Yuan Li
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cong Zeng
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- Hunan Agricultural University, Changsha, Hunan, China
| | - Guo-Yong Yan
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li-Sheng He
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.
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Ayoola AO, Wang Y, Nneji LM, Adeola AC, Ogunjemite BG, Wu DD. Complete mitochondrial genome sequence for the Cercopithecus erythrotis camerunensis (Primate: Cercopithecidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1546138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Affiliation(s)
- Adeola O. Ayoola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yunyu Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Lotanna M. Nneji
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Adeniyi C. Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Babafemi G. Ogunjemite
- Department of Ecotourism and Wildlife Management, School of Agriculture and Agricultural Sciences, The Federal University of Technology, Akure, Ondo State, Nigeria
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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Mu W, Liu J, Zhang H. Complete mitochondrial genome of Benthodytes marianensis (Holothuroidea: Elasipodida: Psychropotidae): Insight into deep sea adaptation in the sea cucumber. PLoS One 2018; 13:e0208051. [PMID: 30500836 PMCID: PMC6267960 DOI: 10.1371/journal.pone.0208051] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/09/2018] [Indexed: 01/01/2023] Open
Abstract
Complete mitochondrial genomes play important roles in studying genome evolution, phylogenetic relationships, and species identification. Sea cucumbers (Holothuroidea) are ecologically important and diverse members, living from the shallow waters to the hadal trench. In this study, we present the mitochondrial genome sequence of the sea cucumber Benthodytes marianensis collected from the Mariana Trench. To our knowledge, this is the first reported mitochondrial genome from the genus Benthodytes. This complete mitochondrial genome is 17567 bp in length and consists of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes (duplication of two tRNAs: trnL and trnS). Most of these genes are coded on the positive strand except for one protein-coding gene (nad6) and five tRNA genes which are coded on the negative strand. Two putative control regions (CRs) have been found in the B. marianensis mitogenome. We compared the order of genes from the 10 available holothurian mitogenomes and found a novel gene arrangement in B. marianensis. Phylogenetic analysis revealed that B. marianensis clustered with Peniagone sp. YYH-2013, forming the deep-sea Elasipodida clade. Positive selection analysis showed that eleven residues (24 S, 45 S, 185 S, 201 G, 211 F and 313 N in nad2; 108 S, 114 S, 322 C, 400 T and 427 S in nad4) were positively selected sites with high posterior probabilities. We predict that nad2 and nad4 may be the important candidate genes for the further investigation of the adaptation of B. marianensis to the deep-sea environment.
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Affiliation(s)
- Wendan Mu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun Liu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Haibin Zhang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- * E-mail:
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11
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Lei R, Frasier CL, Hawkins MTR, Engberg SE, Bailey CA, Johnson SE, McLain AT, Groves CP, Perry GH, Nash SD, Mittermeier RA, Louis EE. Phylogenomic Reconstruction of Sportive Lemurs (genus Lepilemur) Recovered from Mitogenomes with Inferences for Madagascar Biogeography. J Hered 2018; 108:107-119. [PMID: 28173059 DOI: 10.1093/jhered/esw072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 09/30/2016] [Indexed: 11/12/2022] Open
Abstract
The family Lepilemuridae includes 26 species of sportive lemurs, most of which were recently described. The cryptic morphological differences confounded taxonomy until recent molecular studies; however, some species’ boundaries remain uncertain. To better understand the genus Lepilemur, we analyzed 35 complete mitochondrial genomes representing all recognized 26 sportive lemur taxa and estimated divergence dates. With our dataset we recovered 25 reciprocally monophyletic lineages, as well as an admixed clade containing Lepilemur mittermeieri and Lepilemur dorsalis. Using modern distribution data, an ancestral area reconstruction and an ecological vicariance analysis were performed to trace the history of diversification and to test biogeographic hypotheses. We estimated the initial split between the eastern and western Lepilemur clades to have occurred in the Miocene. Divergence of most species occurred from the Pliocene to the Pleistocene. The biogeographic patterns recovered in this study were better addressed with a combinatorial approach including climate, watersheds, and rivers. Generally, current climate and watershed hypotheses performed better for western and eastern clades, while speciation of northern clades was not adequately supported using the ecological factors incorporated in this study. Thus, multiple mechanisms likely contributed to the speciation and distribution patterns in Lepilemur.
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Affiliation(s)
- Runhua Lei
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Cynthia L Frasier
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Melissa T R Hawkins
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Shannon E Engberg
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Carolyn A Bailey
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Steig E Johnson
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada
| | - Adam T McLain
- Department of Mathematics and Sciences, State University of New York Polytechnic Institute, Utica, NY, USA
| | - Colin P Groves
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, Australia
| | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Edward E Louis
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
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12
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The complete mitogenome of Pelochelys cantorii (Guangning) and the comparative analysis of different habitats. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-017-0752-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Zhu KC, Liang YY, Wu N, Guo HY, Zhang N, Jiang SG, Zhang DC. Sequencing and characterization of the complete mitochondrial genome of Japanese Swellshark (Cephalloscyllium umbratile). Sci Rep 2017; 7:15299. [PMID: 29127415 PMCID: PMC5681689 DOI: 10.1038/s41598-017-15702-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/31/2017] [Indexed: 11/18/2022] Open
Abstract
To further comprehend the genome features of Cephalloscyllium umbratile (Carcharhiniformes), an endangered species, the complete mitochondrial DNA (mtDNA) was firstly sequenced and annotated. The full-length mtDNA of C. umbratile was 16,697 bp and contained ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, and a major non-coding control region. Each PCG was initiated by an authoritative ATN codon, except for COX1 initiated by a GTG codon. Seven of 13 PCGs had a typical TAA termination codon, while others terminated with a single T or TA. Moreover, the relative synonymous codon usage of the 13 PCGs was consistent with that of other published Carcharhiniformes. All tRNA genes had typical clover-leaf secondary structures, except for tRNA-Ser (GCT), which lacked the dihydrouridine 'DHU' arm. Furthermore, the analysis of the average Ka/Ks in the 13 PCGs of three Carcharhiniformes species indicated a strong purifying selection within this group. In addition, phylogenetic analysis revealed that C. umbratile was closely related to Glyphis glyphis and Glyphis garricki. Our data supply a useful resource for further studies on genetic diversity and population structure of C. umbratile.
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Affiliation(s)
- Ke-Cheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
- Key Laboratory of Fishery Ecology & Environment, Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
| | - Yin-Yin Liang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
| | - Na Wu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
| | - Hua-Yang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
| | - Shi-Gui Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, Guangdong Province, The People's Republic of China
| | - Dian-Chang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou, 510300, China.
- Engineer Technology Research Center of Marine Biological Seed of Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China.
- Key Laboratory of Fishery Ecology & Environment, Guangdong Province, Guangzhou, Guangdong Province, The People's Republic of China.
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Zhang B, Zhang Y, Wang X, Zhang H, Lin Q. The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep-sea environment. Ecol Evol 2017; 7:4951-4962. [PMID: 28690821 PMCID: PMC5496520 DOI: 10.1002/ece3.3067] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/13/2017] [Accepted: 04/24/2017] [Indexed: 01/14/2023] Open
Abstract
The deep sea is one of the most extensive ecosystems on earth. Organisms living there survive in an extremely harsh environment, and their mitochondrial energy metabolism might be a result of evolution. As one of the most important organelles, mitochondria generate energy through energy metabolism and play an important role in almost all biological activities. In this study, the mitogenome of a deep‐sea sea anemone (Bolocera sp.) was sequenced and characterized. Like other metazoans, it contained 13 energy pathway protein‐coding genes and two ribosomal RNAs. However, it also exhibited some unique features: just two transfer RNA genes, two group I introns, two transposon‐like noncanonical open reading frames (ORFs), and a control region‐like (CR‐like) element. All of the mitochondrial genes were coded by the same strand (the H‐strand). The genetic order and orientation were identical to those of most sequenced actiniarians. Phylogenetic analyses showed that this species was closely related to Bolocera tuediae. Positive selection analysis showed that three residues (31 L and 42 N in ATP6, 570 S in ND5) of Bolocera sp. were positively selected sites. By comparing these features with those of shallow sea anemone species, we deduced that these novel gene features may influence the activity of mitochondrial genes. This study may provide some clues regarding the adaptation of Bolocera sp. to the deep‐sea environment.
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Affiliation(s)
- Bo Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yan‐Hong Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hui‐Xian Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
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15
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Fernández Lázaro G, Zehr S, Alonso García E. Use of Primates in Research: What Do We Know About Captive Strepsirrhine Primates? J APPL ANIM WELF SCI 2016; 20:109-122. [PMID: 27869570 DOI: 10.1080/10888705.2016.1255554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The increasing debate and restrictions on primate research have prompted many surveys about their status. However, there is a lack of information regarding strepsirrhine primates in the literature. This study provides an overview of research on strepsirrhines in captivity by analyzing scientific articles published from 2010 to 2013 and assessing publicly available government reports in Europe and the United States. Data on taxonomy, country, research area, research class, and type of institution were extracted. The 174 qualifying articles showed that species in the Galagidae and Cheirogaleidae families were used more often in invasive studies of neuroscience and metabolism, while the most commonly used species in noninvasive studies of behavior and cognition were true lemurs (family Lemuridae). France conducted the greatest number of invasive research projects, and the Duke Lemur Center was the institution with the most noninvasive studies. This study investigates how strepsirrhines are used in captive research and identifies issues in need of further review, which suggest that increased participation by the scientific community in the monitoring of strepsirrhine research is warranted.
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Affiliation(s)
- Gloria Fernández Lázaro
- a Animal Welfare Group, Animal Welfare Science, Humanities, Ethics and Law-Interdisciplinary Animal Studies (AWSHEL-IAS) , Franklin Institute, Research Institute for North American Studies, University of Alcala , Madrid , Spain
| | - Sarah Zehr
- b Duke Lemur Center, Duke University , Durham , North Carolina , USA
| | - Enrique Alonso García
- a Animal Welfare Group, Animal Welfare Science, Humanities, Ethics and Law-Interdisciplinary Animal Studies (AWSHEL-IAS) , Franklin Institute, Research Institute for North American Studies, University of Alcala , Madrid , Spain
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16
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Characterization of complete mitochondrial genome of fives tripe wrasse (Thalassoma quinquevittatum, Lay & Bennett, 1839) and phylogenetic analysis. Gene 2016; 598:71-78. [PMID: 27816474 DOI: 10.1016/j.gene.2016.10.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/16/2016] [Accepted: 10/28/2016] [Indexed: 11/21/2022]
Abstract
To further supplement the genome-level features in related species, T. quinquevittatum complete mtDNA was firstly sequenced and de novo assembled by next-generation sequencing. The full-length mtDNA of T. quinquevittatum was a 16,896bp fragment, which was atypical of Labridae, with 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, and a major non-coding control region (D-loop region). Additionally, the mtDNA of T. quinquevittatum exhibited characteristics of A (27.1%), T (29.3%), G (17.8%), and C (25.8%) with a high A+T content (56.4%). Furthermore, the analysis of the average Ka/Ks in the 13 PCGs of three Labridae species indicated a strong purifying selection within this group. Additionally, the phylogenetic analysis based on 13 concatenated PCGs nucleotide and amino acid datasets, showed high value support for the following sister clade among the four genera (T. quinquevittatum, Halichoeres trimaculatus, Halichoeres melanurus, Parajulis poecilepterus). The complete mtDNA of the T. quinquevittatum provided important information for the study in population genetics and evolutionary theory.
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17
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Jing H, Yan P, Li W, Li X, Song Z. The complete mitochondrial genome of Triplophysa lixianensis (Teleostei: Cypriniformes: Balitoridae) with phylogenetic consideration. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Rahman MM, Yoon KB, Kim JY, Hussin MZ, Park YC. Complete mitochondrial genome sequence of the Indian pipistrellePipistrellus coromandra(Vespertilioninae). Anim Cells Syst (Seoul) 2016. [DOI: 10.1080/19768354.2016.1150877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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19
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Zhang D, Gong F, Liu T, Guo H, Zhang N, Zhu K, Jiang S. Shotgun assembly of the mitochondrial genome from Fenneropenaeus penicillatus with phylogenetic consideration. Mar Genomics 2015; 24 Pt 3:379-86. [PMID: 26429699 DOI: 10.1016/j.margen.2015.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 08/26/2015] [Accepted: 09/15/2015] [Indexed: 11/25/2022]
Abstract
The complete mitochondrial genome is of great importance for better understanding of the genome-level characteristics and phylogenetic relationships among related species. In this study, Fenneropenaeus penicillatus mitochondrial genome sequence was determined by next-generation sequencing. The complete genome DNA was 16,040 bp in length and consisted of a typical set of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a putative control region (CR). The gene arrangement is identical to the pancrustacean pattern. The overall base composition of its mitochondrial genome is estimated to be 34.1% for A, 34.1% for T, 12.5% for G and 19.3% for C with a high A+T content (68.2%). The analysis of the average Ka/Ks in the 13 mitochondrial protein-coding genes of penaeid shrimps indicated a strong purifying selection within this group. The phylogenetic analysis based on mitochondrial sequences and 13 concatenated protein-coding genes showed strong statistic support for the following relationship among the five genera ((Penaeus s.s+Fenneropenaeus)+(Litopenaeus+Farfantepenaeus))+Marsupenaeus. The sequence data of F. penicillatus can provide useful information for the studies on molecular systematics, population structure, stock evaluation and conservation genetics.
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Affiliation(s)
- Dianchang Zhang
- Key Laboratory of South China Sea Fishery Research Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China.
| | - Fahui Gong
- Key Laboratory of South China Sea Fishery Research Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; College of Fisheries and Life, Shanghai Ocean University, Shanghai; 201306, China
| | - Tiantian Liu
- Key Laboratory of South China Sea Fishery Research Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; College of Fisheries and Life, Shanghai Ocean University, Shanghai; 201306, China
| | - Huayang Guo
- Key Laboratory of South China Sea Fishery Research Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Research Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Kecheng Zhu
- Key Laboratory of South China Sea Fishery Research Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Shigui Jiang
- Key Laboratory of South China Sea Fishery Research Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China.
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20
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Yao H, Gao M, Liu K, Zhao S. Sequence characterization and phylogeny analysis of the complete mitochondrial genome of verreaux's sifaka, Propithecus verreauxi (primates: indriidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4431-4432. [PMID: 26406276 DOI: 10.3109/19401736.2015.1089558] [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
The Verreaux's sifaka, Propithecus verreauxi, is a medium-sized lemur that inhabits in tropical dry lowland and montane forest. Here, we reported the complete mitochondrial genome sequence of this species. The mitogenome of P. verreauxi is 17 106 bp in length and composed of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. The structure about gene order and composition is identical to that of the other lemur species and related genera. The overall base composition of the heavy strand in descending order is A (32.84%), T (27.13%), C (26.95%), and G (13.08%). Most of the genes are encoded on the heavy strand except for the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes. With the exception of COX3, which terminates with an incomplete stop codon (T-), all the other PCGs initiates with a traditional ATN start codon and ends with the typical mitochondrial stop codon (TAG/TAA/AGA). The phylogenetic tree constructed using the complete mitochondrial genome sequences of P. verreauxi together with 15 other closely related species with Neighbor-Joining (NJ) method shows that P. verreauxi is closer to P. coquereli in the phylogenetic relationship.
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Affiliation(s)
- Hongmei Yao
- a Department of Gynecology , Affiliated Hospital of Jining Medical University , Jining , China
| | - Min Gao
- b Department of Clinical Laboratory , Jining NO.1 People's Hospital , Jining , China
| | - Kun Liu
- c Department of Clinical College , Jining Medical University , Jining , China , and
| | - Shaojie Zhao
- d Department of Gynecology , Wuxi Maternal and Child Health Hospital , Wuxi, 214002 , China
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21
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Wei H, Ma H, Ma C, Zhang F, Wang W, Chen W, Ma L. The complete mitochondrial genome sequence and gene organization of Tridentiger trigonocephalus (Gobiidae: Gobionellinae) with phylogenetic consideration. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3725-6. [PMID: 26370266 DOI: 10.3109/19401736.2015.1079876] [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 complete mitochondrial genome plays an important role in studies of genome-level characteristics and phylogenetic relationships. Here we determined the complete mitogenome sequence of Tridentiger trigonocephalus (Perciformes, Gobiidae), and discovered its phylogenetic relationship. This circular genome was 16 662 bp in length, and consisted of 37 typical genes, including 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. The gene order of T. trigonocephalus mitochondrial genome was identical to those observed in most other vertebrates. Of 37 genes, 28 were encoded by heavy strand, while the others were encoded by light strand. The phylogenetic tree constructed by 13 concatenated protein-coding genes showed that T. trigonocephalus was closest to T. bifasciatus, and then to T. barbatus among the 20 species within suborder Gobioidei. This work should facilitate the studies on population genetic diversity, and molecular evolution in Gobioidei fishes.
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Affiliation(s)
- Hongqing Wei
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and.,b College of Fisheries and Life Sciences, Shanghai Ocean University , Shanghai , China
| | - Hongyu Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Chunyan Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Fengying Zhang
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Wei Wang
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Wei Chen
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
| | - Lingbo Ma
- a Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China and
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22
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Lecompte E, Crouau-Roy B, Aujard F, Holota H, Murienne J. Complete mitochondrial genome of the gray mouse lemur, Microcebus murinus (Primates, Cheirogaleidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3514-6. [PMID: 27158869 DOI: 10.3109/19401736.2015.1074196] [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
We report the high-coverage complete mitochondrial genome sequence of the gray mouse lemur Microcebus murinus. The sequencing has been performed on an Illumina Hiseq 2500 platform, with a genome skimming strategy. The total length of this mitogenome is 16 963 bp, containing 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 non-coding region (D-loop region). The genome organization, nucleotide composition and codon usage are similar to those reported from other primate's mitochondrial genomes. The complete mitochondrial genome sequence reported here will be useful for comparative genomics studies in primates.
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Affiliation(s)
- Emilie Lecompte
- a Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, CNRS, Université Toulouse 3 Paul Sabatier , ENFA, Toulouse , France and
| | - Brigitte Crouau-Roy
- a Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, CNRS, Université Toulouse 3 Paul Sabatier , ENFA, Toulouse , France and
| | | | - Hélène Holota
- a Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, CNRS, Université Toulouse 3 Paul Sabatier , ENFA, Toulouse , France and
| | - Jérôme Murienne
- a Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, CNRS, Université Toulouse 3 Paul Sabatier , ENFA, Toulouse , France and
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23
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Yoon KB, Cho CU, Park YC. The mitochondrial genome of the Saunders's gull Chroicocephalus saundersi (Charadriiformes: Laridae) and a higher phylogeny of shorebirds (Charadriiformes). Gene 2015; 572:227-36. [PMID: 26165451 DOI: 10.1016/j.gene.2015.07.022] [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: 08/28/2014] [Revised: 06/20/2015] [Accepted: 07/07/2015] [Indexed: 01/22/2023]
Abstract
The complete mitogenome of Chroicocephalus saundersi was characterized and compared with the 6 published Charadriiformes mitogenomes. The mitogenome of C. saundersi is a closed circular molecule 16,739 bp in size, and contains 37 genes and a control region. The AT and GC skews are positive and negative, respectively, and in agreement with those of the other Charadriiformes mitogenomes. The mitogenome of C. saundersi contains 3 start codons (ATG, GTG, and ATT), 4 stop codons (TAA, TAG, AGG, and AGA), and an incomplete stop codon (T-) in 13 PCGs. A codon usage analysis of all available Charadriiformes mitogenomes showed that the ATG (78%) and TAA (50.5%) were the most common start codon and stop codon, respectively. An unusual start codon, ATT, is commonly found in the ND3s of Charadriiformes mitogenomes, whereas the more common start codons, ATC and ATA, are rarely found. In all the Laridae species, one extra cytosine was inserted at position 174 in ND3. The control region of C. saundersi is 1180-bp long, with a nucleotide composition of 30.2% A, 28.6% T, 27.3% C, and 14.0% G. Variable numbers of tandem repeats (VNTRs) with nine copies of the 10 bp repeat sequence (AACAACAAAC) are found within the CSB domain of the control region. The ML/BI analyses, based on the amino acids of the 13 mitochondrial PCGs, strongly support the monophyly of the order Charadriiformes, with the suborder Lari considered sister to the Scolopaci, which is in turn a sister group to the suborder Charadrii.
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Affiliation(s)
- Kwang Bae Yoon
- Division of Forest Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Chea Un Cho
- Species Restoration Technology Institute, Korea National Park Service, Inje 252-829, Republic of Korea
| | - Yung Chul Park
- Division of Forest Science, Kangwon National University, Chuncheon 200-701, Republic of Korea.
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24
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Pozzi L, Hodgson JA, Burrell AS, Sterner KN, Raaum RL, Disotell TR. Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes. Mol Phylogenet Evol 2014; 75:165-83. [PMID: 24583291 PMCID: PMC4059600 DOI: 10.1016/j.ympev.2014.02.023] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 02/17/2014] [Accepted: 02/19/2014] [Indexed: 01/23/2023]
Abstract
The origins and the divergence times of the most basal lineages within primates have been difficult to resolve mainly due to the incomplete sampling of early fossil taxa. The main source of contention is related to the discordance between molecular and fossil estimates: while there are no crown primate fossils older than 56Ma, most molecule-based estimates extend the origins of crown primates into the Cretaceous. Here we present a comprehensive mitogenomic study of primates. We assembled 87 mammalian mitochondrial genomes, including 62 primate species representing all the families of the order. We newly sequenced eleven mitochondrial genomes, including eight Old World monkeys and three strepsirrhines. Phylogenetic analyses support a strong topology, confirming the monophyly for all the major primate clades. In contrast to previous mitogenomic studies, the positions of tarsiers and colugos relative to strepsirrhines and anthropoids are well resolved. In order to improve our understanding of how fossil calibrations affect age estimates within primates, we explore the effect of seventeen fossil calibrations across primates and other mammalian groups and we select a subset of calibrations to date our mitogenomic tree. The divergence date estimates of the Strepsirrhine/Haplorhine split support an origin of crown primates in the Late Cretaceous, at around 74Ma. This result supports a short-fuse model of primate origins, whereby relatively little time passed between the origin of the order and the diversification of its major clades. It also suggests that the early primate fossil record is likely poorly sampled.
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Affiliation(s)
- Luca Pozzi
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States; New York Consortium in Evolutionary Primatology, United States; Behavioral Ecology and Sociobiology Unit, German Primate Center, Göttingen, Germany.
| | - Jason A Hodgson
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States; New York Consortium in Evolutionary Primatology, United States; Department of Life Sciences, Imperial College London, London, United Kingdom.
| | - Andrew S Burrell
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States.
| | - Kirstin N Sterner
- Department of Anthropology, University of Oregon, Eugene, OR, United States.
| | - Ryan L Raaum
- New York Consortium in Evolutionary Primatology, United States; Department of Anthropology, Lehman College & The Graduate Center, City University of New York, Bronx, NY, United States.
| | - Todd R Disotell
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, NY, United States; New York Consortium in Evolutionary Primatology, United States.
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25
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He L, Zhang Y, Zhang QL, Zhang WJ, Feng HH, Khan MK, Hu M, Zhou YQ, Zhao JL. Mitochondrial genome of Babesia orientalis, apicomplexan parasite of water buffalo (Bubalus babalis, Linnaeus, 1758) endemic in China. Parasit Vectors 2014; 7:82. [PMID: 24580772 PMCID: PMC3941609 DOI: 10.1186/1756-3305-7-82] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 01/26/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Apicomplexan parasites of the genus Babesia, Theileria and Plasmodium are very closely related organisms. Interestingly, their mitochondrial (mt) genomes are highly divergent. Among Babesia, Babesia orientalis is a new species recently identified and specifically epidemic to the southern part of China, causing severe disease to water buffalo. However, no information on the mt genome of B. orientalis was available. METHODS Four pairs of primers were designed based on the full genome sequence of B. orientalis (unpublished data) and by aligning reported mt genomes of B. bovis, B. bigemina, and T. parva. The entire mt genome was amplified by four sets of PCR. The obtained mt genome was annotated by aligning with published apicomplexan mt genomes and Artemis software v11. Phylogenetic analysis was performed by using cox1 and cob amino acid sequences. RESULTS The complete mt genome of B. orientalis (Wuhan strain) was sequenced and characterized. The entire mt genome is 5996 bp in length with a linear form, containing three protein-coding genes including cytochrome c oxidase I (cox1), cytochrome b (cob) and cytochrome c oxidase III (cox3) and six rRNA large subunit gene fragments. The gene arrangement in B. orientalis mt genome is similar to those of B. bovis, B. gibsoni and Theileria parva, but different from those of T. orientalis, T. equi and Plasmodium falciparum. Comparative analysis indicated that cox1 and cob genes were more conserved than cox3. Phylogenetic analysis based on amino acid sequences of cox1, cob and cox1 + cob, respectively, revealed that B. orientalis fell into Babesia clade with the closest relationship to B. bovis. CONCLUSIONS The availability of the entire mt genome sequences of B. orientalis provides valuable information for future phylogenetic, population genetics and molecular epidemiological studies of apicomplexan parasites.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jun-Long Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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26
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The complete sequence of the mitochondrial genome of the African Penguin (Spheniscus demersus). Gene 2014; 534:113-8. [DOI: 10.1016/j.gene.2013.09.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 09/13/2013] [Accepted: 09/16/2013] [Indexed: 11/23/2022]
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27
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Ma H, Ma C, Li X, Xu Z, Feng N, Ma L. The complete mitochondrial genome sequence and gene organization of the mud crab (Scylla paramamosain) with phylogenetic consideration. Gene 2013; 519:120-7. [PMID: 23384716 DOI: 10.1016/j.gene.2013.01.028] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/14/2013] [Accepted: 01/17/2013] [Indexed: 11/24/2022]
Abstract
The complete mitochondrial genome is of great importance for better understanding the genome-level characteristics and phylogenetic relationships among related species. In the present study, we determined the complete mitochondrial genome DNA sequence of the mud crab (Scylla paramamosain) by 454 deep sequencing and Sanger sequencing approaches. The complete genome DNA was 15,824 bp in length and contained a typical set of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a putative control region (CR). Of 37 genes, twenty-three were encoded by the heavy strand (H-strand), while the other ones were encoded by light strand (L-strand). The gene order in the mitochondrial genome was largely identical to those obtained in most arthropods, although the relative position of gene tRNA(His) differed from other arthropods. Among 13 protein-coding genes, three (ATPase subunit 6 (ATP6), NADH dehydrogenase subunits 1 (ND1) and ND3) started with a rare start codon ATT, whereas, one gene cytochrome c oxidase subunit I (COI) ended with the incomplete stop codon TA. All 22 tRNAs could fold into a typical clover-leaf secondary structure, with the gene sizes ranging from 63 to 73 bp. The phylogenetic analysis based on 12 concatenated protein-coding genes showed that the molecular genetic relationship of 19 species of 11 genera was identical to the traditional taxonomy.
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Affiliation(s)
- Hongyu Ma
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, China
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Liu GH, Wang SY, Huang WY, Zhao GH, Wei SJ, Song HQ, Xu MJ, Lin RQ, Zhou DH, Zhu XQ. The complete mitochondrial genome of Galba pervia (Gastropoda: Mollusca), an intermediate host snail of Fasciola spp. PLoS One 2012; 7:e42172. [PMID: 22844544 PMCID: PMC3406003 DOI: 10.1371/journal.pone.0042172] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 07/04/2012] [Indexed: 11/26/2022] Open
Abstract
Complete mitochondrial (mt) genomes and the gene rearrangements are increasingly used as molecular markers for investigating phylogenetic relationships. Contributing to the complete mt genomes of Gastropoda, especially Pulmonata, we determined the mt genome of the freshwater snail Galba pervia, which is an important intermediate host for Fasciola spp. in China. The complete mt genome of G. pervia is 13,768 bp in length. Its genome is circular, and consists of 37 genes, including 13 genes for proteins, 2 genes for rRNA, 22 genes for tRNA. The mt gene order of G. pervia showed novel arrangement (tRNA-His, tRNA-Gly and tRNA-Tyr change positions and directions) when compared with mt genomes of Pulmonata species sequenced to date, indicating divergence among different species within the Pulmonata. A total of 3655 amino acids were deduced to encode 13 protein genes. The most frequently used amino acid is Leu (15.05%), followed by Phe (11.24%), Ser (10.76%) and IIe (8.346%). Phylogenetic analyses using the concatenated amino acid sequences of the 13 protein-coding genes, with three different computational algorithms (maximum parsimony, maximum likelihood and Bayesian analysis), all revealed that the families Lymnaeidae and Planorbidae are closely related two snail families, consistent with previous classifications based on morphological and molecular studies. The complete mt genome sequence of G. pervia showed a novel gene arrangement and it represents the first sequenced high quality mt genome of the family Lymnaeidae. These novel mtDNA data provide additional genetic markers for studying the epidemiology, population genetics and phylogeographics of freshwater snails, as well as for understanding interplay between the intermediate snail hosts and the intra-mollusca stages of Fasciola spp..
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Affiliation(s)
- Guo-Hua Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Shu-Yan Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
- College of Animal Science and Technology, Guangxi Univesity, Nanning, Guangxi Zhuang Nationality Autonomous Region, China
| | - Wei-Yi Huang
- College of Animal Science and Technology, Guangxi Univesity, Nanning, Guangxi Zhuang Nationality Autonomous Region, China
| | - Guang-Hui Zhao
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
- College of Veterinary Medicine, Northwest A & F University, Yangling, Shaanxi Province, China
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hui-Qun Song
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Min-Jun Xu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Rui-Qing Lin
- Laboratory of Parasitology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - Dong-Hui Zhou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province, China
- * E-mail:
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Zhang J, Wu X, Xie M, Li A. The complete mitochondrial genome of Pseudochauhanea macrorchis (Monogenea: Chauhaneidae) revealed a highly repetitive region and a gene rearrangement hot spot in Polyopisthocotylea. Mol Biol Rep 2012; 39:8115-25. [PMID: 22544610 DOI: 10.1007/s11033-012-1659-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 04/16/2012] [Indexed: 02/06/2023]
Abstract
The complete mitochondrial genome of Pseudochauhanea macrorchis was determined and compared with other monogenean mitochondrial genomes from GenBank. The circular genome was 15,031 bp in length and encoded 36 genes (12 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs) typically found in flatworms. Structures of the mitochondrial genome were mostly concordant with that known for Microcotyle sebastis and Polylabris halichoeres, but also contained two noted features-a gene rearrangement hot spot and the highly repetitive region (HRR) in major non-coding region (NCR). The gene rearrangement hot spot located between the cox3 and nad5 genes, including a cluster of tRNA genes, nad6 gene and one major NCR. The HRR seemed to be a unique feature of the polyopisthocotylean mitochondrial genomes. In conclusion, the present study provided new molecular data for future studies of the comparative mitochondrial genomics and also served as a resource of markers for the studies of species populations and monogenean phylogenetics.
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Affiliation(s)
- Juan Zhang
- Key Laboratory for Aquatic Products Safety of Ministry of Education/State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 135 Xingang West Road, Haizhu District, Guangzhou 510275, China
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Liu GH, Wu CY, Song HQ, Wei SJ, Xu MJ, Lin RQ, Zhao GH, Huang SY, Zhu XQ. Comparative analyses of the complete mitochondrial genomes of Ascaris lumbricoides and Ascaris suum from humans and pigs. Gene 2011; 492:110-6. [PMID: 22075400 DOI: 10.1016/j.gene.2011.10.043] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 10/03/2011] [Accepted: 10/20/2011] [Indexed: 12/12/2022]
Abstract
Ascaris lumbricoides and Ascaris suum are parasitic nematodes living in the small intestine of humans and pigs, and can cause the disease ascariasis. For long, there has been controversy as to whether the two ascaridoid taxa represent the same species due to their significant resemblances in morphology. However, the complete mitochondrial (mt) genome data have been lacking for A. lumbricoides in spite of human and animal health significance and socio-economic impact globally of these parasites. In the present study, we sequenced the complete mt genomes of A. lumbricoides and A. suum (China isolate), which was 14,303 bp and 14,311 bp in size, respectively. The identity of the mt genomes was 98.1% between A. lumbricoides and A. suum (China isolate), and 98.5% between A. suum (China isolate) and A. suum (USA isolate). Both genomes are circular, and consist of 36 genes, including 12 genes for proteins, 2 genes for rRNA and 22 genes for tRNA, which are consistent with that of all other species of ascaridoid studied to date. All genes are transcribed in the same direction and have a nucleotide composition high in A and T (71.7% for A. lumbricoides and 71.8% for A. suum). The AT bias had a significant effect on both the codon usage pattern and amino acid composition of proteins. Phylogenetic analyses of A. lumbricoides and A. suum using concatenated amino acid sequences of 12 protein-coding genes, with three different computational algorithms (Bayesian analysis, maximum likelihood and maximum parsimony) all clustered in a clade with high statistical support, indicating that A. lumbricoides and A. suum was very closely related. These mt genome data and the results provide some additional genetic evidence that A. lumbricoides and A. suum may represent the same species. The mt genome data presented in this study are also useful novel markers for studying the molecular epidemiology and population genetics of Ascaris.
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Affiliation(s)
- Guo-Hua Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
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Lin RQ, Qiu LL, Liu GH, Wu XY, Weng YB, Xie WQ, Hou J, Pan H, Yuan ZG, Zou FC, Hu M, Zhu XQ. Characterization of the complete mitochondrial genomes of five Eimeria species from domestic chickens. Gene 2011; 480:28-33. [DOI: 10.1016/j.gene.2011.03.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2010] [Revised: 02/13/2011] [Accepted: 03/03/2011] [Indexed: 10/18/2022]
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