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Li R, Wang Z, Xu H, Jiang C, Wang N, Li X, Qiu X, Wang X. Genetic Diversity among Takifugu rubripes and Takifugu obscurus in Different Regions of China Based on Mitochondrial DNA Sequencing Data. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422120079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Chandran R, Singh A, Singh RK, Mandal S, Ganesan K, Sah P, Paul P, Pathak A, Dutta N, Sah R, Lal KK, Mohindra V. Phenotypic variation of Chitala chitala (Hamilton, 1822) from Indian rivers using truss network and geometric morphometrics. PeerJ 2022; 10:e13290. [PMID: 35462771 PMCID: PMC9022642 DOI: 10.7717/peerj.13290] [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: 11/03/2021] [Accepted: 03/28/2022] [Indexed: 01/13/2023] Open
Abstract
Chitala chitala (Hamilton, 1822) is an economically important food fish species occurring throughout Indian rivers, which also has ornamental value. This study focuses on morphological variations in C. chitala from seven river basins across India namely; Son, Tons, Ken, Brahmaputra, Ganga, Gomti and Gandak. A truss network was constructed by interconnecting nine landmarks to generate 36 morphometric variables extracted from digital images of specimens sampled from the study locations. Transformed truss measurements were subjected to principal component analysis (PCA), canonical discriminant function analysis (CDFA) and discriminant analyses of principal components (DAPC). DAPC function coefficients performed much better in capturing the variation pattern and discrimination between the rivers which was not achieved using CDFA. Eight truss variables were identified with significant and highest loading for truss variables on principal components and coefficients on discriminant function from DAPC contributing to maximum variation between the rivers. Performance graph and functional distribution of identified truss variables clearly indicated distinction between the rivers. Thin plate spline analysis and procrustes shape analysis further showed the variation in morphology between specimens across the rivers. The significant parameters differentiating specimens from different rivers were linked to dorsal fin origin, the base of the pectoral fin and the perpendicular point on the anal fin from the dorsal fin origin. Variation in the hydrodynamics of the rivers studied might be possibly affecting the fin kinematics and consequently leading to adaption seen as phenotypic variation in C. chitala. The results showcased in the present study shall help in better understanding of intra-specific diversity which is significant for management and conservation of a species.
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Affiliation(s)
- Rejani Chandran
- Fish Conservation Division, National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
| | - Achal Singh
- Fish Conservation Division, National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
| | - Rajeev K. Singh
- Fish Conservation Division, National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
| | - Sangeeta Mandal
- Fish Conservation Division, National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
| | - Kantharajan Ganesan
- Fish Conservation Division, National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
| | - Priyanka Sah
- Fish Conservation Division, National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
| | - Pradipta Paul
- Fish Conservation Division, National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India,Department of Fisheries, Bankura, West Bengal, India
| | - Abhinav Pathak
- Fish Conservation Division, National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India,Molecular Biological Sciences, Farelabs Private Limited, Gurugram, India
| | - Nimisha Dutta
- Fish Conservation Division, National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India,Molecular Biological Sciences, Farelabs Private Limited, Gurugram, India
| | - Ramashankar Sah
- Fish Conservation Division, National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
| | - Kuldeep K. Lal
- Fish Conservation Division, National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
| | - Vindhya Mohindra
- Fish Conservation Division, National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh, India
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Nagarajan M, Raja M, Vikram P. Genetic characterization of Bagarius species using cytochrome c oxidase I and cytochrome b genes. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3781-3. [PMID: 26369789 DOI: 10.3109/19401736.2015.1079902] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, we first inferred the genetic variability of two Bagarius bagarius populations collected from Ganges and Brahmaputra rivers of India using two mtDNA markers. Sequence analysis of COI gene did not show significant differences between two populations whereas cytochrome b gene showed significant differences between two populations. Followed by, genetic relationship of B. bagarius and B. yarrielli was analyzed using COI and cytochrome b gene and the results showed a higher level genetic variation between two species. The present study provides support for the suitability of COI and cytochrome b genes for the identification of B. bagarius and B. yarrielli.
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Affiliation(s)
- Muniyandi Nagarajan
- a Department of Genomic Science , School of Biological Sciences, Central University of Kerala , Kasaragod , Kerala , India and
| | - Manikam Raja
- b Department of Biotechnology , Periyar University , Salem , Tamil Nadu , India
| | - Potnuru Vikram
- a Department of Genomic Science , School of Biological Sciences, Central University of Kerala , Kasaragod , Kerala , India and
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Application of microsatellite markers in conservation genetics and fisheries management: recent advances in population structure analysis and conservation strategies. GENETICS RESEARCH INTERNATIONAL 2014; 2014:691759. [PMID: 24808959 PMCID: PMC3997932 DOI: 10.1155/2014/691759] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 02/19/2014] [Accepted: 02/19/2014] [Indexed: 12/22/2022]
Abstract
Microsatellites are the most popular and versatile genetic marker with myriads of applications in population genetics, conservation biology, and evolutionary biology. These are the arrays of DNA sequences, consisting of tandemly repeating mono-, di-, tri-, and tetranucleotide units, which are distributed throughout the genomes of most eukaryotic species. Microsatellites are codominant in nature, highly polymorphic, easily typed, and Mendelian inherited, all properties which make them very suitable for the study of population structure and pedigree analysis and capable of detecting differences among closely related species. PCR for microsatellites can be automated for identifying simple sequence repeat polymorphism. Small amount of blood samples or alcohol preserved tissue is adequate for analyzing them. Most of the microsatellites are noncoding, and therefore variations are independent of natural selection. These properties make microsatellites ideal genetic markers for conservation genetics and fisheries management. This review addresses the applications of microsatellite markers in conservation genetics and recent advances in population structure analysis in the context of fisheries management.
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Gupta A, Lal KK, Mohindra V, Singh RK, Punia P, Dwivedi AK, Gupta BK, Luhariya RK, Masih P, Mishra RM, Jena JK. Genetic divergence in natural populations of bronze featherback, Notopterus notopterus (Osteoglossiformes: Notopteridae) from five Indian rivers, analyzed through mtDNA ATPase6/8 regions. Meta Gene 2013; 1:50-7. [PMID: 25606374 PMCID: PMC4205040 DOI: 10.1016/j.mgene.2013.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 10/07/2013] [Indexed: 11/26/2022] Open
Abstract
The present study characterized 842 bp fragment of mitochondrial ATP synthase 6 and 8 (ATPase6/8) genes in Notopterus notopterus. In all, 97 samples of N. notopterus were collected from five distant rivers; viz Satluj, Gomti, Yamuna, Brahmaputra and Mahanadi representing 4 river basins in India. The analysis of variation revealed presence of 23 haplotypes in ATPase6/8 gene with haplotype diversity (Hd) of 0.899 and nucleotide diversity (π) of 0.00336. The within population variation which was 41.78% of the total variation of 58.22% was found among population. The Fst value of 0.582 (P < 0.05) of the total population was found significant. The results concluded that the polymorphism in ATPase6/8 gene is a potential marker that is important for determining genetic divergence of wild N. notopterus populations. The findings reveal common ancestry of mahanadi population with the populations in rivers of Indo-Gangetic region. However, long evolutionary isolation must be responsible for the high genetic divergence between N. notopterus in Mahanadi and other regions.
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Affiliation(s)
- Arti Gupta
- National Bureau of Fish Genetic Resources, Canal Ring Road, Lucknow 226002, UP, India
| | - Kuldeep K Lal
- National Bureau of Fish Genetic Resources, Canal Ring Road, Lucknow 226002, UP, India
| | - Vindhya Mohindra
- National Bureau of Fish Genetic Resources, Canal Ring Road, Lucknow 226002, UP, India
| | - Rajeev K Singh
- National Bureau of Fish Genetic Resources, Canal Ring Road, Lucknow 226002, UP, India
| | - Peyush Punia
- National Bureau of Fish Genetic Resources, Canal Ring Road, Lucknow 226002, UP, India
| | - Arvind K Dwivedi
- National Bureau of Fish Genetic Resources, Canal Ring Road, Lucknow 226002, UP, India
| | - B K Gupta
- National Bureau of Fish Genetic Resources, Canal Ring Road, Lucknow 226002, UP, India
| | - Rupesh K Luhariya
- National Bureau of Fish Genetic Resources, Canal Ring Road, Lucknow 226002, UP, India
| | - Prachi Masih
- National Bureau of Fish Genetic Resources, Canal Ring Road, Lucknow 226002, UP, India
| | | | - J K Jena
- National Bureau of Fish Genetic Resources, Canal Ring Road, Lucknow 226002, UP, India
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Gupta A, Lal KK, Punia P, Singh RK, Mohindra V, Sah RS, Kumar R, Luhariya RK, Dwivedi AK, Masih P, Mishra RM, Jena JK. Characterization of polymorphic microsatellite markers and genetic diversity in wild bronze featherback, Notopterus notopterus (Pallas, 1769). Mol Biol Rep 2013; 40:6625-31. [PMID: 24072656 DOI: 10.1007/s11033-013-2776-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 09/14/2013] [Indexed: 11/29/2022]
Abstract
Six polymorphic microsatellite DNA loci were identified in the primitive fish, bronze featherback, Notopterus notopterus for the first time and demonstrated significant population genetic structure. Out of the six primers, one primer (NN90) was specific to N. notopterus (microsatellite sequence within the RAG1 gene) and five primers were product of successful cross-species amplification. Sixty-four primers available from 3 fish species of order Osteoglossiformes and families Notopteridae and Osteoglossidae were tested to amplify homologous microsatellite loci in N. notopterus. Fifteen primer pairs exhibited successful cross-priming PCR product. However, polymorphism was detected only at five loci. To assess the significance of these six loci (including NN90) in population genetic study, 215 samples of N. notopterus from five rivers, viz Satluj, Gomti, Yamuna, Brahmaputra and Mahanadi were analyzed. The five sample sets displayed different diversity levels and observed heterozygosity ranged from 0.6036 to 0.7373. Significant genotype heterogeneity (P < 0.0001) and high FST (0.2205) over all loci indicated that the samples are not drawn from the same genepool. The identified microsatellite loci are promising for use in fine-scale population structure analysis of N. notopterus.
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Affiliation(s)
- Arti Gupta
- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226002, Uttar Pradesh, India
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References. Mol Ecol 2012. [DOI: 10.1002/9780470979365.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Aquino LMG, Tango JM, Canoy RJC, Fontanilla IKC, Basiao ZU, Ong PS, Quilang JP. DNA barcoding of fishes of Laguna de Bay, Philippines. ACTA ACUST UNITED AC 2012; 22:143-53. [PMID: 22040082 DOI: 10.3109/19401736.2011.624613] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Laguna de Bay, the largest lake in the Philippines, is an important part of the country's fisheries industry. It is also home to a number of endemic fishes including Gobiopterus lacustris (Herre 1927) of family Gobiidae, Leiopotherapon plumbeus (Kner 1864) of family Terapontidae, Zenarchopterus philippinus (Peters 1868) of family Hemiramphidae and Arius manillensis Valenciennes 1840 of family Ariidae. Over the years, a steady decline has been observed in the abundance and diversity of native fishes in the lake due to anthropogenic disturbances. In this study, a total of 71 specimens of 18 different species belonging to 18 genera, 16 families, and seven orders were DNA barcoded using the mitochondrial cytochrome c oxidase subunit I (COI) gene. All of the fish species were discriminated by their COI sequences and one endemic species G. lacustris, showing deep genetic divergence, was highlighted for further taxonomic investigation. Average Kimura 2-parameter genetic distances within species, family, and order were 1.33%, 18.91%, and 24.22%, respectively. These values show that COI divergence increases as taxa become less exclusive. All of the COI sequences obtained were grouped together according to their species designation in the Neighbor-joining tree that was constructed. This study demonstrated that DNA barcoding has great potential as a tool for fast and accurate species identification and also for highlighting species that warrant further taxonomic investigation.
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Affiliation(s)
- Luis Miguel G Aquino
- DNA Barcoding Laboratory, Institute of Biology, College of Science, University of the Philippines, 1101 Diliman, Quezon City, Philippines
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Comparative assessment of genetic variability in the populations of endemic and endangered yellow catfish, Horabagrus brachysoma (Teleostei: Horabagridae), based on allozyme, RAPD, and microsatellite markers. Biochem Genet 2011; 50:192-212. [PMID: 21938562 DOI: 10.1007/s10528-011-9462-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2010] [Accepted: 07/22/2011] [Indexed: 10/17/2022]
Abstract
The comparative assessment of genetic diversity using allozymes, random amplified polymorphic DNA (RAPD), and microsatellite markers was conducted in endemic and endangered yellow catfish (Horabagrus brachysoma) sampled from three locations in Western Ghats river systems of India. Among the three markers, microsatellites show more polymorphism, having 100% polymorphic loci, whereas allozymes show the least (56%). In RAPD, 60.5% of fragments were polymorphic. Observed heterozygosity and F(ST) values were very high in microsatellites, compared with the other markers. Microsatellite and RAPD markers reported a higher degree of genetic differentiation than allozymes among the populations depicted by pairwise F(ST)/G(ST), AMOVA, Nei's genetic distance, and UPGMA dendrogram. The three classes of markers demonstrated striking genetic differentiation between pairs of H. brachysoma populations. The data emphasize the need for fishery management, conservation, and rehabilitation of this species.
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Mandal A, Mohindra V, Singh RK, Punia P, Singh AK, Lal KK. Mitochondrial DNA variation in natural populations of endangered Indian feather-back fish, Chitala chitala. Mol Biol Rep 2011; 39:1765-75. [PMID: 21637956 DOI: 10.1007/s11033-011-0917-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 05/18/2011] [Indexed: 01/31/2023]
Abstract
Genetic variation at mitochondrial cytochrome b (cyt b) and D-loop region reveals the evidence of population sub-structuring in Indian populations of highly endangered primitive feather-back fish Chitala chitala. Samples collected through commercial catches from eight riverine populations from different geographical locations of India were analyzed for cyt b region (307 bp) and D-loop region (636-716 bp). The sequences of the both the mitochondrial regions revealed high haplotype diversity and low nucleotide diversity. The patterns of genetic diversity, haplotypes networks clearly indicated two distinct mitochondrial lineages and mismatch distribution strongly suggest a historical influence on the genetic structure of C. chitala populations. The baseline information on genetic variation and the evidence of population sub-structuring generated from this study would be useful for planning effective strategies for conservation and rehabilitation of this highly endangered species.
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Affiliation(s)
- Anup Mandal
- National Bureau of Fish Genetic Resources, Canal Ring Road, PO Dilkusha, Lucknow, 226002 UP, India
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