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Yekefenhazi D, He Q, Wang X, Han W, Song C, Li W. Chromosome-level genome assembly of Nibea coibor using PacBio HiFi reads and Hi-C technologies. Sci Data 2022; 9:670. [PMID: 36329044 PMCID: PMC9633807 DOI: 10.1038/s41597-022-01804-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Nibea coibor belongs to Sciaenidae and is distributed in the South China Sea, East China Sea, India and the Philippines. In this study, we sequenced the DNA of a male Nibea coibor using PacBio long-read sequencing and generated chromatin interaction data. The genome size of Nibea coibor was estimated to be 611.85~633.88 Mb based on k-mer counts generated with Jellyfish. PacBio sequencing produced 29.26 Gb of HiFi reads, and Hifiasm was used to assemble a 627.60 Mb genome with a contig N50 of 10.66 Mb. We further found the canonical telomeric repeats "TTAGGG" to be present at the telomeres of all 24 chromosomes. The completeness of the assembly was estimated to be 98.9% and 97.8% using BUSCO and Merqury, respectively. Using the combination of ab initio prediction, protein homology and RNAseq annotation, we identified a total of 21,433 protein-coding genes. Phylogenetic analyses showed that Nibea coibor and Nibea albiflora are closely related. The results provide an important basis for research on the genetic breeding and genome evolution of Nibea coibor.
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Affiliation(s)
- Dinaer Yekefenhazi
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Qiwei He
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Xiaopeng Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Wei Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Chaowei Song
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Wanbo Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China.
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López-Cuamatzi IL, Ortega J, Baeza JA. The complete mitochondrial genome of the 'Zacatuche' Volcano rabbit (Romerolagus diazi), an endemic and endangered species from the Volcanic Belt of Central Mexico. Mol Biol Rep 2021; 49:1141-1149. [PMID: 34783988 DOI: 10.1007/s11033-021-06940-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/23/2021] [Indexed: 12/01/2022]
Abstract
BACKGROUND The 'Zacatuche', 'Teporingo', or Volcano rabbit (Romerolagus diazi) belongs to the family Leporidae, is an endemic species restricted to the Central part of the Trans-Mexican Volcanic Belt, and is considered 'endangered' by the IUCN Red List of Threatened Species. METHODS AND RESULTS This study reports, for the first time, the complete mitochondrial genome of R. diazi and examined the phylogenetic position of R. diazi among other closely related co-familiar species using mitochondrial protein-coding genes (PCGs). The mitogenome of R. diazi was assembled from short Illumina 150 bp pair-end reads with a coverage of 189x. The AT-rich mitochondrial genome of R. diazi is 17,400 bp in length and is comprised of 13 PCGs, two ribosomal RNA genes, and 22 transfer RNA genes. The gene order observed in the mitochondrial genome of R. diazi is identical to that reported for other leporids. Phylogenetic analyses based on PCGs support the basal position of Romerolagus within the Leporidae, at least when compared to the genera Oryctolagus and Lepus. Nonetheless, additional mitochondrial genomes from species belonging to the genera Bunolagus, Sylvilagus, and Pronolagus, among others, are needed before a more robust conclusion about the derived vs basal placement of Romerolagus within the family Leporidae can be reached based on mitochondrial PCGs. CONCLUSIONS This is the first genomic resource developed for R. diazi and it represents a tool to improve our understanding about the ecology and evolutionary biology of this iconic and endangered species.
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Affiliation(s)
- Issachar Leonardo López-Cuamatzi
- Posgrado en Ecología Tropical, Centro de Investigaciones Tropicales, Universidad Veracruzana, José María Morelos 44, Zona Centro, Centro, 91000, Xalapa-Enríquez, Mexico.
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Sto. Tomas, 11340, Ciudad de México, México
| | - J Antonio Baeza
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC, 29634, USA.,Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, FL, 34949, USA.,Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile
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Shan W, Tursun M, Zhou S, Zhang Y, Dai H. Complete mitochondrial genome sequence of Lepus yarkandensis Günther, 1875 (Lagomorpha, Leporidae): characterization and phylogenetic analysis. Zookeys 2021; 1012:135-150. [PMID: 33584111 PMCID: PMC7854563 DOI: 10.3897/zookeys.1012.59035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/28/2020] [Indexed: 11/12/2022] Open
Abstract
Lepusyarkandensis is a national second-class protected animal endemic to China and distributed only in the hot and arid Tarim Basin in Xinjiang. We sequenced and described the complete mitogenome of L.yarkandensis to analyze its characteristics and phylogeny. The species’ DNA is a 17,047 bp circular molecule that includes 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one control region. The overall base composition was as follows: A, 31.50%; T, 29.40%; G, 13.30% and C, 25.80%, with a high A+T bias of 60.9%. In the PCGs, ND6 had deviation ranges for AT skew (–0.303) and GC skew (0.636). The Ka/Ks values of ND1 (1.067) and ND6 (1.352) genes were >1, indicating positive selection, which might play an important role in the adaptation of L.yarkandensis to arid and hot environments. The conserved sequence block, the central conserved domain, and the extended termination-associated sequences of the control region and their features were identified and described. The phylogenetic tree based on the complete mitogenome showed that L.yarkandensis was closely related to the sympatric Lepustibetanuspamirensis. These novel datasets of L.yarkandensis can supply basic data for phylogenetic studies of Lepus spp., apart from providing essential and important resource for further genetic research and the protection of this species.
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Affiliation(s)
- Wenjuan Shan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China, 830046 Xinjiang University Urumqi China
| | - Mayinur Tursun
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China, 830046 Xinjiang University Urumqi China
| | - Shiyu Zhou
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China, 830046 Xinjiang University Urumqi China
| | - Yucong Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China, 830046 Xinjiang University Urumqi China
| | - Huiying Dai
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China, 830046 Xinjiang University Urumqi China
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Zhang YZ, Zhang T, Duan JY, Liu LX, Han QD, Liu YG, Kang DC. The complete mitochondrial DNA sequence of Yimeng black pig ( Sus Scrofa). Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1730722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Yan-Zhen Zhang
- College of Life Sciences and Technology, Xinjiang University, Urumqi, China
- College of Life Sciences, Linyi University, Linyi, China
| | - Tian Zhang
- Tianjin Dongli District Center for Disease Control and Prevention, Tianjin, China
| | - Jia-Yu Duan
- College of Life Sciences, Linyi University, Linyi, China
| | - Ling-Xiao Liu
- Linyi Academy of Agricultural Sciences, Linyi, China
| | - Qing-Dian Han
- College of Life Sciences, Linyi University, Linyi, China
| | - Yun-Guo Liu
- College of Life Sciences, Linyi University, Linyi, China
| | - Da-Cheng Kang
- College of Life Sciences, Linyi University, Linyi, China
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Shan W, Zhang Y, Tursun M, Zhou S, Dai H, Maimaiti M. The complete mitochondrial genome sequence of Lepus tibetanus pamirensis. MITOCHONDRIAL DNA PART B 2020. [DOI: 10.1080/23802359.2020.1736959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Wenjuan Shan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Yucong Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Mayinur Tursun
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Shiyu Zhou
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Huiying Dai
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Mireguli Maimaiti
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
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Ning X, Zhang YZ, Sui ZH, Quan XQ, Zhang HG, Liu LX, Han QD, Liu YG. The complete mitochondrial DNA sequence of Kashgarian loach ( Triplophysa yarkandensis) from Bosten Lake. Mitochondrial DNA B Resour 2020; 5:821-823. [PMID: 33366767 PMCID: PMC7748426 DOI: 10.1080/23802359.2020.1715881] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Triplophysa yarkandensis is a specific cobitidae species that is endemic to Xinjiang Tarim River basin, China. The complete mitochondrial genome sequence of T. yarkandensis from Bosten Lake was determined in this study (Accession number MN821008). The mitogenome (16,552 bp) consists of 22 tRNA genes, 2 ribosomal RNA genes, 13 protein-coding genes, and 1 control region (D-loop region). The complete mitochondrial genome sequence of the T. yarkandensis provides an important data set for further study in genetic mechanism and classification.
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Affiliation(s)
- Xia Ning
- Jinan Zhangqiu District Center for Disease Control and Prevention, Jinan, China
| | - Yan-Zhen Zhang
- College of Life Sciences, Linyi University, Linyi, China
| | - Zhi-Hai Sui
- College of Life Sciences, Linyi University, Linyi, China
| | - Xian-Qing Quan
- College of Life Sciences, Linyi University, Linyi, China
| | | | - Ling-Xiao Liu
- Linyi Academy of Agricultural Sciences, Linyi, China
| | - Qing-Dian Han
- College of Life Sciences, Linyi University, Linyi, China
| | - Yun-Guo Liu
- College of Life Sciences, Linyi University, Linyi, China
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Yao CY, Li YY, Liu LX, Ma C, Liu YG, Liu YH. The complete mitochondrial DNA sequence of Yimeng wool rabbit. Mitochondrial DNA B Resour 2019; 4:3858-3859. [PMID: 33366221 PMCID: PMC7707609 DOI: 10.1080/23802359.2019.1687022] [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: 08/14/2019] [Accepted: 10/26/2019] [Indexed: 11/06/2022] Open
Abstract
Yimeng wool rabbit is a national breed of geographical indication in China. The complete mitochondrial genome sequence of Yimeng wool rabbit was first determined in this study (Accession number MN296708). The mitogenome (16,740 bp) consists of 22 tRNA genes, 2 ribosomal RNA genes, 13 protein-coding genes, and 1 control region (D-loop region). The complete mitochondrial genome sequence of the Yimeng wool rabbit enriches data resource for further study in genetic mechanism and classification.
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Affiliation(s)
- Chang-Yu Yao
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- College of Life Sciences, Linyi University, Linyi, China
| | - Yao-Yao Li
- College of Life Sciences, Linyi University, Linyi, China
- Marine College, Shandong University (Weihai), Weihai, China
| | - Ling-Xiao Liu
- College of Life Sciences, Linyi University, Linyi, China
- Linyi Academy of Agricultural Sciences, Linyi, China
| | - Chao Ma
- College of Life Sciences, Linyi University, Linyi, China
| | - Yun-Guo Liu
- College of Life Sciences, Linyi University, Linyi, China
| | - Ye-Hai Liu
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
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Silva SM, Ruedas LA, Santos LH, e Silva JDS, Aleixo A. Illuminating the obscured phylogenetic radiation of South American SylvilagusGray, 1867 (Lagomorpha: Leporidae). J Mammal 2019. [DOI: 10.1093/jmammal/gyy186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Sofia Marques Silva
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Campus de Pesquisa, Avenida Perimetral, CEP, Belém, Pará, Brazil
| | - Luis A Ruedas
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Campus de Pesquisa, Avenida Perimetral, CEP, Belém, Pará, Brazil
| | - Larissa Hasnah Santos
- Portland State University, Department of Biology and Museum of Natural History, SRTC-246, Portland, OR, USA
| | - José de Sousa e Silva
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Campus de Pesquisa, Avenida Perimetral, CEP, Belém, Pará, Brazil
| | - Alexandre Aleixo
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Campus de Pesquisa, Avenida Perimetral, CEP, Belém, Pará, Brazil
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He YJ, Ma YG, Lin GH, Zhang TZ, Su JP. The complete mitochondrial DNA sequence of the Chinese red pika ( Ochotona erythrotis). Mitochondrial DNA B Resour 2018; 3:852-853. [PMID: 33474343 PMCID: PMC7800179 DOI: 10.1080/23802359.2018.1450663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/06/2018] [Indexed: 12/02/2022] Open
Abstract
In this study, we undertook the first complete Ochotona erythrotis mitochondrial genome. The genome sequence was 16,663 bp in length, including the typical structure of 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes, and the non-coding control region. The overall base composition of O. erythrotis mitogenome is 31.8% A, 26.0% T, 28.6% G, and 13.6% C, with a high A + T content of 57.8%.
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Affiliation(s)
- Yu-Jiao He
- Key Laboratory of Medicinal Plant and Animal Resources in Qinghai-Tibetan Plateau, College of Life Science, Qinghai Normal University, Xining, Qinghai, P.R. China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, P.R. China
| | - Yong-Gui Ma
- Key Laboratory of Medicinal Plant and Animal Resources in Qinghai-Tibetan Plateau, College of Life Science, Qinghai Normal University, Xining, Qinghai, P.R. China
| | - Gong-Hua Lin
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, P.R. China
| | - Tong-Zuo Zhang
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, P.R. China
| | - Jian-Ping Su
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, P.R. China
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Liu YG, Li YY, Meng W, Liu LX. The complete mitochondrial DNA sequence of Xinjiang arctic grayling Thymallus arcticus grubei. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:724-725. [PMID: 33614962 PMCID: PMC7870148 DOI: 10.1080/23802359.2016.1229589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Thymallus arcticus grubei is a specific grayling species that naturally occurs in the Xinjiang Irtysh River basin, China. The complete mitochondrial genome of The Xinjiang arctic grayling T. arcticus grubei was first determined (Accession number LC168675), with a total length of 16,658 nucleotides, of which 15,587 nucleotides are coding DNA, and 1071 nucleotides are non-coding DNA. It has the common feature with those of other grayling with respect to genome structure and gene arrangement. It contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer tRNA genes, and 1 control region (D-loop region). The complete mitochondrial genome of Xinjiang arctic grayling T. arcticus grubei provides an important data set for further study on its classification.
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Affiliation(s)
- Yun-Guo Liu
- College of Life Sciences and technology, Xinjiang University, Urumqi, China
| | - Yao-Yao Li
- College of Life Sciences and technology, Xinjiang University, Urumqi, China
| | - Wei Meng
- College of Life Sciences and technology, Xinjiang University, Urumqi, China
| | - Ling-Xiao Liu
- College of Life Sciences and technology, Xinjiang University, Urumqi, China
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