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Nguyen PT, Lee S, Jeong J, Kim J, Han DW, Kim IC, Lee JH, Park J, Kim JH. Complete mitochondrial genome of Trematomus newnesi (Perciformes, Nototheniidae). Mitochondrial DNA B Resour 2023; 8:1196-1199. [PMID: 38196755 PMCID: PMC10776061 DOI: 10.1080/23802359.2023.2194456] [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: 01/15/2023] [Accepted: 03/19/2023] [Indexed: 01/11/2024] Open
Abstract
The complete mitochondrial genome of Trematomus newnesi was sequenced using an Illumina platform. The 18,602 bp mitogenome contains 13 protein-coding genes, two rRNAs, and 23 tRNAs (tRNAMet is duplicated). The eight stop codons are TAA, TAG, CTT, GTA, AAT, ACT, AGG, and TTA. Two start codons ATG and GTG are present. The GC content is 44.4% and AT content is 55.6%. A phylogenetic tree was generated using 13 species from three families. The results showed that T. newnesi is closely related to Pagothenia borchgrevinki in Nototheniidae. This study provides fundamental data for further genetic evolutionary studies on T. newnesi.
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Affiliation(s)
- Phuong Thi Nguyen
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Korea
- Polar Science, University of Science and Technology, Daejeon, Korea
| | - Seungyeon Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Korea
- Polar Science, University of Science and Technology, Daejeon, Korea
| | - Jihye Jeong
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Korea
| | - Jihun Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Korea
- Polar Science, University of Science and Technology, Daejeon, Korea
| | - Dong-Won Han
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Korea
| | - Il-Chan Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Korea
| | - Jun Hyuck Lee
- Polar Science, University of Science and Technology, Daejeon, Korea
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Inchon, Korea
| | - Jisoo Park
- Polar Science, University of Science and Technology, Daejeon, Korea
- Division of Ocean Sciences, Korea Polar Research Institute, Inchon, Korea
| | - Jin-Hyoung Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Korea
- Polar Science, University of Science and Technology, Daejeon, Korea
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2
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Lu Y, Li W, Li Y, Zhai W, Zhou X, Wu Z, Jiang S, Liu T, Wang H, Hu R, Zhou Y, Zou J, Hu P, Guan G, Xu Q, Canário AVM, Chen L. Population genomics of an icefish reveals mechanisms of glacier-driven adaptive radiation in Antarctic notothenioids. BMC Biol 2022; 20:231. [PMID: 36224580 PMCID: PMC9560024 DOI: 10.1186/s12915-022-01432-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 10/03/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Antarctica harbors the bulk of the species diversity of the dominant teleost fish suborder-Notothenioidei. However, the forces that shape their evolution are still under debate. RESULTS We sequenced the genome of an icefish, Chionodraco hamatus, and used population genomics and demographic modelling of sequenced genomes of 52 C. hamatus individuals collected mainly from two East Antarctic regions to investigate the factors driving speciation. Results revealed four icefish populations with clear reproduction separation were established 15 to 50 kya (kilo years ago) during the last glacial maxima (LGM). Selection sweeps in genes involving immune responses, cardiovascular development, and photoperception occurred differentially among the populations and were correlated with population-specific microbial communities and acquisition of distinct morphological features in the icefish taxa. Population and species-specific antifreeze glycoprotein gene expansion and glacial cycle-paced duplication/degeneration of the zona pellucida protein gene families indicated fluctuating thermal environments and periodic influence of glacial cycles on notothenioid divergence. CONCLUSIONS We revealed a series of genomic evidence indicating differential adaptation of C. hamatus populations and notothenioid species divergence in the extreme and unique marine environment. We conclude that geographic separation and adaptation to heterogeneous pathogen, oxygen, and light conditions of local habitats, periodically shaped by the glacial cycles, were the key drivers propelling species diversity in Antarctica.
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Affiliation(s)
- Ying Lu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education), Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Wenhao Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education), Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Yalin Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education), Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Wanying Zhai
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education), Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Xuming Zhou
- Institute of Zoology, Chinese Academy of Science, Beijing, China
| | - Zhichao Wu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education), Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Shouwen Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education), Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Taigang Liu
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
- College of Information Technology, Shanghai Ocean University, Shanghai, China
| | - Huamin Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education), Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Ruiqin Hu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education), Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Yan Zhou
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education), Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Jun Zou
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education), Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Peng Hu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education), Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Guijun Guan
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education), Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Qianghua Xu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education), Shanghai Ocean University, Shanghai, China.
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China.
| | - Adelino V M Canário
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China.
- Centre of Marine Sciences (CCMAR-CIMAR LA), University of Algarve, Faro, Portugal.
| | - Liangbiao Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education), Shanghai Ocean University, Shanghai, China.
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China.
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3
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Papetti C, Babbucci M, Dettai A, Basso A, Lucassen M, Harms L, Bonillo C, Heindler FM, Patarnello T, Negrisolo E. Not Frozen in the Ice: Large and Dynamic Rearrangements in the Mitochondrial Genomes of the Antarctic Fish. Genome Biol Evol 2021; 13:6133229. [PMID: 33570582 PMCID: PMC7936035 DOI: 10.1093/gbe/evab017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2021] [Indexed: 12/21/2022] Open
Abstract
The vertebrate mitochondrial genomes generally present a typical gene order. Exceptions are uncommon and important to study the genetic mechanisms of gene order rearrangements and their consequences on phylogenetic output and mitochondrial function. Antarctic notothenioid fish carry some peculiar rearrangements of the mitochondrial gene order. In this first systematic study of 28 species, we analyzed known and undescribed mitochondrial genome rearrangements for a total of eight different gene orders within the notothenioid fish. Our reconstructions suggest that transpositions, duplications, and inversion of multiple genes are the most likely mechanisms of rearrangement in notothenioid mitochondrial genomes. In Trematominae, we documented an extremely rare inversion of a large genomic segment of 5,300 bp that partially affected the gene compositional bias but not the phylogenetic output. The genomic region delimited by nad5 and trnF, close to the area of the Control Region, was identified as the hot spot of variation in Antarctic fish mitochondrial genomes. Analyzing the sequence of several intergenic spacers and mapping the arrangements on a newly generated phylogeny showed that the entire history of the Antarctic notothenioids is characterized by multiple, relatively rapid, events of disruption of the gene order. We hypothesized that a pre-existing genomic flexibility of the ancestor of the Antarctic notothenioids may have generated a precondition for gene order rearrangement, and the pressure of purifying selection could have worked for a rapid restoration of the mitochondrial functionality and compactness after each event of rearrangement.
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Affiliation(s)
- Chiara Papetti
- Department of Biology, University of Padova, Padova 35121,Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Roma 00196, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy
| | - Agnes Dettai
- Institut de Systematique, Evolution, Biodiversité (ISYEB) Muséum national d'Histoire naturelle-CNRS-Sorbonne Université-EPHE, MNHN, Paris 75005, France
| | - Andrea Basso
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy
| | - Magnus Lucassen
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, Bremerhaven 27570, Germany
| | - Lars Harms
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, Bremerhaven 27570, Germany.,Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg (HIFMB), Ammerlsity of Oldenburg (HIFMOldenburg 26129, Germany
| | - Celine Bonillo
- Service de Systématique Moléculaire, UMS2700 Acquisition et Analyse de Données (2AD), MNHN, Paris 75005, France
| | | | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy
| | - Enrico Negrisolo
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy.,CRIBI Interdepartmental Research Centre for Innovative Biotechnologies, University of Padova, viale G. Colombo 3, Padova 35121, Italy
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4
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Cao P, Song W, Huang H, Li L, Jiang K, Chen X. The complete mitochondrial genome sequence and gene organization of Cryodraco antarcticus (Perciformes, Channichthyidae) with phylogenetic consideration. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:968-969. [PMID: 33366830 PMCID: PMC7748647 DOI: 10.1080/23802359.2020.1718023] [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: 11/14/2022]
Abstract
The complete mitochondrial genome DNA sequence of Cryodraco antarcticus was 17,857 bp in size. It consists of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and one control region. Among 22 tRNA genes, 8 tRNAs were encoded on the L-strand. The overall base composition of the genome is 26.45% for A, 25.96% for T, 29.78% for C, and 17.81% for G. The phylogenetic tree suggested C. antarcticus was genetically closest to some species in family Channichthyidae. This study could provide valuable information for further studies on population structure, conservation genetics and molecular evolution of C. antarcticus.
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Affiliation(s)
- Ping Cao
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.,College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Wei Song
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.,College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Hongliang Huang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Lingzhi Li
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Keji Jiang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Xuezhong Chen
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
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5
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Wang W, Zhao M, Zhang L, Ma C, Chen W, Liu Z, Zhang F, Ma L. The complete mitochondrial genome sequence and gene organization of Lepidotrigla Kanagashira (Scorpaeniformes, Triglidae) with phylogenetic consideration. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 5:294-295. [PMID: 33366526 PMCID: PMC7721047 DOI: 10.1080/23802359.2019.1698326] [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: 12/02/2022]
Abstract
The complete mitochondrial genome DNA sequence of Lepidotrigla kanagashira was 16,504 bp in length. It consists of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and one control region. Among 22 tRNA genes, 8 tRNAs were encoded on the L-strand. The overall base composition of the genome is 26.65% for A, 25.42% for T, 30.89% for C and17.04% for G. The phylogenetic tree suggested that L. kanagashira was genetically closest to L. microptera and Chelidonichthys kumu among 13 related species. This study could provide some valuable information for further studies on L. kanagashira.
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Affiliation(s)
- Wei Wang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Ming Zhao
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.,College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Linzi Zhang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.,College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Chunyan Ma
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Wei Chen
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Zhiqiang Liu
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Fengying Zhang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Lingbo Ma
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
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6
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Zhang L, Ma C, Zhao M, Zhang F, Wang Y, Ma L. The complete mitochondrial genome sequence and gene organization of Istigobius campbelli (Perciformes, Gobiidae) with phylogenetic consideration. Mitochondrial DNA B Resour 2019; 4:3220-3221. [PMID: 33365928 PMCID: PMC7687455 DOI: 10.1080/23802359.2019.1598809] [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: 02/21/2019] [Accepted: 03/13/2019] [Indexed: 11/14/2022] Open
Abstract
The complete mitochondrial genome DNA sequence of Istigobius campbelli was 16,527 bp in length. It consists of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and 1 control region. 28 of the 37 genes were encoded on the heavy strand, and 9 of them were encoded on the light strand. The overall base composition of the genome is 27.84% A, 25.81% T, 29.68% C, and 16.67% G. The phylogenetic tree suggested I. campbelli was genetically closest to Acentrogobius pflaumii and Oxyurichthys formosanus. This study could provide valuable information for further studies on I. campbelli.
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Affiliation(s)
- Linzi Zhang
- 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
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Chunyan 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, China
| | - Ming Zhao
- 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
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Fengying Zhang
- 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
| | - Yamei Wang
- 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
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Lingbo 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, China
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7
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Kim KY, Yoon M, Yoo JS, Lee DS. The full-length mitochondrial genome of the crocodile icefish, Chionobathyscus dewitti (Teleostei: Perciformes: Channichthyidae). Mitochondrial DNA B Resour 2019; 4:2371-2372. [PMID: 33365549 PMCID: PMC7687568 DOI: 10.1080/23802359.2019.1624635] [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: 05/09/2019] [Accepted: 05/17/2019] [Indexed: 10/30/2022] Open
Abstract
The full-length mitochondrial genome of the crocodile icefish, Chionobathyscus dewitti (Teleostei: Perciformes: Channichthyidae) was analyzed by the primer walking method. The mitogenome was 17,451 bp in total length, comprising 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Its gene order was congruent with those of the other crocodile icefish but different with those of typical vertebrates. In the phylogenetic tree, C. dewitti showed the closest relationship to Chaenocephalus aceratus in the same family.
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Affiliation(s)
| | - Moongeun Yoon
- National Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
| | - Jong Su Yoo
- National Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
| | - Dae-Sung Lee
- National Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
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8
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Cao P, Song W, Huang H, Li L, Zhang F, Jiang K, Chen X, Ma L. The complete mitochondrial genome of Pagetopsis macropterus (Notothenioidei: Channichthyidae) with phylogenetic consideration. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1606681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Ping Cao
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Wei Song
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Hongliang Huang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Lingzhi Li
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Fengying Zhang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Keji Jiang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Xuezhong Chen
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Lingbo Ma
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
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9
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Sang C, Liang S, Song W, Huang H, Jiang K, Chen X. The complete mitochondrial genome of Neopagetopsis ionah (Channichthyidae, neopagetopsis) with phylogenetic consideration. Mitochondrial DNA B Resour 2018; 3:1252-1253. [PMID: 33490576 PMCID: PMC7801004 DOI: 10.1080/23802359.2018.1532350] [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: 08/20/2018] [Accepted: 08/31/2018] [Indexed: 11/01/2022] Open
Abstract
In this study, the complete mitochondrial genome of Neopagetopsis ionah was obtained, which was 17,634 bp including two ribosomal RNAs, 13 protein-coding genes, 22 transfer RNAs, and a non-coding control region. In 13 protein-coding genes, there types of initiation codon (ATC, ATG, and GTG) and four types of stop codons (TAA, TAG, TA, and T) were identified. Among the 22 transfer RNAs, eight tRNAs were encoded by L-strand. The length of D-loop was 1519 bp and its contents of A, T, C, and G were 26.9%, 27.6%, 17.5%, and 30%, respectively. The complete mtDNA sequences of N. ionah and other 13 species were used to reconstruct the phylogenetic tree suggested that N. ionah was closest to some species of Channichthyidae. The study would provide a basic data for further research on population structure, conservation genetics and molecular evolution of N. ionah.
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Affiliation(s)
- Chengde Sang
- School of Ocean, Yantai University, Yantai, Shangdong, China
| | - Shuzhang Liang
- Key Laboratory of Oceanic and Polar Fisheries Ministry of Agriculture, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Wei Song
- Key Laboratory of Oceanic and Polar Fisheries Ministry of Agriculture, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Hongliang Huang
- Key Laboratory of Oceanic and Polar Fisheries Ministry of Agriculture, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China
| | - Keji Jiang
- Key Laboratory of Oceanic and Polar Fisheries Ministry of Agriculture, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China
| | - Xuezhong Chen
- Key Laboratory of Oceanic and Polar Fisheries Ministry of Agriculture, East China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences, Shanghai, China
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10
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Liang S, Song W, Huang H, Qu T, Zhang F, Jiang K, Chen X, Ma L. The complete mitochondrial genome of Chionodraco rastrospinosus (Notothenioidei: Channichthyidae) with phylogenetic consideration. Mitochondrial DNA B Resour 2018; 3:816-817. [PMID: 33490538 PMCID: PMC7800282 DOI: 10.1080/23802359.2018.1483769] [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: 05/22/2018] [Accepted: 05/29/2018] [Indexed: 11/06/2022] Open
Abstract
In this study, the complete mitochondrial genome of Chionodraco rastrospinosus was obtained, which was 17598 bp including 2 ribosomal RNAs, 13 protein-coding genes, 22 transfer RNAs, and a non-coding control region. The length of D-loop was 1332 bp and its contents of A, T, C, and G were 30.3%, 27.6%, 26.8%, and 15.3%. The complete mtDNA sequences of C. rastrospinosus and other 14 species were used to reconstruct the phylogenetic tree, suggested that C. rastrospinosus was closest to two species of Chionodraco. The study would provide a basic data for further research on population structure, conservation genetics and molecular evolution of C. rastrospinosus.
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Affiliation(s)
- Shuzhang Liang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Wei Song
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Hongliang Huang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Taichun Qu
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Fengying Zhang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Keji Jiang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Xuezhong Chen
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Lingbo Ma
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
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11
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Liang S, Song W, Ma C, Zhang F, Jiang K, Wang L, Ma L. The complete mitochondrial genome of Electrona carlsbergi (Myctophiformes, Myctophidae) with phylogenetic consideration. Mitochondrial DNA B Resour 2018; 3:151-152. [PMID: 33474102 PMCID: PMC7800513 DOI: 10.1080/23802359.2017.1383200] [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: 09/03/2017] [Accepted: 09/19/2017] [Indexed: 11/02/2022] Open
Abstract
The complete mitochondrial genome of Electrona carlsbergi was obtained, which was 18,282 bp in size and including 13 protein-coding genes, 2 ribosomal RNAs, 23 transfer RNAs and 1 control region. The overall nucleotide composition is 27.92% for A, 24.66% for T, 30.90% for C and 16.52% for G. Among 23 tRNA genes, 8 tRNAs were encoded on the L-strand. Further, the phylogenetic tree, which based on complete mtDNA sequences, revealed that the E. carlsbergi was genetically closest to species E. antarctica and Krefftichthys anderssoni. This study could provide a basic data for the studies on evolution for low temperature adaptability, stock evaluation and conservation genetics.
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Affiliation(s)
- Shuzhang Liang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Wei Song
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Chunyan Ma
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Fengying Zhang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Keji Jiang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Luming Wang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Lingbo Ma
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
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Lee-Estevez M, Larama G, Figueroa E, Ulloa-Rodríguez P, Díaz R, Valdebenito I, Farías JG. Complete mitochondrial genome sequence of Patagonian blenny, Eleginops maclovinus (Perciformes: Eleginopidae) with phylogenetic consideration. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0954-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Song W, Li L, Huang H, Chen F, Zhao M, Jiang K, Zhang F, Ma C, Chen X, Ma L. Isolation and characterization of the mitochondrial genome of Gymnodraco acuticeps (Perciformes: Bathydraconidae) with phylogenetic consideration. Mitochondrial DNA B Resour 2017; 2:526-527. [PMID: 33473885 PMCID: PMC7799673 DOI: 10.1080/23802359.2017.1361361] [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: 07/11/2017] [Accepted: 07/26/2017] [Indexed: 12/03/2022] Open
Abstract
Gymnodraco acuticepsis is an Antarctic fish living in the Southern Ocean. Until now, studies on G. acuticeps are still limited. As an Antarctic fish, obtaining and characterization of the mitochondrial genome of G. acuticeps will be important for elucidation of the mechanism of cold-adapting evolution in mitochondrion. In this study, we first isolated and characterized the mitochondrial genome sequence of G. acuticeps with 15,987 bp in length. It contained of 34 genes (12 protein-coding genes, 20 transfer RNA genes, 2 ribosomal RNA genes) and a partial putative control region. Gene organization and nucleotide composition of obtained mito-genome were similar to those of other Antarctic fish. Twenty-eight genes were encoded by heavy strand, while six genes were encoded by light strand. Further, the phylogenetic tree, which based on 12 protein-coding genes, revealed that the G. acuticeps was genetically closest to species Parachaenichthys charcoti among 18 species. We hope this work would be helpful for the population genetics and molecular evolution studies.
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Affiliation(s)
- Wei Song
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Lingzhi Li
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Hongliang Huang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Fenfang Chen
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Ming Zhao
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Keji Jiang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Fengying Zhang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Chunyan Ma
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Xuezhong Chen
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Lingbo Ma
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
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