151
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Lim LWK, Chung HH, Lau MML, Aziz F, Gan HM. Improving the phylogenetic resolution of Malaysian and Javan mahseer (Cyprinidae), Tor tambroides and Tor tambra: Whole mitogenomes sequencing, phylogeny and potential mitogenome markers. Gene 2021; 791:145708. [PMID: 33984441 DOI: 10.1016/j.gene.2021.145708] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/19/2021] [Accepted: 05/06/2021] [Indexed: 11/29/2022]
Abstract
The true mahseer (Tor spp.) is one of the highest valued fish in the world due to its high nutritional value and great unique taste. Nevertheless, its morphological characterization and single mitochondrial gene phylogeny in the past had yet to resolve the ambiguity in its taxonomical classification. In this study, we sequenced and assembled 11 complete mahseer mitogenomes collected from Java of Indonesia, Pahang and Terengganu of Peninsular Malaysia as well as Sarawak of East Malaysia. The mitogenome evolutionary relationships among closely related Tor spp. samples were investigated based on maximum likelihood phylogenetic tree construction. Compared to the commonly used COX1 gene fragment, the complete COX1, Cytb, ND2, ND4 and ND5 genes appear to be better phylogenetic markers for genetic differentiation at the population level. In addition, a total of six population-specific mitolineage haplotypes were identified among the mahseer samples analyzed, which this offers hints towards its taxonomical landscape.
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Affiliation(s)
- Leonard Whye Kit Lim
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia.
| | - Hung Hui Chung
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia.
| | - Melinda Mei Lin Lau
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia.
| | - Fazimah Aziz
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia.
| | - Han Ming Gan
- GeneSEQ Sdn Bhd, Bukit Beruntung, 48300 Rawang, Selangor, Malaysia; Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia.
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152
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Santos RP, Melo BF, Yazbeck GM, Oliveira RS, Hilário HO, Prosdocimi F, Carvalho DC. Diversification of
Prochilodus
in the eastern Brazilian Shield: Evidence from complete mitochondrial genomes (Teleostei, Prochilodontidae). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Rosiane P. Santos
- Laboratório de Genética da Conservação Programa de Pós‐Graduação em Biologia dos Vertebrados Pontifícia Universidade Católica de Minas Gerais Belo Horizonte Brazil
- Laboratório de Recursos Genéticos Programa de Pós‐Graduação em Ecologia Universidade Federal de São João del‐Rei São João del‐Rei Brazil
| | - Bruno F. Melo
- Departamento de Biologia Estrutural e Funcional Instituto de Biociências Universidade Estadual Paulista Botucatu Brazil
| | - Gabriel M. Yazbeck
- Laboratório de Recursos Genéticos Programa de Pós‐Graduação em Ecologia Universidade Federal de São João del‐Rei São João del‐Rei Brazil
| | - Rafael S. Oliveira
- Programa de Pós‐Graduação em Ciência da Computação Universidade Federal de São João del‐Rei São João del‐Rei Brazil
| | - Heron O. Hilário
- Laboratório de Genética da Conservação Programa de Pós‐Graduação em Biologia dos Vertebrados Pontifícia Universidade Católica de Minas Gerais Belo Horizonte Brazil
| | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade Instituto de Bioquímica Médica Leopoldo de MeisUniversidade Federal do Rio de Janeiro Rio de Janeiro Brazil
| | - Daniel C. Carvalho
- Laboratório de Genética da Conservação Programa de Pós‐Graduação em Biologia dos Vertebrados Pontifícia Universidade Católica de Minas Gerais Belo Horizonte Brazil
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153
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Sam KK, Lau NS, Shu-Chien AC, Muchlisin ZA, Nugroho RA. Complete Mitochondrial Genomes of Paedocypris micromegethes and Paedocypris carbunculus Reveal Conserved Gene Order and Phylogenetic Relationships of Miniaturized Cyprinids. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.662501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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154
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Zhang R, Li C, Yu M, Huang X, Zhang M, Liu S, Pan S, Xue W, Wang C, Mao C, Zhang H, Fan G. Chromosome-level genome assembly of the humpback puffer, Tetraodon palembangensis. GIGABYTE 2021; 2021:gigabyte17. [PMID: 36824331 PMCID: PMC9632004 DOI: 10.46471/gigabyte.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/31/2021] [Indexed: 11/09/2022] Open
Abstract
The humpback puffer, Tetraodon palembangensis, is a poisonous freshwater pufferfish species mainly distributed in Southeast Asia (Thailand, Laos, Malaysia and Indonesia). The humpback puffer has many interesting biological features, such as inactivity, tetrodotoxin production and body expansion. Here, we report the first chromosome-level genome assembly of the humpback puffer. The genome size is 362 Mb, with a contig N50 value of ∼1.78 Mb and a scaffold N50 value of ∼15.8 Mb. Based on this genome assembly, ∼61.5 Mb (18.11%) repeat sequences were identified, 19,925 genes were annotated, and the function of 90.01% of these genes could be predicted. Finally, a phylogenetic tree of ten teleost fish species was constructed. This analysis suggests that the humpback puffer and T. nigroviridis share a common ancestor 18.1 million years ago (MYA), and diverged from T. rubripes 45.8 MYA. The humpback puffer genome will be a valuable genomic resource to illustrate possible mechanisms of tetrodotoxin synthesis and tolerance.
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Affiliation(s)
- Rui Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Chang Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Mengjun Yu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | | | - Mengqi Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Shanshan Pan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Weizhen Xue
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Congyan Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Chunyan Mao
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - He Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
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155
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Singh B, Kumar A, Uniyal VP, Gupta SK. Phylogeography and population genetic structure of red muntjacs: evidence of enigmatic Himalayan red muntjac from India. BMC Ecol Evol 2021; 21:49. [PMID: 33757420 PMCID: PMC7989103 DOI: 10.1186/s12862-021-01780-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/11/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Identifying factors shaping population genetic structure across continuous landscapes in the context of biogeographic boundaries for lineage diversification has been a challenging goal. The red muntjacs cover a wide range across multiple vegetation types, making the group an excellent model to study South and Southeast Asian biogeography. Therefore, we analysed mitogenomes and microsatellite loci, confirming the number of red muntjac lineages from India, gaining insights into the evolutionary history and phylogeography of red muntjacs. RESULTS Our results indicated the Northwestern population of red muntjac or the Himalayan red muntjac (M. aureus) in India as genetically diverse and well-structured, with significant genetic differentiation implying a low level of gene flow. The phylogenetic, population genetic structure, as well as species delimitation analyses, confirm the presence of the lineage from Western Himalayan in addition to the previously identified red muntjac lineages. Relatively low genetic diversity was observed in M. aureus compared to M. vaginalis, M. malabaricus and M. muntjak. The M. aureus and M. vaginalis lineages have split during the late Pleistocene, ~ 1.01 million years ago (Mya), making M. aureus the youngest lineage; whereas, M. malabaricus split earlier, ~ 2.2 Mya and appeared as the oldest lineage among red muntjacs. CONCLUSIONS Pronounced climate fluctuations during the Quaternary period were pivotal in influencing the current spatial distribution of forest-dwelling species' restriction to Northwestern India. Our finding confirms the distinct Himalayan red muntjac (M. aureus) within the red muntjac group from Northwestern India that should be managed as an Evolutionary Significant Unit (ESU). We recommend a reassessment of the conservation status of red muntjacs for effective conservation and management.
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Affiliation(s)
- Bhim Singh
- Wildlife Institute of India, Chandrabani, Dehradun, 248001, UK, India
| | - Ajit Kumar
- Wildlife Institute of India, Chandrabani, Dehradun, 248001, UK, India
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156
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Complete Mitochondrial DNA Genome of Nine Species of Sharks and Rays and Their Phylogenetic Placement among Modern Elasmobranchs. Genes (Basel) 2021; 12:genes12030324. [PMID: 33668210 PMCID: PMC7995966 DOI: 10.3390/genes12030324] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 11/16/2022] Open
Abstract
Chondrichthyes occupy a key position in the phylogeny of vertebrates. The complete sequence of the mitochondrial genome (mitogenome) of four species of sharks and five species of rays was obtained by whole genome sequencing (DNA-seq) in the Illumina HiSeq2500 platform. The arrangement and features of the genes in the assembled mitogenomes were identical to those found in vertebrates. Both Maximum Likelihood (ML) and Bayesian Inference (BI) analyses were used to reconstruct the phylogenetic relationships among 172 species (including 163 mitogenomes retrieved from GenBank) based on the concatenated dataset of 13 individual protein coding genes. Both ML and BI analyses did not support the “Hypnosqualea” hypothesis and confirmed the monophyly of sharks and rays. The broad notion in shark phylogeny, namely the division of sharks into Galeomorphii and Squalomorphii and the monophyly of the eight shark orders, was also supported. The phylogenetic placement of all nine species sequenced in this study produced high statistical support values. The present study expands our knowledge on the systematics, genetic differentiation, and conservation genetics of the species studied, and contributes to our understanding of the evolutionary history of Chondrichthyes.
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157
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Sahoo B, Das G, Sahoo L, Mahapatra KD, Meher PK, Udit UK, Sundaray JK, Das P. The complete mitochondrial genome of Labeo catla (Hamilton, 1822) using long read sequencing. Mitochondrial DNA B Resour 2021; 6:402-403. [PMID: 33628875 PMCID: PMC7889109 DOI: 10.1080/23802359.2020.1870879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Labeo catla is a widely cultured species in monoculture and polyculture systems of the Indian subcontinent. In this study, the complete mitochondrial genome sequence of catla was reconstructed from Oxford Nanopore sequence data. The mitochondrial genome is 16,600 bp in length (accession no. is MN830943) which is larger than the previously reported catla mitogenomes. Like other vertebrate mitochondrial genomes, it has 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a putative control region. Most of the mitogenes are encoded on H-strand. Phylogenetic analysis showed that Labeo catla is more closely related to Labeo rohita than other labeo species. The catla mtgenome reported here will facilitate population genetics, phylogenetics and molecular taxonomy of Indian major carps.
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Affiliation(s)
- Bismay Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Gargee Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Lakshman Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Kanta Das Mahapatra
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Prem K Meher
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Uday Kumar Udit
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Jitendra Kumar Sundaray
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Paramananda Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
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158
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Sun CH, Liu HY, Xu N, Zhang XL, Zhang Q, Han BP. Mitochondrial Genome Structures and Phylogenetic Analyses of Two Tropical Characidae Fishes. Front Genet 2021; 12:627402. [PMID: 33633787 PMCID: PMC7901900 DOI: 10.3389/fgene.2021.627402] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/13/2021] [Indexed: 11/13/2022] Open
Abstract
The Characidae family contains the largest number of tropical fish species. Morphological similarities make species identification difficult within this family. Here, the complete mitogenomes of two Characidae fish were determined and comparatively analyzed with those of nine other Characidae fish species. The two newly sequenced complete mitogenomes are circular DNA molecules with sizes of 16,701 bp (Hyphessobrycon amandae; MT484069) and 16,710 bp (Hemigrammus erythrozonus; MT484070); both have a highly conserved structure typical of Characidae, with the start codon ATN (ATG/ATT) and stop codon TAR (TAA/TAG) or an incomplete T--/TA-. Most protein-coding genes of the 11 Characidae mitogenomes showed significant codon usage bias, and the protein-coding gene cox1 was found to be a comparatively slow-evolving gene. Phylogenetic analyses via the maximum likelihood and Bayesian inference methods confirmed that H. amandae and H. erythrozonus belong to the family Characidae. In all Characidae species studied, one genus was well supported; whereas other two genera showed marked differentiation. These findings provide a phylogenetic basis for improved classification of the family Characidae. Determining the mitogenomes of H. erythrozonus and H. amandae improves our understanding of the phylogeny and evolution of fish species.
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Affiliation(s)
- Cheng-He Sun
- Department of Ecology, Jinan University, Guangzhou, China
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Hong-Yi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Nan Xu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Xiao-Li Zhang
- Department of Ecology, Jinan University, Guangzhou, China
| | - Qun Zhang
- Department of Ecology, Jinan University, Guangzhou, China
| | - Bo-Ping Han
- Department of Ecology, Jinan University, Guangzhou, China
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159
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Jia C, Zhang X, Xu S, Yang T, Yanagimoto T, Gao T. Comparative analysis of the complete mitochondrial genomes of three rockfishes (Scorpaeniformes, Sebastiscus) and insights into the phylogenetic relationships of Sebastidae. Biosci Rep 2020; 40:BSR20203379. [PMID: 33245090 PMCID: PMC7736627 DOI: 10.1042/bsr20203379] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/26/2020] [Accepted: 11/26/2020] [Indexed: 01/09/2023] Open
Abstract
Mitochondrial genome is a powerful molecule marker to provide information for phylogenetic relationships and revealing molecular evolution in ichthyological studies. Sebastiscus species, a marine rockfish, are of essential economic value. However, the taxonomic status and phylogenetic relationships of Sebastidae have been controversial so far. Here, the mitochondrial genomes (mitogenomes) of three species, S. tertius, S. albofasciatus, and S. marmoratus, were systemically investigated. The lengths of the mitogenomes' sequences of S. tertius, S. albofasciatus, and S. marmoratus were 16910, 17056, and 17580 bp, respectively. It contained 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNA (tRNA) genes, and one identical control region (D-loop) among the three species. The genetic distance and Ka/Ks ratio analyses indicated 13 PCGs were suffering purifying selection and the selection pressures were different from certain deep-sea fishes, which were most likely due to the difference in their living environment. The phylogenetic tree was constructed by Bayesian Inference (BI) and Maximum Likelihood (ML). Most interestingly, the results indicated that Sebastidae and Scorpaenidae were grouped into a separate branch, so the taxonomic status of Sebastidae should be classified into subfamily Sebastinae. Our results may lead to a taxonomic revision of Scorpaenoidei.
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Affiliation(s)
- Chenghao Jia
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Xiumei Zhang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
- Function Laboratory for Marine, Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
| | - Shengyong Xu
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Tianyan Yang
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Takashi Yanagimoto
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
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160
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Complete mitogenome of Ganges river dolphin, Platanista gangetica gangetica and its phylogenetic relationship with other cetaceans. Mol Biol Rep 2020; 48:315-322. [PMID: 33296067 DOI: 10.1007/s11033-020-06048-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/28/2020] [Indexed: 10/22/2022]
Abstract
The Ganges river dolphin, Platanista gangetica gangetica is one of the endangered cetaceans. Due to increasing anthropogenic activities, it has faced a significant reduction in distribution range since the late 1800s and has even gone extinct from most of the early localities. The investigation of complete mitogenome holds significant relevance for identifying evolutionary relationships and monitoring the endangered species. Herein, we report and characterize for the first time the 16,319 bp complete mitochondrial genome of P. g. gangetica. It comprises 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and one control region (CR). The genome composition was A + T biased (59.6%) and exhibited a positive AT-skew (0.104) and negative GC-skew (- 0.384). All the genes were encoded on the heavy strand, except eight tRNAs and the ND6 gene. In the CR, an 18 bp tandem repeat sequence was observed. Our Bayesian Inference (BI) and Maximum Likelihood (ML) based phylogenetic analysis indicated that studied river dolphins were polyphyletic and the placement of Platanista was to be more basal than other river dolphins (Lipotes, Inia and Pontoporia). The pairwise genetic distance of Platanista with other cetaceans was varied, with an overall close affinity with whales. The model-based BI and ML phylogenetic analysis indicated that Platanista clustering with Ziphiidae with high to moderate supportive values (PP/BP = 98/68). The results of this study provide insights important for the conservation genetics and further evolutionary studies of the freshwater river dolphins.
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161
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Rocha-Reis DA, Pasa R, Menegidio FB, Heslop-Harrison JS, Schwarzacher T, Kavalco KF. The Complete Mitochondrial Genome of Two Armored Catfish Populations of the Genus Hypostomus (Siluriformes, Loricariidae, Hypostominae). Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.579965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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162
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Sequencing and characterisation of complete mitogenome DNA for Rasbora sarawakensis (Cypriniformes: Cyprinidae: Rasbora) with phylogenetic consideration. Comput Biol Chem 2020; 89:107403. [PMID: 33120127 DOI: 10.1016/j.compbiolchem.2020.107403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/18/2020] [Accepted: 10/11/2020] [Indexed: 11/23/2022]
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163
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Sharma A, Siva C, Ali S, Sahoo PK, Nath R, Laskar M, Sarma D. The complete mitochondrial genome of the medicinal fish, Cyprinion semiplotum: Insight into its structural features and phylogenetic implications. Int J Biol Macromol 2020; 164:939-948. [DOI: 10.1016/j.ijbiomac.2020.07.142] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 01/24/2023]
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164
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Miyazawa S. Pattern blending enriches the diversity of animal colorations. SCIENCE ADVANCES 2020; 6:eabb9107. [PMID: 33268371 PMCID: PMC7710386 DOI: 10.1126/sciadv.abb9107] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 10/20/2020] [Indexed: 05/10/2023]
Abstract
Animals exhibit a fascinating variety of skin patterns, but mechanisms underlying this diversity remain largely unknown, particularly for complex and camouflaged colorations. A mathematical model predicts that intricate color patterns can be formed by "pattern blending" between simple motifs via hybridization. Here, I analyzed the skin patterns of 18,114 fish species and found strong mechanistic associations between camouflaged labyrinthine patterns and simple spot motifs, showing remarkable consistency with the pattern blending hypothesis. Genomic analyses confirmed that the coloring on multiple labyrinthine fish species has originated from pattern blending by hybridization, and phylogenetic comparative analyses have further substantiated the pattern blending hypothesis in multiple major fish lineages. These findings provide a plausible mechanistic explanation for the characteristic diversity of animal markings and suggest a novel evolutionary process of complex and camouflaged colorations by means of pattern blending.
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Affiliation(s)
- Seita Miyazawa
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
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165
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Mitochondrial genomes of four American characins and phylogenetic relationships within the family Characidae (Teleostei: Characiformes). Gene 2020; 762:145041. [DOI: 10.1016/j.gene.2020.145041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/11/2020] [Accepted: 08/04/2020] [Indexed: 01/08/2023]
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166
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Weiss SJ, Gonçalves DV, Secci-Petretto G, Englmaier GK, Gomes-Dos-Santos A, Denys GPJ, Persat H, Antonov A, Hahn C, Taylor EB, Froufe E. Global systematic diversity, range distributions, conservation and taxonomic assessments of graylings (Teleostei: Salmonidae; Thymallus spp.). ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-020-00468-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
AbstractGraylings (Thymallus) are among the less well-studied groups of salmonid fishes, especially across their Asian distribution range. Here we perform a comprehensive global review of their phylogeography, systematic diversity and range distributions, including biogeographic reconstruction and assessment of both conservation and taxonomic status of each species. Based on a mitogenomic phylogenetic analysis, three approaches to the delineation of molecular operational units, and evaluation of 15 a-priori defined species, we provide biological support for the recognition of 13 grayling species, plus two additional species tentatively. Several instances of paraphyly and its potential effect on systematic inferences are discussed. Overall, the genus displays increasing species diversity and decreasing range size from higher to lower latitudes and ancestral trait reconstruction supports an East Asian origin for extant diversity, most likely centred in the Amur River drainage. Europe’s colonization by Thymallus took place as early as the late Miocene, at least two colonisations of North America are supported, and multiple dispersal events likely took place into Western Siberia. The conservation status for the 15 taxa was estimated to be: 6 least concern, 1 near-threatened, 2 vulnerable, 3 endangered and 3 data deficient.
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167
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Hughes LC, Ortí G, Saad H, Li C, White WT, Baldwin CC, Crandall KA, Arcila D, Betancur-R R. Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics. Mol Ecol Resour 2020; 21:816-833. [PMID: 33084200 DOI: 10.1111/1755-0998.13287] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 10/09/2020] [Indexed: 11/28/2022]
Abstract
Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogues that can mislead phylogenetic analysis. We present seven new probe sets for current target-capture phylogenomic protocols that capture 1,104 exons explicitly filtered for paralogues using gene trees. These seven probe sets span the diversity of teleost fishes, including four sets that target five hyperdiverse percomorph clades which together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + Pelagiaria combined). We additionally included probes to capture legacy nuclear exons and mitochondrial markers that have been commonly used in fish phylogenetics (despite some exons being flagged for paralogues) to facilitate integration of old and new molecular phylogenetic matrices. We tested these probes experimentally for 56 fish species (eight species per probe set) and merged new exon-capture sequence data into an existing data matrix of 1,104 exons and 300 ray-finned fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data from raw reads to alignments for downstream analysis. We show that legacy loci with known paralogues are at risk of assembling duplicated sequences with target-capture, but we also assembled many useful orthologous sequences that can be integrated with many PCR-generated matrices. These probe sets are a valuable resource for advancing fish phylogenomics because targeted exons can easily be extracted from increasingly available whole genome and transcriptome data sets, and also may be integrated with existing PCR-based exon and mitochondrial data.
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Affiliation(s)
- Lily C Hughes
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Computational Biology Institute, Milken Institute of Public Health, George Washington University, Washington, DC, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Guillermo Ortí
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Hadeel Saad
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | - Chenhong Li
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - William T White
- CSIRO Australian National Fish Collection, National Research Collections of Australia, Hobart, TAS, Australia
| | - Carole C Baldwin
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Keith A Crandall
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Computational Biology Institute, Milken Institute of Public Health, George Washington University, Washington, DC, USA
| | - Dahiana Arcila
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Sam Noble Oklahoma Museum of Natural History, Norman, OK, USA.,Department of Biology, University of Oklahoma, Norman, OK, USA
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168
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Yang L, Xu Z, Zeng H, Sun N, Wu B, Wang C, Bo J, Li L, Dong Y, He S. FishDB: an integrated functional genomics database for fishes. BMC Genomics 2020; 21:801. [PMID: 33203359 PMCID: PMC7670658 DOI: 10.1186/s12864-020-07159-9] [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] [Received: 11/18/2019] [Accepted: 10/19/2020] [Indexed: 11/29/2022] Open
Abstract
Background Hundreds of genomes and transcriptomes of fish species have been sequenced in recent years. However, fish scholarship currently lacks a comprehensive, integrated, and up-to-date collection of fish genomic data. Results Here we present FishDB, the first database for fish multi-level omics data, available online at http://fishdb.ihb.ac.cn. The database contains 233 fish genomes, 201 fish transcriptomes, 5841 fish mitochondrial genomes, 88 fish gene sets, 16,239 miRNAs of 65 fishes, 1,330,692 piRNAs and 4852 lncRNAs of Danio rerio, 59,040 Mb untranslated regions (UTR) of 230 fishes, and 31,918 Mb coding sequences (CDS) of 230 fishes. Among these, we newly generated a total of 11 fish genomes and 53 fish transcriptomes. Conclusions This release contains over 410,721.67 Mb sequences and provides search functionality, a BLAST server, JBrowse, and PrimerServer modules. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07159-9.
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Affiliation(s)
- Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zetan Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Honghui Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ning Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baosheng Wu
- University of Chinese Academy of Sciences, Beijing, 100049, China.,Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Cheng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Bo
- University of Chinese Academy of Sciences, Beijing, 100049, China.,Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Lin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. .,Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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169
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Duangjai S, Srisodsuk S, Chuaynkern C, Chuaynkern Y. Complete mitochondrial genome of Tropidophorus hangnam (Squamata: Scincidae) with phylogenetic analysis. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3701-3702. [PMID: 33367066 PMCID: PMC7655071 DOI: 10.1080/23802359.2020.1832928] [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: 11/25/2022]
Abstract
The complete mitochondrial genome (mitogenome) of Tropidophorus hangnam was sequenced from its paratype (GenBank accession no. MN977920). It was 16,777 bp in length with a base composition of 31.99% A, 29.49% C, 14.34% G, and 24.18% T, and a GC content of 43.83%. The genome includes 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region (D loop). Most T. hangnam genes are located on the H strand, except for the ND6 gene and eight tRNA genes, which are located on the L strand. Phylogenetic analyses based on 13 PCGs indicated that T. hangnam is sister to the clade composed of the genera Scincella and Sphenomorphus. The newly sequenced T. hangnam mitogenome will provide basic data for further studies on the genetic diversity and molecular phylogenetic relationships of the genus Tropidophorus.
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Affiliation(s)
- Sutee Duangjai
- Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Suttikarn Srisodsuk
- Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Chantip Chuaynkern
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Yodchaiy Chuaynkern
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
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170
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Lv W, Jiang H, Bo J, Wang C, Yang L, He S. Comparative mitochondrial genome analysis of Neodontobutis hainanensis and Perccottus glenii reveals conserved genome organization and phylogeny. Genomics 2020; 112:3862-3870. [DOI: 10.1016/j.ygeno.2020.06.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/14/2020] [Accepted: 06/22/2020] [Indexed: 10/23/2022]
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171
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Patel E, Bernard AM, Mehlrose M, Harned S, Finnegan KA, Fitzpatrick CK, Lea JS, Shivji MS. The complete mitochondrial genome of a gray reef shark, Carcharhinus amblyrhynchos (Carcharhiniformes: Carcharhinidae), from the Western Indian Ocean. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3498-3499. [PMID: 33458217 PMCID: PMC7782100 DOI: 10.1080/23802359.2020.1827064] [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
We present the mitochondrial genome sequence of a gray reef shark, Carcharhinus amblyrhynchos (Bleeker 1856), a coral reef associated species. This is the first mitogenome for this species from the western Indian Ocean. The mitogenome is 16,705 bp in length, has 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region, and demonstrates a gene arrangement congruent with other shark and most vertebrate species. This mitogenome provides a genomic resource for assisting with population, evolutionary and conservation studies for the gray reef shark, which is increasingly under threat from fisheries.
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Affiliation(s)
- Ela Patel
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, Florida, USA.,Trinity Preparatory School, Florida, USA
| | - Andrea M Bernard
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, Florida, USA
| | - Marissa Mehlrose
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, Florida, USA
| | - Sydney Harned
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, Florida, USA
| | - Kimberly A Finnegan
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, Florida, USA
| | - Cristín K Fitzpatrick
- State Fisheries Genomics Lab, Department of Fisheries and Wildlife, Oregon State University, Oregon, USA
| | - James S Lea
- Save Our Seas Foundation, Geneva, Switzerland.,Department of Zoology, University of Cambridge, Cambridge, UK
| | - Mahmood S Shivji
- Save Our Seas Foundation Shark Research Center, Nova Southeastern University, Florida, USA
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172
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Petean FF, Naylor GJP, Lima SMQ. Integrative taxonomy identifies a new stingray species of the genus Hypanus Rafinesque, 1818 (Dasyatidae, Myliobatiformes), from the Tropical Southwestern Atlantic. JOURNAL OF FISH BIOLOGY 2020; 97:1120-1142. [PMID: 32743805 DOI: 10.1111/jfb.14483] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/25/2020] [Accepted: 07/30/2020] [Indexed: 06/11/2023]
Abstract
An integrative approach by the congruence of genetics, morphology and ecological niche modelling (ENM) was used to delimit a new species of Hypanus (Rafinesque, 1818), a recently resurrected genus of marine stingrays comprising eight species, five of which occur in the western Atlantic. The species with the widest distribution, Hypanus americanus (Hildebrand and Schroeder, 1928), from the northeastern coast of the United States to southeastern Brazil, was demonstrated to be paraphyletic based on protein-coding mitochondrial genome analyses. This data set also indicates that the genetic distance between the new species Hypanus berthalutzae sp. nov. and its three closely related species (H. americanus, H. longus and H. rudis) varies from 0.82% to 3.14%. In addition, Bayesian Analysis of Population Similarity using the mitochondrial gene mt-nd2 supports the separation of H. berthalutzae sp. nov. (southwestern Atlantic) from its sister species H. rudis (eastern Atlantic). Similarly, morphological and morphometric analyses corroborated four morphotypes within the H. americanus species group and indicated the ventral caudal fold height and length and interspiracular and interorbital lengths as useful measurements to distinguish among them. Claspers of adult males also exhibit morphological differences among species. The ENM agreed with molecular and morphological analyses and delimits the distribution of H. berthalutzae sp. nov. to shallow areas close to shore along the Brazilian coast, from the mouth of the Amazon River to São Paulo State, including the northeastern oceanic islands, suggesting that the great outflow of fresh water and sediments and the Mid-Atlantic Ridge might act as barriers. The integration of these data to describe a new species provides information relevant to their conservation status, because all species of the H. americanus species group are under the "data-deficient" status.
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Affiliation(s)
- Flávia F Petean
- Laboratório de Ictiologia Sistemática e Evolutiva, Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Gavin J P Naylor
- Florida Program for Shark Research, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - Sergio M Q Lima
- Laboratório de Ictiologia Sistemática e Evolutiva, Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Brazil
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173
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Yang L, Feng C, Cai MM, Chen JH, Ding P. Complete chloroplast genome sequence of Amomum villosum and comparative analysis with other Zingiberaceae plants. CHINESE HERBAL MEDICINES 2020; 12:375-383. [PMID: 36120171 PMCID: PMC9476707 DOI: 10.1016/j.chmed.2020.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 05/24/2020] [Accepted: 05/31/2020] [Indexed: 10/28/2022] Open
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174
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Liu D, Zhang Y, Zhang M, Yang J, Tang W. Complete mitochondrial genome of Iniistius trivittatus and unique variation in two observed inserts between rRNA and tRNA genes in wrasses. BMC Evol Biol 2020; 20:125. [PMID: 32957913 PMCID: PMC7507615 DOI: 10.1186/s12862-020-01683-8] [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: 02/11/2019] [Accepted: 09/07/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The family Labridae made up of 519 species in the world. The functional evolution of the feeding-related jaws leaded to differentiation of species, and the pharyngeal jaw apparatus evolved independently, but evolutionary mechanism still remain unaddressed in wrasses. Mitogenomes data can be used to infer genetic diversification and investigate evolutionary history of wrasses, whereas only eight complete mitogenomes in this family have been sequenced to date. Here, we sequenced the complete mitogenomes of Iniistius trivittatus to investigate genetic differentiation among wrasse species. RESULTS We sequenced the complete mitogenomes of I. trivittatus using a novel PCR strategy. The I. trivittatus mitogenomes is 16,820 bp in length and includes 13 protein -coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region. Compared to eight known mitochondrial genome, 2 additional noncoding regions (lengths of 121 and 107 bp), or so-called inserts, are found in the intergenic regions 12S rRNA - tRNAVal - 16S rRNA. The presumed origin of the two rare inserts is from tRNA- related retrotransposons. Compared with cytochrome b gene, the two insert sequences are highly conserved at the intraspecies level, but they showed significant variation and low similarity (< 70%) at the interspecies level. The insert events were only observed in I. trivittatus by checking the phylogenetic trees based on the complete mitogenomes of Labrida species. This finding provides evidence that in the mitogenomes, retrotransposon inserts result in intraspecific homoplasmy and interspecific heteroplasmy by natural selection and adaptation to various environments. CONCLUSIONS This study found additional mitogenome inserts limited in wrasse species. The rRNA genes with inserts might have experienced a selective pressure for adaptation to feeding modes. Such knowledge can enable a better understanding of molecular mechanism underlying morphological evolution in wrasses.
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Affiliation(s)
- Dong Liu
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306 China
- Key Laboratory of Exploration and Utilization Aquatic Genetic Resources, Ministry of Education, Shanghai, 201306 China
- Shanghai Ocean University, National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306 China
| | - Yuanyuan Zhang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306 China
| | - Ming Zhang
- Department of Epidemiology and Biostatistics, University of Georgia, GA, 30602 USA
| | - Jinquan Yang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306 China
| | - Wenqiao Tang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306 China
- Key Laboratory of Exploration and Utilization Aquatic Genetic Resources, Ministry of Education, Shanghai, 201306 China
- Shanghai Ocean University, National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306 China
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175
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Balakirev ES, Kravchenko AY, Semenchenko AA. Genetic Evidence for a Mixed Composition of the Genus Myoxocephalus (Cottoidei: Cottidae) Necessitates Generic Realignment. Genes (Basel) 2020; 11:E1071. [PMID: 32933022 PMCID: PMC7564937 DOI: 10.3390/genes11091071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/22/2020] [Accepted: 09/09/2020] [Indexed: 11/16/2022] Open
Abstract
Sculpin fishes belonging to the family Cottidae represent a large and complex group, inhabiting a wide range of freshwater, brackish-water, and marine environments. Numerous studies based on analysis of their morphology and genetic makeup frequently provided controversial results. In the present work, we sequenced complete mitochondrial (mt) genomes and fragments of nuclear ribosomal DNA (rDNA) of the fourhorn sculpin Myoxocephalus quadricornis and some related cottids to increase the power of phylogenetic and taxonomic analyses of this complex fish group. A comparison of the My. quadricornis mt genomes obtained by us with other complete mt genomes available in GenBank has revealed a surprisingly low divergence (3.06 ± 0.12%) with Megalocottus platycephalus and, at the same time, a significantly higher divergence (7.89 ± 0.16%) with the species of the genus Myoxocephalus. Correspondingly, phylogenetic analyses have shown that My. quadricornis is clustered with Me. platycephalus but not with the Myoxocephalus species. Completely consistent patterns of divergence and tree topologies have been obtained based on nuclear rDNA. Thus, the multi-gene data in the present work indicates obvious contradictions in the relationships between the Myoxocephalus and Megalocottus species studied. An extensive phylogenetic analysis has provided evidence for a closer affinity of My. quadricornis with the species of the genus Megalocottus than with the species of the genus Myoxocephalus. A recombination analysis, along with the additional GenBank data, excludes introgression and/or incorrect taxonomic identification as the possible causative factors responsible for the observed closer affinity between the two species from different genera. The above facts necessitate realignment of the genera Myoxocephalus and Megalocottus. The genetic data supports the two recognized genera, Myoxocephalus and Megalocottus, but suggests changing their compositions through transferring My. quadricornis to the genus Megalocottus. The results of the present study resolve the relationships within a complex group of sculpin fishes and show a promising approach to phylogenetic systematics (as a key organizing principle in biodiversity research) for a better understanding of the taxonomy and evolution of fishes and for supplying relevant information to address various fish biodiversity conservation and management issues.
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Affiliation(s)
- Evgeniy S. Balakirev
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690041, Russia;
- School of Biomedicine, Far Eastern Federal University, Vladivostok 690950, Russia
| | - Alexandra Yu. Kravchenko
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690041, Russia;
- Laboratory of Ecology and Evolutionary Biology of Aquatic Organisms, School of Natural Sciences, Far Eastern Federal University, Vladivostok 690950, Russia;
| | - Alexander A. Semenchenko
- Laboratory of Ecology and Evolutionary Biology of Aquatic Organisms, School of Natural Sciences, Far Eastern Federal University, Vladivostok 690950, Russia;
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176
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Comprehensive whole genome survey analyses of male and female brown-spotted flathead fish Platycephalus sp.1. Genomics 2020; 112:4742-4748. [PMID: 32871221 DOI: 10.1016/j.ygeno.2020.08.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/14/2020] [Accepted: 08/25/2020] [Indexed: 01/20/2023]
Abstract
The flathead fish Platycephalus sp.1 is an ecologically and commercially important marine fish in the northwestern Pacific with notable sexual differences in growth and development. Yet the genomic data of this species is lacking. In the present study, whole genome sequencing of two individuals (one male and one female) of Platycephalus sp.1 were conducted to provide fundamental genomic information. The genome sizes were estimated to be 674.96 Mb (male) and 684.15 Mb (female) by using k-mer analyses. The heterozygosity and repeat ratios suggested possible male heterogamety of this species. The draft genome sequences were initially assembled and genome-wide microsatellite motifs were identified. Besides, the complete mitochondrial genome sequences were assembled and the phylogenetic analyses genetically supported the validation of Platycephalus sp.1. The reported genomic data and genetic markers in this study could be useful in future comparative genomics and evolutionary biology studies.
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177
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Bobier KE. The complete mitochondrial genome of the yellowfin shiner, Notropis lutipinnis. Mitochondrial DNA B Resour 2020; 5:3185-3187. [PMID: 33458105 PMCID: PMC7782857 DOI: 10.1080/23802359.2020.1809541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/01/2020] [Indexed: 11/22/2022] Open
Abstract
The complete mitochondrial genome of the yellowfin shiner (Notropis lutipinnis) 16,706 bp and contained 13 protein coding genes, 2 rRNAs, 22tRNAs, and one control region. The overall base composition was A (28.8%), T (27.0%), C (26.7%), G (17.5%). Phylogenetics analyses of N. Lutipinnis and 29 closely related species found discrepancies between genetic relationships and taxonomic delineations, highlighting the need for further studies of phylogenetic and biogeographic relationships among the closely related taxa of the subfamily Pogonichthyinae.
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Affiliation(s)
- Karen E. Bobier
- Department of Genetics, University of Georgia, Athens, Georgia
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178
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Porter TM, Hajibabaei M. Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00248] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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179
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Chung HH, Kamar CKA, Lim LWK, Roja JS, Liao Y, Lam TTY, Chong YL. Sequencing and characterization of complete mitogenome DNA of Rasbora tornieri (Cypriniformes: Cyprinidae: Rasbora) and its evolutionary significance. J Genet 2020. [DOI: 10.1007/s12041-020-01221-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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180
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Wilson RE, Sonsthagen SA, Smé N, Gharrett AJ, Majewski AR, Wedemeyer K, Nelson RJ, Talbot SL. Mitochondrial genome diversity and population mitogenomics of polar cod (Boreogadus saida) and Arctic dwelling gadoids. Polar Biol 2020. [DOI: 10.1007/s00300-020-02703-5] [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]
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181
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Jahari PNS, Abdul Malik NF, Shamsir MS, Gilbert MP, Mohd Salleh F. The first complete mitochondrial genome data of Hippocampus kuda originating from Malaysia. Data Brief 2020; 31:105721. [PMID: 32490085 PMCID: PMC7260291 DOI: 10.1016/j.dib.2020.105721] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 11/26/2022] Open
Abstract
The spotted seahorse, Hippocampus kuda population is exponentially decreasing globally due to habitat loss contributed by massive coastal urbanization as well as its large exploitation for Chinese herbal medicine. Genomic data would be highly useful to improve biomonitoring of seahorse populations in Malaysia via the usage of non-invasive approaches such as water environmental DNA. Here we report the first complete mitogenome of two H. kuda individuals originating from Malaysia, generated using BGISEQ-500RS sequencer. The lengths of both mitogenomes are 16,529bp, consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. The overall base composition was 32.46% for A, 29.40% for T, 14.73% for G and 23.41% for C with AT rich features (61.86%). The gene organization of Malaysian H. kuda were similar to that of most teleost species. A phylogenetic analysis of the genome against mtDNA data from other Hippocampus species showed that Malaysian H. kuda samples clustered with H. capensis, H. reidi and H. kuda. Notably however, analysis of the data using BLASTn revealed they had 99.18% similarity to H. capensis, and only 97.66% to H. kuda and H. reidi, which are all part of the unresolved H. kuda complex. The mitogenomes are deposited in Genbank under the accession number MT221436 (HK1) and MT221436 (HK2).
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Affiliation(s)
- Puteri Nur Syahzanani Jahari
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia
| | - Nur Fatihah Abdul Malik
- Johor Biotechnology & Biodiversity Corporation (J-Biotech), Level 2, Bio-XCell Malaysia, No. 2, Jalan Bioteknologi 1, SiLC Industrial Park, 79200 Iskandar Puteri, Johor, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, 84600 Muar, Johor, Malaysia
| | - M. Thomas P. Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5a, 1353, Copenhagen, Denmark
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia
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182
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Gamage CD, Sato Y, Kimura R, Yamashiro T, Toma C. Understanding leptospirosis eco-epidemiology by environmental DNA metabarcoding of irrigation water from two agro-ecological regions of Sri Lanka. PLoS Negl Trop Dis 2020; 14:e0008437. [PMID: 32701971 PMCID: PMC7377381 DOI: 10.1371/journal.pntd.0008437] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
Background Leptospirosis is one of the most significant zoonoses across the world not only because of its impact on human and animal health but also because of the economic and social impact on agrarian communities. Leptospirosis is endemic in Sri Lanka where paddy farming activities, the use of draught animals in agriculture, and peridomestic animals in urban and rural areas play important roles in maintaining the infection cycle of pathogenic Leptospira, especially concerning animals as a potential reservoir. In this study, an environmental DNA (eDNA) metabarcoding methodology was applied in two different agro-ecological regions of Sri Lanka to understand the eco-epidemiology of leptospirosis. Methodology/Principal findings Irrigation water samples were collected in Kandy District (wet zone mid-country region 2) and Girandurukotte, Badulla District (intermediate zone low-country region 2); and analysed for the presence of pathogenic Leptospira, associated microbiome and the potential reservoir animals. Briefly, we generated PCR products for high-throughput sequencing of multiple amplicons through next-generation sequencing. The analysis of eDNA showed different environmental microbiomes in both regions and a higher diversity of Leptospira species circulating in Kandy than in Girandurukotte. Moreover, the number of sequence reads of pathogenic Leptospira species associated with clinical cases such as L. interrogans was higher in Kandy than in Girandurukotte. Kandy also showed more animal species associated with pathogenic bacterial species than Girandurukotte. Finally, several pathogenic bacterial species including Arcobacter cryaerophilus, responsible for abortion in animals, was shown to be associated with pathogenic Leptospira. Conclusions/Significance Leptospirosis has been considered to be endemic in wet regions, consistently, leptospiral sequences were detected strongly in Kandy. The great Leptospira species diversity in Kandy observed in this study shows that the etiological agents of leptospirosis in Sri Lanka might be underestimated. Furthermore, our eDNA metabarcoding can be used to discriminate bacterial and animal species diversity in different regions and to explore environmental microbiomes to identify other associated bacterial pathogens in the environment. Leptospirosis is a widespread bacterial zoonosis with increasing importance due to its vast range of reservoir hosts. Early symptoms are shared by other infectious diseases common in tropical and sub-tropical regions, where the real burden and risk factors need to be known. In Sri Lanka, leptospirosis is mostly an occupational disease associated with freshwater or animal exposure in agriculture communities. Thus, there is a need for understanding the epidemiology of leptospirosis in agrarian regions of the country for developing better prevention and intervention strategies. In this study, we applied an environmental DNA metabarcoding methodology to understand the environmental microbiome, potential reservoir animals and the Leptospira species circulating in two different agro-ecological regions of Sri Lanka: Kandy (wet region mid-country region 2) and Girandurukotte (intermediate region low-country region 2). It is known that pathogenic Leptospira are excreted through the urine of reservoir animals in the environment, where they can persist in humid conditions. Congruently, this study showed a higher detection of pathogenic Leptospira in the environment of Kandy where the environmental microbiome showed a higher diversity than Girandurukotte. Potential animal reservoirs were also detected in samples positive for pathogenic Leptospira, suggesting that environmental DNA metabarcoding can provide important information for management and intervention strategies to control leptospirosis.
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Affiliation(s)
- Chandika D. Gamage
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Kandy, Sri Lanka
| | - Yukuto Sato
- Center for Strategic Research Project, Organization for Research Promotion, University of the Ryukyus, Nishihara, Okinawa, Japan
- * E-mail: (YS); (CT)
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Tetsu Yamashiro
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Claudia Toma
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
- * E-mail: (YS); (CT)
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183
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Zheng Y, Feng L, Liu H, Song R, Xu S, Shi H, Gao T. The complete mitochondrial genome of Hapalogenys analis (Perciformes, Haemulidea) except for control region, obtained by whole genome sequencing. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2807-2808. [PMID: 33457955 PMCID: PMC7782058 DOI: 10.1080/23802359.2020.1788463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
In this study, we obtained the complete mitochondrial genome of Hapalogenys analis using whole genome sequencing. With the exception for control region, this mitochondrial genome, consisting of 16,355 base pairs (bp), contains 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), and 21 transfer RNAs (tRNAs). This mitochondrial genome also lacks a tRNA-Pro gene after tRNA-Thr gene. The overall base composition shows 25.45% of T, 29.73% of C, 28.68% of A and 16.14% of G, with a slight A + T rich feature (54.13%). Sanger sequencing is needed to confirm the accuracy of control region, as well as the lack of tRNA-Pro gene. The mitogenome data provides useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis and conservation genetics.
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Affiliation(s)
- Yunya Zheng
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Linxiao Feng
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Haoyu Liu
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Riyu Song
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Shengyong Xu
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Huilai Shi
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang, China.,Zhejiang Province Key Lab of Mariculture and Enhancement, Marine Fisheries Research Institute of Zhejiang, Zhoushan, Zhejiang, China
| | - Tianxiang Gao
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
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184
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Carter JK, Innes P, Goebl AM, Johnson B, Gebert M, Attia Z, Gabani Z, Li R, Melie T, Dart C, Mares A, Greidanus C, Paterson J, Wall B, Cortese G, Thirouin K, Glime G, Rutten J, Poyd C, Post E, Wall B, Elhadi AA, Feldmann K, Danz A, Blanchard T, Amato S, Reinert S, Pogoda CS, Scordato ESC, Hund AK, Safran RJ, Kane NC. Complete mitochondrial genomes provide current refined phylogenomic hypotheses for relationships among ten Hirundo species. Mitochondrial DNA B Resour 2020; 5:2881-2885. [PMID: 33457987 PMCID: PMC7783031 DOI: 10.1080/23802359.2020.1790999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Hirundo is the most species-rich genus of the passerine swallow family (Hirundinidae) and has a cosmopolitan distribution. Here we report the complete, annotated mitochondrial genomes for 25 individuals from 10 of the 14 extant Hirundo species; these include representatives from four subspecies of the barn swallow, H. rustica. Mitogenomes were conserved in size, ranging from 18,500 to 18,700 base pairs. They all contained 13 protein-coding regions, 22 tRNAs, a control region, and large and small ribosomal subunits. Phylogenetic analysis resolved most of the relationships between the studied species and subspecies which were largely consistent with previously published trees. Several new relationships were observed within the phylogeny that could have only been discovered with the increased amount of genetic material. This study represents the largest Hirundo mitochondrial phylogeny to date, and could serve as a vital tool for other studies focusing on the evolution of the Hirundo genus.
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Affiliation(s)
- Javan K. Carter
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Peter Innes
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - April M. Goebl
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Benjamin Johnson
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Matthew Gebert
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Ziv Attia
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Zachariah Gabani
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Ruiqi Li
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Tina Melie
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Chiara Dart
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Ali Mares
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Chrisopher Greidanus
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Jaime Paterson
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Brianna Wall
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Gabriela Cortese
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Kevin Thirouin
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Gabrielle Glime
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Joseph Rutten
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Cameron Poyd
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Erin Post
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Brianna Wall
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Ahmed A. Elhadi
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Katherine Feldmann
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - August Danz
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Thomas Blanchard
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Samantha Amato
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Stephan Reinert
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Cloe S. Pogoda
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | | | - Amanda K. Hund
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
| | - Rebecca J. Safran
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
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185
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Liu K, Ma HJ, Feng XY, Xie N. Complete mitochondrial genome of the hybrid of Culter alburnus (♀) × Megalobrama terminalis (♂). Mitochondrial DNA B Resour 2020; 5:2316-2317. [PMID: 33457773 PMCID: PMC7782101 DOI: 10.1080/23802359.2020.1772690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we determined the complete mitochondrial DNA sequence of the hybrid of Culter alburnus (♀) x Megalobrama terminalis (♂) for the first time. The complete mitochondrial genome of the hybrid was sequenced to be 16,622 bp in size following the female parent, C. alburnus. The genome contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and two main non-coding regions (the control region and the origin of light strand replication). Sequence alignment between the mitochondrial genomes of the hybrid and its female parent showed that a total of 35 mutation sites were identified in 14 genes or regions. The genome information presented here may play an important role in further study on the genetic mechanisms of mitochondrial DNA in hybrids.
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Affiliation(s)
- Kai Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Heng-jia Ma
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Xiao-yu Feng
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
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186
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Freitas A, Carneiro J, Guimarães-Costa A, Schneider H, Sampaio I. The complete mitochondrial genome of Menticirrhus littoralis (Sciaenidae, Perciformes) and its phylogeny. Mitochondrial DNA B Resour 2020; 5:2286-2287. [PMID: 33367010 PMCID: PMC7510665 DOI: 10.1080/23802359.2020.1772681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/16/2020] [Indexed: 12/05/2022] Open
Abstract
We describe the mitochondrial genome of the Menticirrhus littoralis and infer the phylogenetic position of Menticirrhus in the family Sciaenidae. The genome contains 16,499 base pairs distributed in gene regions (13 protein-coding regions, 2 rRNAs and 22 tRNAs) and a control region (CR). Our phylogenetic analysis suggests, with strong statistical support, that Menticirrhus is a sister group of the other sciaenids.
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Affiliation(s)
- Adrianne Freitas
- Genomics and Systems Biology Center, Universidade Federal do Pará, Belém, Brazil
| | - Jeferson Carneiro
- Genomics and Systems Biology Center, Universidade Federal do Pará, Belém, Brazil
- Institute of Coastal Studies, Universidade Federal do Pará, Bragança, Brazil
| | | | - Horacio Schneider
- Genomics and Systems Biology Center, Universidade Federal do Pará, Belém, Brazil
- Institute of Coastal Studies, Universidade Federal do Pará, Bragança, Brazil
| | - Iracilda Sampaio
- Genomics and Systems Biology Center, Universidade Federal do Pará, Belém, Brazil
- Institute of Coastal Studies, Universidade Federal do Pará, Bragança, Brazil
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187
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Delaval A, Schwanck T, Kopp MEL, Hoarau G, Jones CS, Noble LR. The complete mitochondrial genome of the blue skate Dipturus batis. Mitochondrial DNA B Resour 2020; 5:2488-2489. [PMID: 33457838 PMCID: PMC7781903 DOI: 10.1080/23802359.2020.1778572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
The complete mitochondrial genome of the blue skate Dipturus batis is described from shotgun sequencing on an Illumina next-generation sequencing platform. We report a 16,911 bp long sequence similar in size to other members of the genus, containing 13 protein-coding regions, 22 tRNA genes, 2 rRNA genes, and 2 non-coding areas. Phylogenetic analysis was performed using the complete mitochondrial genomes of 17 related species, placing D. batis within the Rajini tribe of the Rajidae family, consistent with current taxonomy. The new resource adds to a growing database of rajid mitogenomes which will help resolve phylogenetic relationships within the family.
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Affiliation(s)
- Aurélien Delaval
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Tanja Schwanck
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | | | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Leslie R Noble
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
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188
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Tan H, Yang Y, Zhang M, Chen X. The complete mitochondrial genome of Rhinogobius duospilus (Gobiidae: Gobionellinae). Mitochondrial DNA B Resour 2020; 5:3406-3407. [PMID: 33458187 PMCID: PMC7781900 DOI: 10.1080/23802359.2020.1823279] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Rhinogobius duospilus is a small freshwater fish with brilliant color in southern China, belonging to the subfamily Gobionellinae. In this study, the complete mitochondrial genome of 16,496 bp from R. duospilus was reported for the first time. It composed of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 non-coding genes. Phylogenetic tree showed that R. duospilus formed a separate lineage. The findings here would be helpful to further researches of R. duospilus.
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Affiliation(s)
- Hongyu Tan
- Guangxi Colleges and Universities Key Laboratory of Aquatic Healthy Breeding and Nutrition Regulation, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Yanyan Yang
- Guangxi Colleges and Universities Key Laboratory of Aquatic Healthy Breeding and Nutrition Regulation, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Man Zhang
- School of Marine Sciences, Guangxi University, Nanning, Guangxi, China
| | - Xiuli Chen
- Guangxi Academy of Fishery Sciences, Nanning, Guangxi, China
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189
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Li Z, Li M, Xu S, Liu L, Chen Z, Zou K. Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations. Int J Mol Sci 2020; 21:E4685. [PMID: 32630142 PMCID: PMC7370159 DOI: 10.3390/ijms21134685] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 12/31/2022] Open
Abstract
Carangidae are ecologically and economically important marine fish. The complete mitogenomes of three Carangidae species (Alectis indicus, Decapterus tabl, and Alepes djedaba) were sequenced, characterized, and compared with 29 other species of the family Carangidae in this study. The length of the three mitogenomes ranged from 16,530 to 16,610 bp, and the structures included 2 rRNA genes (12S rRNA and 16S rRNA), 1 control region (a non-coding region), 13 protein-coding genes, and 22 tRNA genes. Among the 22 tRNA genes, only tRNA-Ser (GCT) was not folded into a typical cloverleaf secondary structure and had no recognizable DHU stem. The full-length sequences and protein-coding genes (PCGs) of the mitogenomes of the three species all had obvious AT biases. The majority of the AT-skew and GC-skew values of the PCGs among the three species were negative, demonstrating bases T and C were more plentiful than A and G. Analyses of Ka/Ks and overall p-genetic distance demonstrated that ATP8 showed the highest evolutionary rate and COXI/COXII were the most conserved genes in the three species. The phylogenetic tree based on PCGs sequences of mitogenomes using maximum likelihood and Bayesian inference analyses showed that three clades were divided corresponding to the subfamilies Caranginae, Naucratinae, and Trachinotinae. The monophyly of each superfamily was generally well supported. The divergence time analyses showed that Carangidae evolved during three geological periods, the Cretaceous, Paleogene, and Neogene. A. indicus began to differentiate from other species about 27.20 million years ago (Mya) in the early Miocene, while D. tabl (21.25 Mya) and A. djedaba (14.67 Mya) differentiated in the middle Oligocene.
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Affiliation(s)
- Zhenhai Li
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agriculture University, Guangzhou 510642, China; (Z.L.); (L.L.)
| | - Min Li
- Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (M.L.); (S.X.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Shannan Xu
- Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (M.L.); (S.X.)
| | - Li Liu
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agriculture University, Guangzhou 510642, China; (Z.L.); (L.L.)
| | - Zuozhi Chen
- Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; (M.L.); (S.X.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Keshu Zou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agriculture University, Guangzhou 510642, China; (Z.L.); (L.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agriculture University, Guangzhou 510642, China
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190
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Ji D, Sun Z, Song N, Gao T, Xu S. The complete mitochondrial genome of Jaydia lineata (Perciformes, Apogonidae) obtained by next-generation sequencing. MITOCHONDRIAL DNA PART B 2020. [DOI: 10.1080/23802359.2020.1780970] [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)
- Dongping Ji
- Agricultural Machinery Service Center of Fangchenggang, Fangchenggang, China
| | - Zhicheng Sun
- Fisheries College, Ocean University of China, Qingdao, China
| | - Na Song
- Fisheries College, Ocean University of China, Qingdao, China
| | - Tianxiang Gao
- Fisheries College, Zhejiang Ocean University, Zhoushan, China
| | - Shengyong Xu
- Fisheries College, Zhejiang Ocean University, Zhoushan, China
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191
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Ji D, Liang J, Li P, Gao T, Xu S. The complete mitochondrial genome of Hexagrammos agrammus (Scorpaeniformes: Hexagrammidae) by next-generation sequencing. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2509-2511. [PMID: 33457844 PMCID: PMC7782902 DOI: 10.1080/23802359.2020.1780971] [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: 11/15/2022]
Abstract
The complete mitochondrial genome of the Hexagrammos agrammus is presented in this study. The mitochondrial genome is 16,512 bp long and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. The gene order and composition were similar to those of most other vertebrates. The nucleotide compositions of the heavy strand are 17.27% of G, 26.10% of T, 26.85% of A, and 29.78% of C. With the exception of the NADH dehydrogenase subunit 6 (ND6) and 8 tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The phylogenetic analysis by neighbour-joining (NJ) method showed that H. agrammus has the closer relationship with Hexagrammos otakii and Hexagrammos lagocephalus in the phylogenetic relationship.
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Affiliation(s)
- Dongping Ji
- Agricultural Machinery Service Center of Fangchenggang, Fangchenggang, Guangxi, China
| | - Jun Liang
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Zhoushan, Zhejiang, China
| | - Pengfei Li
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Zhoushan, Zhejiang, China
| | - Tianxiang Gao
- Key Laboratory of Sustainable Utilization of Technology Research for Fishery Resource of Zhejiang Province, Zhoushan, Zhejiang, China.,Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, P.R. China
| | - Shengyong Xu
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, P.R. China
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192
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Osborne MJ, Cameron AC, Fitzgerald BP, McKitrick SA, Paulk MR, Turner TF. The complete mitochondrial genomes of three imperiled cyprinid fishes Bonytail ( Gila elegans), Rio Grande Silvery Minnow ( Hybognathus amarus) and Loach Minnow ( Tiaroga cobitis). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2368-2370. [PMID: 33457794 PMCID: PMC7782156 DOI: 10.1080/23802359.2020.1774435] [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: 12/01/2022]
Abstract
Gila elegans, Hybognathus amarus, and Tiaroga cobitis (Family Cyprinidae, Order Cypriniformes) are endemic and endangered fishes in the southwestern United States. We present complete mitochondrial genomes for each species. Each mitochondrion consisted of 13 protein-coding genes, 2 ribosomal (rRNA) genes, 22 transfer RNA (tRNA) genes, and a single control region (D-loop), and gene order was consistent with other cyprinid fishes. Total genome lengths were 16,593 base pairs (bp) for G. elegans, 16,705 bp for H. amarus, and 16,802 for T. cobitis. The GC content in G. elegans and H. amarus was 44%, but higher in T. cobitis at 48%. Phylogenetic trees were generated to confirm relationships inferred via novel mitogenomes, and best-supported trees were consistent with previous research.
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Affiliation(s)
- Megan J Osborne
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Alexander C Cameron
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Brian P Fitzgerald
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Samuel A McKitrick
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Madison R Paulk
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Thomas F Turner
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
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193
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Cao M, Tang L, Chen J, Zhang X, Easy RH, You P. The mitogenome of freshwater loach Homatula laxiclathra (Teleostei: Nemacheilidae) with phylogenetic analysis of Nemacheilidae. Ecol Evol 2020; 10:5990-6000. [PMID: 32607206 PMCID: PMC7319148 DOI: 10.1002/ece3.6338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 11/11/2022] Open
Abstract
The complete mitogenome can provide valuable genetic information to reconstruct relationships between species. In this study, we sequenced a stone loach, Homatula laxiclathra (Teleostei: Nemacheilidae), which is found in the northern region of the Qinling Mountains in China. The size of the H. laxiclathra mitogenome is 16,570 bp, which contains 37 typical mitochondrial genes including 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a control region (D-loop) with a total AT content of 55.8%. This is similar to other Nemacheilidae sequences published in GenBank. Furthermore, a mito-phylogenomic analysis of 46 Nemacheilidae species places H. laxiclathra in a robust monophyletic Homatula cluster with other Homatula species. Our results contribute toward a better understanding of a true phylogeny of these species based on large-scale taxonomic samplings as well as to help grasp the evolution of fish mitogenomes.
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Affiliation(s)
- Mengfei Cao
- School of Life SciencesShaanxi Normal UniversityXi'anChina
| | - Ling Tang
- School of Life SciencesShaanxi Normal UniversityXi'anChina
| | - Juan Chen
- School of Life SciencesShaanxi Normal UniversityXi'anChina
| | - Xiaoyu Zhang
- School of Life SciencesShaanxi Normal UniversityXi'anChina
| | | | - Ping You
- School of Life SciencesShaanxi Normal UniversityXi'anChina
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194
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Wiley G, Miller MJ. A Highly Contiguous Genome for the Golden-Fronted Woodpecker ( Melanerpes aurifrons) via Hybrid Oxford Nanopore and Short Read Assembly. G3 (BETHESDA, MD.) 2020; 10:1829-1836. [PMID: 32317270 PMCID: PMC7263694 DOI: 10.1534/g3.120.401059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/17/2020] [Indexed: 12/31/2022]
Abstract
Woodpeckers are found in nearly every part of the world and have been important for studies of biogeography, phylogeography, and macroecology. Woodpecker hybrid zones are often studied to understand the dynamics of introgression between bird species. Notably, woodpeckers are gaining attention for their enriched levels of transposable elements (TEs) relative to most other birds. This enrichment of TEs may have substantial effects on molecular evolution. However, comparative studies of woodpecker genomes are hindered by the fact that no high-contiguity genome exists for any woodpecker species. Using hybrid assembly methods combining long-read Oxford Nanopore and short-read Illumina sequencing data, we generated a highly contiguous genome assembly for the Golden-fronted Woodpecker (Melanerpes aurifrons). The final assembly is 1.31 Gb and comprises 441 contigs plus a full mitochondrial genome. Half of the assembly is represented by 28 contigs (contig L50), each of these contigs is at least 16 Mb in size (contig N50). High recovery (92.6%) of bird-specific BUSCO genes suggests our assembly is both relatively complete and relatively accurate. Over a quarter (25.8%) of the genome consists of repetitive elements, with 287 Mb (21.9%) of those elements assignable to the CR1 superfamily of transposable elements, the highest proportion of CR1 repeats reported for any bird genome to date. Our assembly should improve comparative studies of molecular evolution and genomics in woodpeckers and allies. Additionally, the sequencing and bioinformatic resources used to generate this assembly were relatively low-cost and should provide a direction for development of high-quality genomes for studies of animal biodiversity.
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Affiliation(s)
- Graham Wiley
- Clinical Genomics Center, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma and
| | - Matthew J Miller
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, Oklahoma
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195
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Mitochondrial genome to aid species delimitation and effective conservation of the Sharpnose Guitarfish (Glaucostegus granulatus). Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100648] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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196
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The first complete mitochondrial genome sequence of the endangered mountain anoa (Bubalus quarlesi) (Artiodactyla: Bovidae) and phylogenetic analysis. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2020. [DOI: 10.1016/j.japb.2020.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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197
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Greiner S, Lehwark P, Bock R. OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res 2020; 47:W59-W64. [PMID: 30949694 PMCID: PMC6602502 DOI: 10.1093/nar/gkz238] [Citation(s) in RCA: 982] [Impact Index Per Article: 245.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/18/2019] [Accepted: 03/25/2019] [Indexed: 11/12/2022] Open
Abstract
Organellar (plastid and mitochondrial) genomes play an important role in resolving phylogenetic relationships, and next-generation sequencing technologies have led to a burst in their availability. The ongoing massive sequencing efforts require software tools for routine assembly and annotation of organellar genomes as well as their display as physical maps. OrganellarGenomeDRAW (OGDRAW) has become the standard tool to draw graphical maps of plastid and mitochondrial genomes. Here, we present a new version of OGDRAW equipped with a new front end. Besides several new features, OGDRAW now has access to a local copy of the organelle genome database of the NCBI RefSeq project. Together with batch processing of (multi-)GenBank files, this enables the user to easily visualize large sets of organellar genomes spanning entire taxonomic clades. The new OGDRAW server can be accessed at https://chlorobox.mpimp-golm.mpg.de/OGDraw.html.
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Affiliation(s)
- Stephan Greiner
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Pascal Lehwark
- Die Freiraum.Company Web & Code UG, Glogauer Straße 31, D-10999 Berlin, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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198
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Dunn N, Johri S, Curnick D, Carbone C, Dinsdale EA, Chapple TK, Block BA, Savolainen V. Complete mitochondrial genome of the gray reef shark, Carcharhinus amblyrhynchos (Carcharhiniformes: Carcharhinidae). Mitochondrial DNA B Resour 2020; 5:2080-2082. [PMID: 33457750 PMCID: PMC7782339 DOI: 10.1080/23802359.2020.1765208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report the first mitochondrial genome sequences for the gray reef shark, Carcharhinus amblyrhynchos. Two specimens from the British Indian Ocean Territory were sequenced independently using two different next generation sequencing methods, namely short read sequencing on the Illumina HiSeq and long read sequencing on the Oxford Nanopore Technologies’ MinION sequencer. The two sequences are 99.9% identical and are 16,705 base pairs (bp) and 16,706 bp in length. The mitogenome contains 22 tRNA genes, two rRNA genes, 13 protein-coding genes and two non-coding regions; the control region and the origin of light-strand replication (OL).
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Affiliation(s)
- Nicholas Dunn
- Institute of Zoology, Zoological Society of London, London, UK.,Department of Life Sciences, Imperial College London, Ascot, UK
| | - Shaili Johri
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA.,Department of Biology, San Diego State University, San Diego, CA, USA
| | - David Curnick
- Institute of Zoology, Zoological Society of London, London, UK
| | - Chris Carbone
- Institute of Zoology, Zoological Society of London, London, UK
| | | | - Taylor K Chapple
- Coastal Oregon Marine Experiment Station, Oregon State University, Newport, OR, USA
| | - Barbara A Block
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
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199
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Donath A, Jühling F, Al-Arab M, Bernhart SH, Reinhardt F, Stadler PF, Middendorf M, Bernt M. Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes. Nucleic Acids Res 2020; 47:10543-10552. [PMID: 31584075 PMCID: PMC6847864 DOI: 10.1093/nar/gkz833] [Citation(s) in RCA: 240] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 08/30/2019] [Accepted: 09/29/2019] [Indexed: 11/13/2022] Open
Abstract
With the rapid increase of sequenced metazoan mitochondrial genomes, a detailed manual annotation is becoming more and more infeasible. While it is easy to identify the approximate location of protein-coding genes within mitogenomes, the peculiar processing of mitochondrial transcripts, however, makes the determination of precise gene boundaries a surprisingly difficult problem. We have analyzed the properties of annotated start and stop codon positions in detail, and use the inferred patterns to devise a new method for predicting gene boundaries in de novo annotations. Our method benefits from empirically observed prevalances of start/stop codons and gene lengths, and considers the dependence of these features on variations of genetic codes. Albeit not being perfect, our new approach yields a drastic improvement in the accuracy of gene boundaries and upgrades the mitochondrial genome annotation server MITOS to an even more sophisticated tool for fully automatic annotation of metazoan mitochondrial genomes.
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Affiliation(s)
- Alexander Donath
- Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander Koenig (ZFMK), Adenauerallee 160, D-53113 Bonn, Germany
| | - Frank Jühling
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, 3 Rue Koeberlé, F-67000 Strasbourg, France.,Université de Strasbourg, 4 Rue Blaise Pascal, F-67081 Strasbourg, France
| | - Marwa Al-Arab
- Bioinformatics, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.,Doctoral School of Science and Technology, AZM Center for Biotechnology Research, Lebanese University, Tripoli, Lebanon
| | - Stephan H Bernhart
- Bioinformatics, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
| | - Franziska Reinhardt
- Bioinformatics, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.,Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, German Centre for Integrative Biodiversity Research (iDiv), and Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany.,Fraunhofer Institut for Cell Therapy and Immunology, Perlickstraße 1, D-04103 Leipzig, Germany.,Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.,Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Martin Middendorf
- Swarm Intelligence and Complex Systems, Department of Computer Science, Universität Leipzig, Augustusplatz 10, D-04109 Leipzig, Germany
| | - Matthias Bernt
- Swarm Intelligence and Complex Systems, Department of Computer Science, Universität Leipzig, Augustusplatz 10, D-04109 Leipzig, Germany.,Helmholtz Centre for Environmental Research - UFZ, Young Investigators Group Bioinformatics and Transcriptomics Permoserstraße 15, D-04318 Leipzig, Germany
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200
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Wang Y, Li Z, Li Y, Jiang J, Ouyang G, Liu S, Liu HY, Xiong F. Complete mitochondrial genome of Lepturichthys fimbriata and phylogenetic analysis of family Balitoridae. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1732846] [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)
- Ying Wang
- School of Life Sciences, Jianghan University, Wuhan, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Jianghan University, Wuhan, China
| | - Zhaoyang Li
- School of Life Sciences, Jianghan University, Wuhan, China
| | - Yihuan Li
- School of Life Sciences, Jianghan University, Wuhan, China
| | - Junchao Jiang
- School of Life Sciences, Jianghan University, Wuhan, China
| | - Guolei Ouyang
- School of Life Sciences, Jianghan University, Wuhan, China
| | - Shijin Liu
- School of Life Sciences, Jianghan University, Wuhan, China
| | - Hong-yan Liu
- School of Life Sciences, Jianghan University, Wuhan, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Jianghan University, Wuhan, China
| | - Fei Xiong
- School of Life Sciences, Jianghan University, Wuhan, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Jianghan University, Wuhan, China
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