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Das G, Das SP, Sahoo L, Swain SK, Raghavendra CH, Sahoo SK, Jayasankar P, Sundaray JK, Das P. High Genetic Differentiation and Genetic Diversity in Endangered Mahseer Tor khudree (Sykes, 1839) as Revealed from Concatenated ATPase 6/8 and Cyt b Mitochondrial Genes. Biochem Genet 2024:10.1007/s10528-023-10623-2. [PMID: 38231360 DOI: 10.1007/s10528-023-10623-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 12/06/2023] [Indexed: 01/18/2024]
Abstract
The Deccan mahseer, Tor khudree (Sykes 1839), belonging to family Cyprinidae is an important food and a game fish distributed in peninsular India. Due to overfishing and habitat destruction, the species is declared endangered and placed on the IUCN red list. Therefore, a well-designed conservation program may be essential to get this species protected in its natural habitat. We used a total of 152 samples from four rivers of peninsular India to assess the genetic diversity and structure of the mahseer using concatenated sequences of two mitochondrial genes, ATPase 6/8 (790 bp) and Cyt b (1000 bp). High haplotypic diversity was seen with 44 haplotypes. Individual gene wise haplotypes included 10 and 21 haplotypes for ATPase6/8 and Cyt b, respectively. AMOVA revealed most of the genetic variations (71.02%) to be within the populations. Significant genetic differentiation was observed between all population pairs, with FST values ranging from 0.121 to 0.372, with minimum between Tunga and Tungabhadra population and maximum between Tunga and Periyar population. Haplotype network showed one ancestral haplotype (TKACH04). Significant negative Fu's F and unimodal mismatch distribution suggested recent demographic expansion. The results of the present study would serve as a useful resource for further research on population genetics and conservation programs of the species.
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Affiliation(s)
- Gargee Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | | | - Lakshman Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Subrat Kumar Swain
- Institute of Medical Sciences & SUM Hospital, Siksha O Anusandhan University, Bhubaneswar, India
| | | | - Sangram Ketan Sahoo
- Aquaculture Production and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Pallipuram Jayasankar
- Department of Marine Biotechnology, Fish Nutrition and Health, ICAR-Central Marine Fisheries Research Institute, Kochi, India
| | - Jitendra Kumar Sundaray
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Paramananda Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India.
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Phan GH, Lam TTH, Dinh QM, Nguyen THD. Phylogenics of the genus Glossogobius in the Mekong Delta based on the mitochondrial cytochrome b ( cytb) gene. Heliyon 2023; 9:e16106. [PMID: 37215891 PMCID: PMC10199184 DOI: 10.1016/j.heliyon.2023.e16106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023] Open
Abstract
The Glossogobius species play an essential role in food supply and are distributed widely from the marine to freshwater, especially in the Mekong Delta, Vietnam (VMD). Some of their morphometrics and meristics are observed to vary with species and sampling sites. Therefore, the present study aims to verify if their mitochondrial Cytochrome b (Cytb) gene, one of the popular gene sequences used in fish phylogenic variation assessment, varies with species and sampling sites in the VMD. The Cytb gene size was 1300 bp for GcytbH/GcytbL primer pair and 1045 bp for GluMuq1-F/Mixcyto937-2R. The genetic distances within and among these three fish species groups were 0-11%. The Cytb gene sequences' similarity between this study and the NCBI database was 85.84-100%. The Glossogobius specimens were observed to disperse in small branches of the phylogenetic tree with a low K2P value, suggesting that the Cytb genetic diversity may be low among species.
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Affiliation(s)
- Gieo Hoang Phan
- Department of Molecular Biotechnology, Institute of Food and Biotechnology, Can Tho University, Xuan Khanh Ward, Ninh Kieu District, Can Tho, 900000, Viet Nam
- Kien Giang University, Minh Luong Town, Chau Thanh District, Kien Giang, 920000, Viet Nam
| | - Tran Thi Huyen Lam
- Department of Molecular Biotechnology, Institute of Food and Biotechnology, Can Tho University, Xuan Khanh Ward, Ninh Kieu District, Can Tho, 900000, Viet Nam
- Institute of High Quality Biotechnology - Food Technology, Cuu Long University, National Road 1A, Phu Quoi Ward, Long Ho District, Vinh Long, 850000, Viet Nam
| | - Quang Minh Dinh
- Department of Biology, School of Education, Can Tho University, Xuan Khanh Ward, Ninh Kieu District, Can Tho, 900000, Viet Nam
| | - Ton Huu Duc Nguyen
- Department of Biology, School of Education, Can Tho University, Xuan Khanh Ward, Ninh Kieu District, Can Tho, 900000, Viet Nam
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Davidović S, Marinković S, Kukobat M, Mihajlović M, Tanasić V, Hribšek I, Tanasković M, Stamenković-Radak M. Genetic Diversity Analysis of Mitochondrial Cytb Gene, Phylogeny and Phylogeography of Protected Griffon Vulture (Gyps fulvus) from Serbia. Life (Basel) 2022; 12:life12020164. [PMID: 35207453 PMCID: PMC8880743 DOI: 10.3390/life12020164] [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: 12/27/2021] [Revised: 01/13/2022] [Accepted: 01/19/2022] [Indexed: 11/16/2022] Open
Abstract
Once a widespread and common species across the region of southeast Europe, the Griffon vulture is now confined to small and isolated populations across the Balkan Peninsula. The population from Serbia with 290 couples represents its biggest and most viable population that can serve as an important reservoir of genetic diversity from which the birds can be used for the region’s reintroduction or recolonization programs. To estimate the level of genetic diversity, the mitochondrial Cytb gene from 58 unrelated birds sampled during the marking in the nests was sequenced and compared to the homologous Griffon vulture sequences available in publicly accessible online databases. Phylogeographic analysis based on Cytb sequences showed that the most frequent haplotype is found in all Griffon vulture populations and that each population possesses private haplotypes. Our data suggest that the Griffon vulture population from Serbia should be used as a source population for restocking and reintroduction programs in the region. The observed genetic differentiation between the populations from the Iberian and Balkan Peninsulas suggest that the introduction of foreign birds from remote populations should be avoided and that birds from indigenous or neighboring populations, if available, should be used instead.
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Affiliation(s)
- Slobodan Davidović
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (M.T.); (M.S.-R.)
- Correspondence:
| | - Saša Marinković
- Department of Ecology, Institute for Biological Research “Siniša Stanković”—National Institute of Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia;
| | - Mila Kukobat
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia;
| | - Milica Mihajlović
- Center for Forensic and Applied Molecular Genetics, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (M.M.); (V.T.)
| | - Vanja Tanasić
- Center for Forensic and Applied Molecular Genetics, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (M.M.); (V.T.)
| | - Irena Hribšek
- Birds of Prey Protection Foundation, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia;
| | - Marija Tanasković
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (M.T.); (M.S.-R.)
| | - Marina Stamenković-Radak
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (M.T.); (M.S.-R.)
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia;
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Skorupski J. Characterisation of the Complete Mitochondrial Genome of Critically Endangered Mustela lutreola (Carnivora: Mustelidae) and Its Phylogenetic and Conservation Implications. Genes (Basel) 2022; 13:genes13010125. [PMID: 35052465 PMCID: PMC8774856 DOI: 10.3390/genes13010125] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/28/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023] Open
Abstract
In this paper, a complete mitochondrial genome of the critically endangered European mink Mustela lutreola L., 1761 is reported. The mitogenome was 16,504 bp in length and encoded the typical 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes, and harboured a putative control region. The A+T content of the entire genome was 60.06% (A > T > C > G), and the AT-skew and GC-skew were 0.093 and −0.308, respectively. The encoding-strand identity of genes and their order were consistent with a collinear gene order characteristic for vertebrate mitogenomes. The start codons of all protein-coding genes were the typical ATN. In eight cases, they were ended by complete stop codons, while five had incomplete termination codons (TA or T). All tRNAs had a typical cloverleaf secondary structure, except tRNASer(AGC) and tRNALys, which lacked the DHU stem and had reduced DHU loop, respectively. Both rRNAs were capable of folding into complex secondary structures, containing unmatched base pairs. Eighty-one single nucleotide variants (substitutions and indels) were identified. Comparative interspecies analyses confirmed the close phylogenetic relationship of the European mink to the so-called ferret group, clustering the European polecat, the steppe polecat and the black-footed ferret. The obtained results are expected to provide useful molecular data, informing and supporting effective conservation measures to save M. lutreola.
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Affiliation(s)
- Jakub Skorupski
- Institute of Marine and Environmental Sciences, University of Szczecin, Adama Mickiewicza 16 St., 70-383 Szczecin, Poland; ; Tel.: +48-91-444-16-85
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
- The European Mink Centre, 71-415 Szczecin, Poland
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5
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Mitochondrial DNA based diversity studies reveal distinct and sub-structured populations of pearlspot, Etroplus suratensis (Bloch, 1790) in Indian waters. J Genet 2022. [DOI: 10.1007/s12041-021-01341-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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6
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SriHari M, Abidi ZJ, Ayyathurai K. Lack of genetic differentiation in milkfish, Chanos chanos (Forsskål, 1775), revealed by mitochondrial ATPase 6/8 genes. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:511-516. [PMID: 30836041 DOI: 10.1080/24701394.2019.1568425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The milkfish, Chanos chanos, is a commercially important cultured species which is distributed throughout south and southeast Asian countries. Captive breeding and seed production techniques have been standardized recently in India and there is a need for analyzing its population structure along the Indian coast. A total of 80 samples from four different locations across the Indian coast were analyzed by using ATPase 6/8 genes. Analysis revealed the existence of 25 haplotypes across populations with the haplotype diversity in the range of 0.5684-0.8053 and the nucleotide diversity varied from 0.001838 to 0.002519. The variation within and among populations accounted for 97.43% and 2.75%, respectively. The observed FST values were found to be non-significant (p > 0.05). Results from this study indicated that there is lack of genetic divergence between the populations of milkfish along the Indian coast.
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Affiliation(s)
- Murugesan SriHari
- a Department of Fisheries Resource Management, ICAR-Central Institute of Fisheries Education , Mumbai , India
| | - Zeba Jaffer Abidi
- a Department of Fisheries Resource Management, ICAR-Central Institute of Fisheries Education , Mumbai , India
| | - Kathirvelpandian Ayyathurai
- b Peninsular and Marine Fish Genetic Resources Centre , ICAR - National Bureau of Fish Genetic Resources , Cochin , India
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Vernygora OV, Davis CS, Murray AM, Sperling FAH. Delimitation of Alosa species (Teleostei: Clupeiformes) from the Sea of Azov: integrating morphological and molecular approaches. JOURNAL OF FISH BIOLOGY 2018; 93:1216-1228. [PMID: 30367487 DOI: 10.1111/jfb.13847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 10/22/2018] [Indexed: 06/08/2023]
Abstract
Shads of the genus Alosa are essential to commercial fisheries across North America and Europe, but in some areas their species boundaries remain controversial. Traditional morphology-based taxonomy of Alosa spp. has relied heavily on the number of gill rakers and body proportions, but these can be highly variable. We use mitochondrial (mt)DNA (coI and cytb) and genome-wide single nucleotide polymorphisms (SNP) along with morphological characters to assess differentiation among endemic Ponto-Caspian shads in the Sea of Azov. Morphological species assignments based on gill-raker number were not congruent with genetic lineages shown by mtDNA and SNPs. Iterative analysis revealed that genetic lineages were associated with sampling location and several other morphometric traits (caudal peduncle depth, pre-anal length and head length). Phylogenetic analysis of the genus placed Ponto-Caspian Alosa spp. in the same evolutionary lineage as endangered Alosa spp. endemic to Greece, highlighting the importance of these findings to conservation management. We conclude that gill-raker number is not reliable for delimiting species of Alosa. This taxonomic uncertainty should be addressed by examining type material to provide a robust integrative classification for these commercially important fishes.
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Affiliation(s)
- Oksana V Vernygora
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Corey S Davis
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Alison M Murray
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
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8
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Sharma L, Ali S, Barat A, Kumar R, Pande V, Laskar MA, Sahoo PK, Sumer S. Molecular identification and genetic diversity analysis of Chocolate mahseer (Neolissochilus hexagonolepis) populations of Northeast India, using mitochondrial DNA markers. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:397-406. [DOI: 10.1080/24701394.2018.1526929] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Lata Sharma
- ICAR-Directorate of Coldwater Fisheries Research, Nainital, India
| | - Shahnawaz Ali
- ICAR-Directorate of Coldwater Fisheries Research, Nainital, India
| | - Ashoktaru Barat
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, India
| | - Rohit Kumar
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Nainital, India
| | | | - Prabhati K. Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, India
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9
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Yacoub HA, Sadek MA, Uversky VN. On the potential of using peculiarities of the protein intrinsic disorder distribution in mitochondrial cytochrome b to identify the source of animal meats. INTRINSICALLY DISORDERED PROTEINS 2017; 5:e1264350. [PMID: 28331777 PMCID: PMC5351768 DOI: 10.1080/21690707.2016.1264350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/17/2016] [Accepted: 11/19/2016] [Indexed: 10/20/2022]
Abstract
This study was conducted to identify the source of animal meat based on the peculiarities of protein intrinsic disorder distribution in mitochondrial cytochrome b (mtCyt-b). The analysis revealed that animal and avian species can be discriminated based on the proportions of the two groups of residues, Leu+Ile, and Ser+Pro+Ala, in the amino acid sequences of their mtCyt-b. Although levels of the overall intrinsic disorder in mtCyt-b is not very high, the peculiarities of disorder distribution within the sequences of mtCyt-b from different species varies in a rather specific way. In fact, positions and intensities of disorder/flexibility "signals" in the corresponding disorder profiles are relatively unique for avian and animal species. Therefore, it is possible to devise a set of simple rules based on the peculiarities of disorder profiles of their mtCyt-b proteins to discriminate among species. This intrinsic disorder-based analysis represents a new technique that could be used to provide a promising solution for identification of the source of meats.
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Affiliation(s)
- Haitham A. Yacoub
- Department of Biological Sciences, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
- Department of Cell Biology, Genetic Engineering and Biotechnology Division, National Research Centre, Dokki, Gizza, Egypt
| | - Mahmoud A. Sadek
- Department of Biological Sciences, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
- EgyBlood, Vacsera, Cairo, Egypt
| | - Vladimir N. Uversky
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Molecular Medicine and USF Health Byrd Alzheimer Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
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10
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Zhao L, Chenoweth EL, Liu Q. Population structure and genetic diversity of Sinibrama macrops from Ou River and Ling River based on mtDNA D-loop region analysis, China. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:303-311. [PMID: 28129728 DOI: 10.1080/24701394.2016.1278533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In order to understand the influence of human activities such as habitat fragmentation on freshwater fish population evolution, we investigated and compared the genetic diversity and phylogeography of Sinibrama macrops populations in the Oujiang River and Ling River. Mitochondrial control region sequences (D-loop region) of 131 specimens from six populations were obtained and analyzed. The diversity of main stream in the Ou River was lower than that in Ling River. Changtan population showed the lowest diversity (H = 0.646 ± 0.077; π = 0.00060 ± 0.00820). Pairwise FST, gene flow (Nm), and genetic distance (Da) indicated that Longquan and Changtan significantly differentiate from other populations. Nested clade phylogeographical analysis (NCPA) showed some clades and total cladogram experienced isolation by distance. In conclusion, the populations from severely fragmented Ou River have the lower diversity and more intense differentiation than that from the mainstream of Ling River, Changtan population present the lowest diversity and were isolated by the dam construction.
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Affiliation(s)
- Liangjie Zhao
- a The Key Laboratory of Aquatic Genetic Resources and Utilization (AGRU) of the Ministry of Agriculture , Shanghai Ocean University , Shanghai , P. R. China.,b Fishery Biological Engineering Technology Research Center of Henan Province, Xinyang Agriculture and Forestry University , Xinyang , P. R. China
| | - Erica L Chenoweth
- c Gene Conservation Laboratory, Alaska Department of Fish & Game , Anchorage , AK , USA
| | - Qigen Liu
- a The Key Laboratory of Aquatic Genetic Resources and Utilization (AGRU) of the Ministry of Agriculture , Shanghai Ocean University , Shanghai , P. R. China
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11
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Guo M, Huang H, Gao Y. Complete mitochondrial genome of darkfin hind Cephalopholis urodeta (Perciformes, Epinephelidae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:913-916. [PMID: 33473676 PMCID: PMC7799697 DOI: 10.1080/23802359.2016.1214542] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Darkfin hind, Cephalopholis urodeta, belongs to the subfamily Epinephelinae. It is one of the most important fish species in coral-reef ecosystem. In this study, the complete mitochondrial (mt) genome of C. urodeta has been determined. It was 16,592 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 2 non-coding regions. The mitogenome sequence of C. urodeta shared 94% and 92% similarity to that of C. sonnerati and C.sexmaculata, respectively. Phylogenetic tree was made based on the concatenated sequences of 12 protein-coding genes on mtH-strand. All the results provide insights into the evolution in the subfamily Epinephelinae.
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Affiliation(s)
- Minglan Guo
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Hui Huang
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
| | - Yongli Gao
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,The Center of Instruments and Determination, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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12
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Yacoub HA, Sadek MA. Identification of fraud (with pig stuffs) in chicken-processed meat through information of mitochondrial cytochrome b. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:855-859. [DOI: 10.1080/24701394.2016.1197220] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Haitham A. Yacoub
- Biological Sciences Department, Faculty of Sciences, King Abdul Aziz University, Jeddah, Kingdom of Saudi Arabia
- Cell Biology Department, Genetic Engineering and Biotechnology Division, National Research Centre, Gizza, Egypt
| | - Mahmoud A. Sadek
- Biological Sciences Department, Faculty of Sciences, King Abdul Aziz University, Jeddah, Kingdom of Saudi Arabia
- EgyBlood, Vacsera, Cairo, Egypt
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13
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Shan B, Song N, Han Z, Wang J, Gao T, Yokogawa K. Complete mitochondrial genomes of three sea basses Lateolabrax (Perciformes, Lateolabracidae) species: Genome description and phylogenetic considerations. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Kumar R, Gopalakrishnan A, Divya PR, Basheer VS, Singh RK, Mohindra V, Lal KK, Jena JK. Population genetic structure of Macrobrachium rosenbergii (Palaemonidae) from Indian waters using mitochondrial ATPase 6/8 gene. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:602-605. [PMID: 27159702 DOI: 10.3109/24701394.2016.1149829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Macrobrachium rosenbergii, giant freshwater prawn, is one of the most commercially important crustaceans. In the present study, primers for ATPase 6/8 region of mt-DNA were designed and successfully amplified (827 bp) in the species. The nucleotide variation in ATPase 6/8 gene revealed the population structuring in natural populations of M. rosenbergii in Indian waters. A total of 35 haplotypes were observed in 93 individuals collected from different locations. Low nucleotide diversity and high haplotype diversity were noticed for the ATPase 6/8 gene. Significant pairwise FST and, haplotype network indicated occurrence of distinct populations. Observed mismatch distribution and Tajima's D test suggested demographical stability of giant freshwater prawn. The genetic stock structure revealed in this study will be helpful for conservation and management of stocks of M. rosenbergii in Indian waters.
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Affiliation(s)
- Raj Kumar
- a Peninsular and Marine Fish Genetic Resources Centre (PMFGR), National Bureau of Fish Genetic Resources , CMFRI Campus , Kochi , Kerala , India
| | - A Gopalakrishnan
- b Central Marine Fisheries Research Institute , Kochi , Kerala , India
| | - P R Divya
- a Peninsular and Marine Fish Genetic Resources Centre (PMFGR), National Bureau of Fish Genetic Resources , CMFRI Campus , Kochi , Kerala , India
| | - V S Basheer
- a Peninsular and Marine Fish Genetic Resources Centre (PMFGR), National Bureau of Fish Genetic Resources , CMFRI Campus , Kochi , Kerala , India
| | - Rajeev K Singh
- c National Bureau of Fish Genetic Resources , Lucknow , UP , India
| | - Vindya Mohindra
- c National Bureau of Fish Genetic Resources , Lucknow , UP , India
| | - Kuldeep K Lal
- c National Bureau of Fish Genetic Resources , Lucknow , UP , India
| | - J K Jena
- c National Bureau of Fish Genetic Resources , Lucknow , UP , India
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15
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Kumar R, Pandey BK, Sarkar UK, Nagpure NS, Baisvar VS, Agnihotri P, Awasthi A, Mishra A, Kumar N. Population genetic structure and geographic differentiation in butter catfish, Ompok bimaculatus, from Indian waters inferred by cytochrome b mitochondrial gene. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:442-450. [PMID: 27159686 DOI: 10.3109/19401736.2015.1137898] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Documentation of genetic differentiation among the populations of a species can provide useful information that has roles in conservation, breeding, and management plans. In the present study, we examined the genetic structure and phylogenetic relationships among the 149 individuals of Ompok bimaculatus belonging to 24 populations, collected from Indian waters, using cytochrome b gene. The combined analyses of data suggested that the Indian O. bimaculatus consist of three distinct mtDNA lineages with star-like haplotypes network, which exhibited high genetic variation and haplotypic diversity. Analysis of molecular variance indicated that most of the observed genetic variation was found among the populations suggesting restricted gene flow. Long-term interruption of gene flow was also evidenced by high overall Fst values (0.82367) that could be favored by the discontinuous distributions of the lineages.
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Affiliation(s)
- Ravindra Kumar
- a ICAR - National Bureau of Fish Genetic Resources , Lucknow , Uttar Pradesh , India
| | - Brijesh Kumar Pandey
- a ICAR - National Bureau of Fish Genetic Resources , Lucknow , Uttar Pradesh , India
| | - Uttam Kumar Sarkar
- a ICAR - National Bureau of Fish Genetic Resources , Lucknow , Uttar Pradesh , India
| | | | | | - Praveen Agnihotri
- a ICAR - National Bureau of Fish Genetic Resources , Lucknow , Uttar Pradesh , India
| | - Abhishek Awasthi
- a ICAR - National Bureau of Fish Genetic Resources , Lucknow , Uttar Pradesh , India
| | - Abha Mishra
- b Babasaheb Bhimrao Ambedkar University (A Central University) , Vidya Vihar , Lucknow , Uttar Pradesh , India
| | - Narendra Kumar
- a ICAR - National Bureau of Fish Genetic Resources , Lucknow , Uttar Pradesh , India
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Bar I, Smith A, Bubner E, Yoshizaki G, Takeuchi Y, Yazawa R, Chen BN, Cummins S, Elizur A. Assessment of yellowtail kingfish (Seriola lalandi) as a surrogate host for the production of southern bluefin tuna (Thunnus maccoyii) seed via spermatogonial germ cell transplantation. Reprod Fertil Dev 2016. [DOI: 10.1071/rd15136] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Germ cell transplantation is an innovative technology for the production of interspecies surrogates, capable of facilitating easier and more economical management of large-bodied broodstock, such as the bluefin tuna. The present study explored the suitability of yellowtail kingfish (Seriola lalandi) as a surrogate host for transplanted southern bluefin tuna (Thunnus maccoyii) spermatogonial cells to produce tuna donor-derived gametes upon sexual maturity. Germ cell populations in testes of donor T. maccoyii males were described using basic histology and the molecular markers vasa and dead-end genes. The peripheral area of the testis was found to contain the highest proportions of dead-end-expressing transplantable Type A spermatogonia. T. maccoyii Type A spermatogonia-enriched preparations were transplanted into the coelomic cavity of 6–10-day-old post-hatch S. lalandi larvae. Fluorescence microscopy and polymerase chain reaction analysis detected the presence of tuna cells in the gonads of the transplanted kingfish fingerlings at 18, 28, 39 and 75 days after transplantation, indicating that the transplanted cells migrated to the genital ridge and had colonised the developing gonad. T. maccoyii germ cell-derived DNA or RNA was not detected at later stages, suggesting that the donor cells were not maintained in the hosts’ gonads.
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Rodríguez RA, Herrera AM, Santander J, Miranda JV, Fernández-Rodríguez MJ, Quirós Á, Riera R, Fernández-Palacios JM, Otto R, Escudero CG, Jiménez-Rodríguez A, Navarro-Cerrillo RM, Perdomo ME, Delgado JD. Uncertainty principle in niche assessment: A solution to the dilemma redundancy vs. competitive exclusion, and some analytical consequences. Ecol Modell 2015. [DOI: 10.1016/j.ecolmodel.2015.07.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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Kirczuk L, Rymaszewska A, Czerniawski R, Pilecka-Rapacz M, Domagała J. Genetic structure of the cisco (Coregonus albula L.) from lakes of glacial origin in northern Poland. Open Life Sci 2015. [DOI: 10.1515/biol-2015-0046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractEuropean cisco (Coregonus albula L.) is one of the
most precious species of the European lake ichtyofauna,
however, due to progressive eutrophication of water,
the range of its occurrence has decreased. Deteriorating
ecological conditions are the main cause of this decline
in population, and most of the existing populations in
lakes are maintained thanks to reintroduction. Thus, it
is important to determine the genetic structure of the
European cisco. The study involved PCR-RFLP-based
genetic analysis of C. albula caught in 15 lakes in northern
Poland, including four lakes located in national parks.
The analysis covered 3 genes located in the mitochondrial
DNA: ND1, ND3/4 and cytochrome b, as well as a control
region (D-loop). The PCR product was digested with
4 endonucleases (RsaI, MspI, BsuI and HhaI) and the
resulting haplotypes were grouped into combinations.
Statistical analysis were then performed on these
groups. Based on the genetic distance, a phenogram was
constructed in which two groups could be distinguished.
One group was represented by C. albula populations from
most lakes in north-western Poland, including the three
protected lakes. The other group consisted of the European
cisco population from Lake Wigry (north-eastern Poland)
and commercially exploited lakes from the southern part
of the investigated north-western Poland area. The results
of the study of C. albula from northern Poland present a
valuable molecular characterization of the populations
and can be a starting point for further genetic monitoring.
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Affiliation(s)
- L. Kirczuk
- 1Department of General Zoology, University of Szczecin, Felczaka 3c Street, 71-415 Szczecin, Poland
| | - A. Rymaszewska
- 2Department of Genetics, University of Szczecin, Felczaka 3c Street, 71-415 Szczecin, Poland
| | - R. Czerniawski
- 1Department of General Zoology, University of Szczecin, Felczaka 3c Street, 71-415 Szczecin, Poland
| | - M. Pilecka-Rapacz
- 1Department of General Zoology, University of Szczecin, Felczaka 3c Street, 71-415 Szczecin, Poland
| | - J. Domagała
- 1Department of General Zoology, University of Szczecin, Felczaka 3c Street, 71-415 Szczecin, Poland
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19
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Molina WF, Martinez PA, Bertollo LAC, Bidau CJ. Preferential accumulation of sex and Bs chromosomes in biarmed karyotypes by meiotic drive and rates of chromosomal changes in fishes. AN ACAD BRAS CIENC 2015; 86:1801-12. [PMID: 25590717 DOI: 10.1590/0001-3765201420130489] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 05/13/2014] [Indexed: 08/20/2023] Open
Abstract
Mechanisms of accumulation based on typical centromeric drive or of chromosomes carrying pericentric inversions are adjusted to the general karyotype differentiation in the principal Actinopterygii orders. Here, we show that meiotic drive in fish is also supported by preferential establishment of sex chromosome systems and B chromosomes in orders with predominantly bi-brachial chromosomes. The mosaic of trends acting at an infra-familiar level in fish could be explained as the interaction of the directional process of meiotic drive as background, modulated on a smaller scale by adaptive factors or specific karyotypic properties of each group, as proposed for the orthoselection model.
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Affiliation(s)
- Wagner F Molina
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, Brasil
| | - Pablo A Martinez
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, Brasil
| | - Luiz A C Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brasil
| | - Claudio J Bidau
- Departamento de Ingeniería en Biotecnología, Universidad Nacional de Río Negro, Villa Regina, Argentina
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20
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Qi D, Guo S, Chao Y, Kong Q, Li C, Xia M, Xie B, Zhao K. The biogeography and phylogeny of schizothoracine fishes (Schizopygopsis) in the Qinghai-Tibetan Plateau. ZOOL SCR 2015. [DOI: 10.1111/zsc.12116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Delin Qi
- Animal Science Department of Agriculture and Animal Husbandry College; Qinghai University; Xining 810016 China
| | - Songchang Guo
- Key laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining 810001 China
| | - Yan Chao
- Animal Science Department of Agriculture and Animal Husbandry College; Qinghai University; Xining 810016 China
| | - Qinghui Kong
- Animal Science Department of Agriculture and Animal Husbandry College; Qinghai University; Xining 810016 China
| | - Changzhong Li
- College of Eco-Environmental Engineering; Qinghai University; Xining 810016 China
| | - Mingzhe Xia
- Animal Science Department of Agriculture and Animal Husbandry College; Qinghai University; Xining 810016 China
| | - Baosheng Xie
- College of Eco-Environmental Engineering; Qinghai University; Xining 810016 China
| | - Kai Zhao
- Key laboratory of Adaptation and Evolution of Plateau Biota; Northwest Institute of Plateau Biology; Chinese Academy of Sciences; Xining 810001 China
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21
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Garcia G, Pereyra S, Gutierrez V, Oviedo S, Miller P, Domingo A. Population structure of Squatina guggenheim (Squatiniformes, Squatinidae) from the south-western Atlantic Ocean. JOURNAL OF FISH BIOLOGY 2015; 86:186-202. [PMID: 25424738 DOI: 10.1111/jfb.12560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 09/24/2014] [Indexed: 06/04/2023]
Abstract
Population genetic analyses based on both mitochondrial cytochrome b and the internal transcribed spacer 2 of recombinant (r)DNA genes were implemented to examine hypotheses of population differentiation in the angular angel shark Squatina guggenheim, one of the four most-widespread endemic species inhabiting coastal ecosystems in the south-western Atlantic Ocean. A total of 82 individuals of S. guggenheim from 10 sampling sites throughout the Río de la Plata mouth, its maritime front, the outer shelf at the subtropical confluence and the coastal areas of the south-west Atlantic Ocean, were included. The analysis of molecular variance (AMOVA) based on the second internal transcribed spacer (its-2) region supports that the samples from the outer shelf represent an isolated group from other sites. Historical gene flow in a coalescent-based approach revealed significant immigration and emigration asymmetry between sampling sites. Based on the low level of genetic diversity, the existence of a long-term population decline or a past recent population expansion following a population bottleneck could be proposed in S. guggenheim. This demographic differentiation suggests a degree of vulnerability to overexploitation in this endemic and endangered south-west Atlantic Ocean shark, given its longevity and low reproductive potential.
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Affiliation(s)
- G Garcia
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225, CP. 11400, Montevideo, Uruguay
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22
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Wei T, Sun Y, Zhang B, Wang R, Xu T. A mitogenomic perspective on the phylogenetic position of the Hapalogenys genus (Acanthopterygii: Perciformes) and the evolutionary origin of Perciformes. PLoS One 2014; 9:e103011. [PMID: 25077480 PMCID: PMC4117523 DOI: 10.1371/journal.pone.0103011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 06/26/2014] [Indexed: 11/18/2022] Open
Abstract
The Hapalogenys genus was the most controversial and problematic in phylogenetic position of Percoidei. In this study, we rechecked the taxonomic status of Hapalogenys in Percoidei using complete mitochondrial genome data. We purposefully added a new complete mitochondrial sequence from chosen species of Hapalogenys and conducted phylogenetic analyses using a large complete mitochondrial data set. The resultant tree topologies were congruent from partitioned Bayesian and Maximum-likelihood methods. The results indicated that Hapalogenys was distantly related to Haemulidae and could be removed from Haemulidae. The results supported the Hapalogeny was upgraded to a family rank titled Hapalogenyidae, and it should be recognized in a separate family of Hapalogenyidae. A relaxed molecular-clock Bayesian analysis indicated that the divergence times of Perciformes groups had a much older than the available old fossil records. The origin of the common ancestral lineage of Perciformes fish was estimated in the late Jurassic about 149 Myr ago.
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Affiliation(s)
- Tao Wei
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Yuena Sun
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Bo Zhang
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Rixin Wang
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Tianjun Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
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23
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Kathirvelpandian A, Gopalakrishnan A, Lakra WS, Krishna G, Sharma R, Divya PR, Kumar R, Jena JK. Mitochondrial ATPase 6/8 genes reveal genetic divergence in the Coilia dussumieri (Valenciennes, 1848) populations of north east and northwest coasts of India. Mol Biol Rep 2014; 41:3723-31. [DOI: 10.1007/s11033-014-3237-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 02/06/2014] [Indexed: 11/29/2022]
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24
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Genetic diversity of Echinococcus granulosus in southwest China determined by the mitochondrial NADH dehydrogenase subunit 2 gene. ScientificWorldJournal 2014; 2014:867839. [PMID: 24592194 PMCID: PMC3925532 DOI: 10.1155/2014/867839] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 11/24/2013] [Indexed: 12/21/2022] Open
Abstract
We evaluated genetic diversity and structure of Echinococcus granulosus by analyzing the complete mitochondrial NADH dehydrogenase subunit 2 (ND2) gene in 51 isolates of E. granulosus sensu stricto metacestodes collected at three locations in this region. We detected 19 haplotypes, which formed a distinct clade with the standard sheep strain (G1). Hence, all 51 isolates were identified as E. granulosus sensu stricto (G1–G3). Genetic relationships among haplotypes were not associated with geographical divisions, and fixation indices (Fst) among sampling localities were low. Hence, regional populations of E. granulosus in the southwest China are not differentiated, as gene flow among them remains high. This information is important for formulating unified region-wide prevention and control measures. We found large negative Fu's Fs and Tajima's D values and a unimodal mismatch distribution, indicating that the population has undergone a demographic expansion. We observed high genetic diversity among the E. granulosus s. s. isolates, indicating that the parasite population in this important bioregion is genetically robust and likely to survive and spread. The data from this study will prove valuable for future studies focusing on improving diagnosis and prevention methods and developing robust control strategies.
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25
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Wang L, Liu S, Zhuang Z, Guo L, Meng Z, Lin H. Population genetic studies revealed local adaptation in a high gene-flow marine fish, the small yellow croaker (Larimichthys polyactis). PLoS One 2013; 8:e83493. [PMID: 24349521 PMCID: PMC3861527 DOI: 10.1371/journal.pone.0083493] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 11/04/2013] [Indexed: 12/02/2022] Open
Abstract
The genetic differentiation of many marine fish species is low. Yet local adaptation may be common in marine fish species as the vast and changing marine environment provides more chances for natural selection. Here, we used anonymous as well as known protein gene linked microsatellites and mitochondrial DNA to detect the population structure of the small yellow croaker (Larimichthys polyactis) in the Northwest Pacific marginal seas. Among these loci, we detected at least two microsatellites, anonymous H16 and HSP27 to be clearly under diversifying selection in outlier tests. Sequence cloning and analysis revealed that H16 was located in the intron of BAHCC1 gene. Landscape genetic analysis showed that H16 mutations were significantly associated with temperature, which further supported the diversifying selection at this locus. These marker types presented different patterns of population structure: (i) mitochondrial DNA phylogeny showed no evidence of genetic divergence and demonstrated only one glacial linage; (ii) population differentiation using putatively neutral microsatellites presented a pattern of high gene flow in the L. polyactis. In addition, several genetic barriers were identified; (iii) the population differentiation pattern revealed by loci under diversifying selection was rather different from that revealed by putatively neutral loci. The results above suggest local adaptation in the small yellow croaker. In summary, population genetic studies based on different marker types disentangle the effects of demographic history, migration, genetic drift and local adaptation on population structure and also provide valuable new insights for the design of management strategies in L. polyactis.
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Affiliation(s)
- Le Wang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shufang Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
| | - Zhimeng Zhuang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
| | - Liang Guo
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Haoran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
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26
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Cao L, Liang XF, Du Y, Zheng H, Yang M, Huang W. Genetic population structure in Siniperca scherzeri (Perciformes: Siniperca) in China inferred from mitochondrial DNA sequences and microsatellite loci. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.08.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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27
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Phylogeography of Coreoperca whiteheadi (Perciformes: Coreoperca) in China based on mitochondrial and nuclear gene sequences. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.04.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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28
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Sati J, Kumar R, Sahoo PK, Patiyal RS, Ali S, Barat A. Genetic characterization of Golden mahseer (Tor putitora) populations using mitochondrial DNA markers. ACTA ACUST UNITED AC 2013; 26:68-74. [DOI: 10.3109/19401736.2013.823170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Jyoti Sati
- Molecular Genetics Laboratory, Directorate of Coldwater Fisheries Research, Indian Council of Agricultural Research, Bhimtal, Nainital, Uttarakhand, India
| | - Rohit Kumar
- Molecular Genetics Laboratory, Directorate of Coldwater Fisheries Research, Indian Council of Agricultural Research, Bhimtal, Nainital, Uttarakhand, India
| | - Prabhati Kumari Sahoo
- Molecular Genetics Laboratory, Directorate of Coldwater Fisheries Research, Indian Council of Agricultural Research, Bhimtal, Nainital, Uttarakhand, India
| | - Rabindar S. Patiyal
- Molecular Genetics Laboratory, Directorate of Coldwater Fisheries Research, Indian Council of Agricultural Research, Bhimtal, Nainital, Uttarakhand, India
| | - Shahnawaz Ali
- Molecular Genetics Laboratory, Directorate of Coldwater Fisheries Research, Indian Council of Agricultural Research, Bhimtal, Nainital, Uttarakhand, India
| | - Ashoktaru Barat
- Molecular Genetics Laboratory, Directorate of Coldwater Fisheries Research, Indian Council of Agricultural Research, Bhimtal, Nainital, Uttarakhand, India
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29
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Shen M, Shi X, Qu M, Chen J. Complete mitochondrial genome of squaretail coralgrouper Plectropomus areolatus (Perciformes, Epinephelidae). MITOCHONDRIAL DNA 2013; 24:365-367. [PMID: 23387393 DOI: 10.3109/19401736.2012.762579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The complete mitochondrial genome (mitogenome) sequence of squaretail coralgrouper Plectropomus areolatus was determined with long PCR approach. The genome was 16,770 bp in length and contained 13 protein-coding genes, 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and 2 non-coding regions, with the gene content and order being similar to most other teleosts. The overall base composition of the mitogenome was estimated to be 28.81% A, 27.63% T, 27.24% C, and 16.33% G, with a high AT content of 56.44%, indicating an obvious anti-guanine bias commonly observed in fishes. It shared 90.7%, 78.8%, and 78.7% mitogenome sequence with Plectropomus leopardus, Epinephelus moara, and Epinephelus coioides, respectively.
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Affiliation(s)
- Minghui Shen
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
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30
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Genetic variation and Phylogeography of Sinibrama Macrops (Teleostei: Cyprinidae) in Qiantang River Basin, China. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna. Proc Natl Acad Sci U S A 2013; 110:11061-6. [PMID: 23781100 DOI: 10.1073/pnas.1302051110] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values, the open-ocean lifestyle of tuna, in which effective sensing systems such as color vision are required for capture of prey, has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna, we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis), using next-generation sequencing technology. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified five common fish visual pigment genes: red-sensitive (middle/long-wavelength sensitive; M/LWS), UV-sensitive (short-wavelength sensitive 1; SWS1), blue-sensitive (SWS2), rhodopsin (RH1), and green-sensitive (RH2) opsin genes. Sequence comparison revealed that tuna's RH1 gene has an amino acid substitution that causes a short-wave shift in the absorption spectrum (i.e., blue shift). Pacific bluefin tuna has at least five RH2 paralogs, the most among studied fishes; four of the proteins encoded may be tuned to blue light at the amino acid level. Moreover, phylogenetic analysis suggested that gene conversions have occurred in each of the SWS2 and RH2 loci in a short period. Thus, Pacific bluefin tuna has undergone evolutionary changes in three genes (RH1, RH2, and SWS2), which may have contributed to detecting blue-green contrast and measuring the distance to prey in the blue-pelagic ocean. These findings provide basic information on behavioral traits of predatory fish and, thereby, could help to improve the technology to culture such fish in captivity for resource management.
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32
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Identification, phylogenetic relationships and a new maximum size of two rudd populations (Scardinius, Cyprinidae) from the Adriatic Sea drainage, Croatia. Biologia (Bratisl) 2013. [DOI: 10.2478/s11756-013-0179-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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33
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Yacoub HA, Fathi MM, Mahmoud WM. DNA barcode through cytochrome b gene information of mtDNA in native chicken strains. ACTA ACUST UNITED AC 2013; 24:528-37. [PMID: 23464748 DOI: 10.3109/19401736.2013.770489] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
This study was carried out to figure out the potentiality of a cytochrome b gene as a barcoding tool in discriminating native chicken strains and other Gallus gallus species. We performed PCR amplification using universal primer to amplify around 415 bp fragment of cytochrome b gene of mtDNA. The results revealed that all Saudi chicken strains were identical to each other but when compared with other species of Gallus the differences were exciting. The phylogenetic tree revealed that there were seven clusters represented for native strains and were clustered together especially in black strain and dark brown ones. The results have confirmed that using cytochrome b gene to discriminate between Saudi chicken strains and other species of G. gallus fowl was a very sufficient tool. Moreover, we can consider short fragment of cytochrome b gene of mtDNA as a universal DNA barcode region. It was a much more accurate and efficient tool to discriminate interspecies than intraspecies. We think it needs more studies to confirm this concept, and we have to apply that tool for many species of vertebrate and invertebrate as well.
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Affiliation(s)
- Haitham Ahmed Yacoub
- Cell Biology Department, Genetic Engineering and Biotechnology Division, National Research Center , Cairo , Egypt
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34
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Genetic divergence and historical demography in the endangered large yellow croaker revealed by mtDNA. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2012.09.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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35
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Kraitsek S, Klossa-Kilia E, Kilias G. Nuclear and mitochondrial phylogenetic analysis of big-scale sand smelt Atherina boyeri complex in Greece. JOURNAL OF FISH BIOLOGY 2012; 81:1559-1577. [PMID: 23020561 DOI: 10.1111/j.1095-8649.2012.03404.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Genetic differentiation and phylogenetic relationships of big-scale sand smelt Atherina boyeri specimens from 23 sampling sites in Greece and one from a lake in Turkey were investigated. A total of 2180 base pairs (bp) corresponding to the partial sequence of the mitochondrial gene cytochrome oxidase I (coI), cytochrome b (cytb) and control region, as well as of the nuclear protein-coding gene rhodopsin (rh), were determined for the 143 specimens studied. Phylogenetic analysis of each gene segment separately and of the combined dataset revealed the existence of three different and well divergent lineages in Greece. The first corresponds to the lagoon form, in which a clear distinction between the Aegean and Ionian Sea was observed. The other two correspond to the punctuated and non-punctuated marine forms that have been previously reported. The fact that in the present study a population without black spots on the flanks is clustered with the punctuated form and vice versa, however, suggests that differences in colour pattern do not seem to be a sufficient marker to discriminate the two marine forms. In contrast, the presence of a different length insertion between transfer RNA (tRNA) glutamic acid (tRNA(glu)) and cytb genes in the lagoon and in one of the two forms of marine populations, and its absence from the rest marine-form specimens confirms that this character is conserved and capable to be used for distinguishing the different forms. Even though the divergence values among the different forms were high, their phylogenetic relationships were not able to be resolved.
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Affiliation(s)
- S Kraitsek
- Department of Biology, Division of Genetics, Cell Biology and Development, University of Patras, Patras 26500, Greece
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Shi X, Su Y, Wang J, Ding S, Mao Y. Complete mitochondrial genome of black porgy Acanthopagrus schlegelii (Perciformes, Sparidae). ACTA ACUST UNITED AC 2012; 23:310-2. [PMID: 22591205 DOI: 10.3109/19401736.2012.683182] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Black porgy, Acanthopagrus schlegelii, is a marine protandrous hermaphrodite and belongs to one of the most important species commercialized for food in various areas of Asia. In this study, the complete mitochondrial genome of A. schlegelii has been determined. The mitogenome was 16,649 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding regions. It shared 90.2%, 82.3%, and 82.1% mitogenome sequence with Acanthopagrus latus, Parargyrops edita, and Pagrus major, respectively.
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Affiliation(s)
- Xiaofeng Shi
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, PR China
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Lévy-Hartmann L, Roussel V, Letourneur Y, Sellos DY. Global and New Caledonian patterns of population genetic variation in the deep-sea splendid alfonsino, Beryx splendens, inferred from mtDNA. Genetica 2012; 139:1349-65. [PMID: 22527688 DOI: 10.1007/s10709-012-9628-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 01/02/2012] [Indexed: 10/28/2022]
Abstract
Splendid alfonsino Beryx splendens is a commercial species in several countries, but is not currently exploited in New Caledonia. Information on species biology and genetics can influence the development of fisheries and assist in their management, but the genetic structuring and diversity of B. splendens populations remain largely unknown. To improve knowledge of genetic parameters, we used mitochondrial DNA sequences to conduct a comparative study of populations from throughout the world. Fragments of 815 bp of cytochrome b gene were sequenced and used to interpret the species history. We analyzed 204 individuals representing 14 geographical populations worldwide. A special focus was put on populations from New Caledonia. Analysis of variation between sequences, based on pairwise F statistics and AMOVA, demonstrated a population subdivision between the Atlantic and Indo-Pacific Oceans (Fst = 0.11-0.32; P < 0.05). Minimum-spanning network analysis revealed a mainly star-shaped pattern, with two lineages that may represent population expansion following a bottleneck/founder event and/or suggest colonization by migratory events over large distances. Our observations demonstrated that the species seems to follow the oceanic currents. Analysis of the nucleotide sequences revealed 122 variable sites, which defined numerous haplotypes, some associated with particular geographical regions. These data suggest an extremely high intra-specific genetic diversity, even at small scales. Focusing on the New Caledonia area, statistical analysis did not reveal sub-structuring among samples, suggesting again that at least a fraction of individuals migrate. No significant isolation by distance pattern was observed in this species (R = -0.22; P = 0.79) among seamount populations in the EEZ.
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Affiliation(s)
- Lauriana Lévy-Hartmann
- Laboratoire Insulaire du Vivant et de l'Environnement, Université de la Nouvelle-Calédonie, BP R4, 98851, Nouméa Cedex, New Caledonia, France.
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Cheng J, Ma GQ, Song N, Gao TX. Complete mitochondrial genome sequence of bighead croaker Collichthys niveatus (Perciformes, Sciaenidae): a mitogenomic perspective on the phylogenetic relationships of Pseudosciaeniae. Gene 2011; 491:210-23. [PMID: 21989484 DOI: 10.1016/j.gene.2011.09.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2011] [Revised: 09/20/2011] [Accepted: 09/20/2011] [Indexed: 11/25/2022]
Abstract
The monophyly and phylogenetic relationships of Pseudosciaeniae have long been controversial. Here we describe the mitochondrial genome (mitogenome) sequence of Collichthys niveatus. It is a circular double-stranded DNA molecule of 16,450 base pairs (bp) in length with a standard set of 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), 13 protein-coding genes as well as a non-coding control region. The mitogenome of C. niveatus shared common features with those of other bony fishes in terms of gene arrangement, base composition, and tRNA structures. The C. niveatus mitogenome exhibited pronounced strand-specific asymmetry in nucleotide composition, which was also reflected in the codon usage of genes oriented in opposite directions. Contrary to the typical structure of the control region, the central conserved blocks (CSB-D, -E, and -F) could not be detected in C. niveatus mitogenome. Phylogenetic analysis based on whole mitogenome sequences provided strong support for the monophyly of Pseudosciaeniae, and sister-group relationships of C. niveatus+Collichthys lucidus and Larimichthys crocea+Larimichthys polyactis, which was consistent with the traditional taxonomy. Unexpected divergence was found in two C. niveatus mitogenomes and several hypotheses were proposed to explain this observation including misidentification and introgressive hybridization between C. niveatus and L. polyactis, and polyphyletic origin of C. niveatus. We considered species misidentification to be the main hypothesis. However, additional data is essential to test these proposed hypotheses.
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Affiliation(s)
- Jiao Cheng
- Fisheries College, Ocean University of China, Yushan Road, 5, Qingdao 266003, China
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39
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Singh M, Lakra WS, Bahuguna SN, Kartavtsev YP. Cytochrome b gene sequence divergence of seven sisorid species of catfish genus Glyptothorax (siluriformes, sisoridae) from India. Mol Biol Rep 2011; 39:4275-82. [PMID: 21789484 DOI: 10.1007/s11033-011-1214-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 07/14/2011] [Indexed: 11/28/2022]
Abstract
Samples of seven Sisorid catfish species of the genus Glyptothorax (G. garhwali, G. dakpathari, G. brevipinnis, G. ngapang, G. granulus, G. ventrolineatus, and G. davissinghi) were collected from the Himalayan region and the Western Ghats of India. They were analyzed for the mitochondrial cytochrome b gene (Cyt b). Out of 1152 nucleotide positions analyzed, 269 (23.3%) were found to be variable and 235 (20.3%) were parsimoniously informative. The sequences showed 111 (9.6%) fourfold degenerate sites. The overall transition/transversion bias was R = 3.457. The average proportion of base substitutions measured as P-distance for all sequences of seven Glyptothorax species and other five species comprising four comparison groups was intraspecies, P = 0.17 ± 0.05%, intragenus, P = 10.75 ± 0.48%, intrafamily, P = 20.07 ± 1.43%, and intraorder, P = 21.10 ± 0.45%. Within the Glyptothorax genus maximum divergence was obtained among G. brevipinnis sequences, whereas the least divergence was obtained within G. davissinghi. The phylogenetic trees for 193 and 47 sequences of Sisorid catfishes together were developed using the Cyt b gene and four different analytical approaches: Bayesian (BA), neighbour-joining (NJ), maximum parsimony (MP), and maximum likelihood (ML). The analysis revealed a monophyletic origin for the all investigated representatives of the genus Glyptothorax (99, 100, 99, and 73% support level in our BA, NJ, MP, and ML analyses respectively) and with some reservations for Sisoridae, which is the principal family investigated. The monophyletic origin of the two subfamilies of Sisorid catfish defined in the literature was partly also supported by molecular phylogenetic data.
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Affiliation(s)
- Mahender Singh
- National Bureau of Fish Genetic Resources, Lucknow, 226002, Uttra Pradesh, India.
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Cheng J, Ma GQ, Miao ZQ, Shui BN, Gao TX. Complete mitochondrial genome sequence of the spinyhead croaker Collichthys lucidus (Perciformes, Sciaenidae) with phylogenetic considerations. Mol Biol Rep 2011; 39:4249-59. [PMID: 21786157 DOI: 10.1007/s11033-011-1211-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 07/14/2011] [Indexed: 11/29/2022]
Abstract
The complete mitochondrial genome of the spinyhead croaker Collichthys lucidus was determined using long-PCR and primer walking methods. It is a circular molecule of 16,451 bp in length with a standard set of 22 tRNAs, 2 rRNAs, 13 protein-coding genes as well as a non-coding control region in the same order as those of the other bony fishes. C. lucidus mitogenome exhibited a clear strand-specific bias in nucleotide composition, as evidence by a GC- skew of the H-strand of -0.319. The strand-specific bias was also reflected in the codon usage of genes oriented in opposite directions. All tRNA genes except for tRNA( Ser(AGY)) harbored the typical cloverleaf secondary structures and possessed anticodons that matched the vertebrate mitochondrial genetic code. Contrary to the typical structure of control region consistig of TAS, central, and CSB domains, there were no central conserved blocks available in C. lucidus mitogenome. Despite extensive studies based on both morphology and molecules, phylogenetic position of C. lucidus with Sciaenidae is still controversial. Our phylogenetic results provided more evidence to support previous morphological studies and consistently placed C. lucidus as a sister taxon to Collichthys niveatus, with both of these taxa forming the monophyletic Collichthys.
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Affiliation(s)
- Jiao Cheng
- Fisheries College, Ocean University of China, Qingdao, 266003, China
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Abstract
AbstractThe use of both morphological and molecular methods has allowed a fast and reliable species assignment of a fish that local fishermen with over thirty years of experience had never seen before. The identified species, Schedophilus medusophagus, is rare along Italian coasts, and this is the first documented record in the Central Tyrrhenian Sea for over 35 years. Its abundance should be evaluated on a continuous basis, as it might reflect biological consequences of environmental and climatic change. The mitochondrial sequences obtained in this study constitute a useful molecular tag for future research and may contribute to the phylogenetic debate on the status of the genus Schedophilus, of which S. medusophagus is the type species. Based on the existing literature, these preliminary molecular data support the hypothesis that the genus is not monophyletic.
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Yap FC, Yan YJ, Loon KT, Zhen JLN, Kamau NW, Kumaran JV. Phylogenetic analysis of different breeds of domestic chickens in selected area of Peninsular Malaysia inferred from partial cytochrome b gene information and RAPD markers. Anim Biotechnol 2011; 21:226-40. [PMID: 20967642 DOI: 10.1080/10495398.2010.506334] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The present investigation was carried out in an attempt to study the phylogenetic analysis of different breeds of domestic chickens in Peninsular Malaysia inferred from partial cytochrome b gene information and random amplified polymorphic DNA (RAPD) markers. Phylogenetic analysis using both neighbor-joining (NJ) and maximum parsimony (MP) methods produced three clusters that encompassed Type-I village chickens, the red jungle fowl subspecies and the Japanese Chunky broilers. The phylogenetic analysis also revealed that majority of the Malaysian commercial chickens were randomly assembled with the Type-II village chickens. In RAPD assay, phylogenetic analysis using neighbor-joining produced six clusters that were completely distinguished based on the locality of chickens. High levels of genetic variations were observed among the village chickens, the commercial broilers, and between the commercial broilers and layer chickens. In this study, it was found that Type-I village chickens could be distinguished from the commercial chickens and Type-II village chickens at the position of the 27th nucleotide of the 351 bp cytochrome b gene. This study also revealed that RAPD markers were unable to differentiate the type of chickens, but it showed the effectiveness of RAPD in evaluating the genetic variation and the genetic relationships between chicken lines and populations.
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Affiliation(s)
- Fook Choy Yap
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
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KOKITA TOMOYUKI, NOHARA KENJI. Phylogeography and historical demography of the anadromous fish Leucopsarion petersii in relation to geological history and oceanography around the Japanese Archipelago. Mol Ecol 2010; 20:143-64. [DOI: 10.1111/j.1365-294x.2010.04920.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Brykov VA, Oleinik AG, Polyakova NE, Skurikhina LA, Semina AV, Podlesnykh AV, Kukhlevsky AD. Punctuate divergent evolution in fish from the Northern Pacific. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410070112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Yan J, Liu L, Liu S, Guo X, Liu Y. Comparative analysis of mitochondrial control region in polyploid hybrids of red crucian carp (Carassius auratus) x blunt snout bream (Megalobrama amblycephala). FISH PHYSIOLOGY AND BIOCHEMISTRY 2010; 36:263-272. [PMID: 18815893 DOI: 10.1007/s10695-008-9251-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Accepted: 07/21/2008] [Indexed: 05/26/2023]
Abstract
The entire sequences of the mitochondrial (mt)DNA control region (CR) and portions of its flanking genes in the red crucian carp (RC) and blunt snout bream (BSB) as well as their polyploid hybrids (3nRB, 4nRB and 5nRB) were determined and subjected to a comparative analysis. The mtDNA-CRs of these five fish species ranged from 923 to 937 bp in length, they had the same flanking gene arrangement as other vertebrates and the pattern of nucleotide substitution bias was also similar to that in other vertebrates. Our data are consistent with the viewpoint of three domains [extended terminal associated sequence (ETAS domain), central conserved sequence block domain and conserved sequence block (CSB) domain] within the mtDNA-CR of mammals. On the basis our comparative analysis of the mtDNA-CRs of these five fish species, we were able to identify the consensus sequences of functional conserved units, including the ETAS, CSB-F, CSB-D, CSB-E, CSB1, CSB2 and CSB3 and putative promoter. The percentage of variable nucleotide positions (41.98%) in the central domain was lower than those in the ETAS and conserved domain (71.70 and 47.12%, respectively), suggesting that the central domain was the most conserved part of the mtDNA-CR. These results provide useful and important information for the further study of mtDNA-CR structure in fish. The sequence similarities of mtDNA-CR among the 3nRB, 4nRB, 5nRB hybrids and their respective female parents were higher than those among the 3nRB, 4nRB, 5nRB hybrids and their respective male parents, providing the direct evidence of stringent maternal inheritance of mtDNA-CR in the 3nRB, 4nRB and 5nRB hybrids.
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Affiliation(s)
- Jinpeng Yan
- College of Life Science, Hunan Normal University, Changsha 410081, Hunan, People's Republic of China
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46
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Ku CC, Lu CH, Wang CS. Establishment and characterization of a fibroblast cell line derived from the dorsal fin of red sea bream, Pagrus major (Temminck & Schlegel). JOURNAL OF FISH DISEASES 2010; 33:187-196. [PMID: 20102463 DOI: 10.1111/j.1365-2761.2009.01104.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The establishment and partial characterization of a continuous cell line from the dorsal fin of red sea bream, Pagrus major, are described. The cell line, designated RSBF-2, has been subcultured for more than 100 passages since its initiation in November 2000. It was optimally maintained at 28 degrees C in Leibovitz L-15 medium with 10% foetal bovine serum. Propagation of RSBF-2 cells was serum dependent and exhibited low plating efficiency (<1.7%). Aside from long-term cryopreservation, the cells could also be kept at 4 degrees C for 72 days. The distribution of the chromosome number was 38-98 with a mode of 48. The RSBF-2 cell line was susceptible to red sea bream iridovirus but only produced a few rounded and refractory cells. Virus-inoculated RSBF-2 cells were then subcultured to generate a persistently infected cell line. RSBF-2 was also very sensitive to the extracellular products of Photobacterium damselae ssp. piscicida and produced significant fluorescent signals after transfection with pEGFP-C3. Analysis of mitochondrial cytochrome b gene sequences revealed 99% identity between the cell line and Pagrus major.
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Affiliation(s)
- C-C Ku
- Department of Aquaculture, National Penghu University, Penghu, Taiwan.
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47
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Ci HX, Lin GH, Cai ZY, Tang LZ, Su JP, Liu JQ. Population history of the plateau pika endemic to the Qinghai-Tibetan Plateau based on mtDNA sequence data. J Zool (1987) 2009. [DOI: 10.1111/j.1469-7998.2009.00635.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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48
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Ketmaier V, Finamore F, Largiadèr C, Milone M, Bianco PG. Phylogeography of bleaks Alburnus spp. (Cyprinidae) in Italy, based on cytochrome b data. JOURNAL OF FISH BIOLOGY 2009; 75:997-1017. [PMID: 20738595 DOI: 10.1111/j.1095-8649.2009.02357.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Sequence variation of a fragment of the mitochondrial DNA encoding for the cytochrome b gene was used to reconstruct the phylogeography of the two species of bleaks occurring in Italy: the alborella Alburnus arborella in northern Italy and the vulturino Alburnus albidus in southern Italy. The study includes four populations of the alborella and 14 populations of the vulturino. A total of 57 haplotypes were identified; these could not be sorted into two reciprocally monophyletic clusters. Multiple phylogenetic methods and nested clade phylogeographical analysis consistently retrieved three well-supported clades, two of which contained both Northern and Southern Italian haplotypes. A third clade is limited to southern Italy. This clade is tentatively assigned to the vulturino. The placement in the same clade of northern and southern Italian haplotypes is explained in light of the introductions of fishes operated from northern to central and southern Italy. The origin of the vulturino dates back to the last two million years. This divergence time estimate identifies the Pleistocene confluences between adjacent river basins along the Adriatic slope of the Italian peninsula and their subsequent isolation as the cause that triggered the diversification of the genus in the area. The existence of a clade endemic to southern Italy supports the recognition of the area as a new peri-Mediterranean ichthyogeographic district, the borders of which correspond to the northern and southern edges of the vulturino range.
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Affiliation(s)
- V Ketmaier
- Unit of Evolutionary Biology-Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Haus 25, D-14476 Potsdam, Germany.
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A comparative analysis of the complete mitochondrial genome of the Eurasian otter Lutra lutra (Carnivora; Mustelidae). Mol Biol Rep 2009; 37:1943-55. [DOI: 10.1007/s11033-009-9641-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Accepted: 07/21/2009] [Indexed: 10/20/2022]
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50
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Hwang DS, Hwang DS, Ki JS, Hwang DS, Ki JS, Jeong DH, Kim BH, Lee BK, Han SH, Lee JS. A comprehensive analysis of three Asiatic black bear mitochondrial genomes (subspeciesussuricus,formosanusandmupinensis), with emphasis on the complete mtDNA sequence ofUrsus thibetanus ussuricus(Ursidae). ACTA ACUST UNITED AC 2009. [DOI: 10.1080/19401730802389525] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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