1
|
Baisvar VS, Kushwaha B, Kumar R, Kumar MS, Singh M, Rai A, Sarkar UK. BAC-FISH Based Physical Map of Endangered Catfish Clarias magur for Chromosome Cataloguing and Gene Isolation through Positional Cloning. Int J Mol Sci 2022; 23:ijms232415958. [PMID: 36555603 PMCID: PMC9781557 DOI: 10.3390/ijms232415958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/01/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Construction of a physical chromosome map of a species is important for positional cloning, targeted marker development, fine mapping of genes, selection of candidate genes for molecular breeding, as well as understanding the genome organization. The genomic libraries in the form of bacterial artificial chromosome (BAC) clones are also a very useful resource for physical mapping and identification and isolation of full-length genes and the related cis acting elements. Some BAC-FISH based studies reported in the past were gene based physical chromosome maps of Clarias magur (magur) to understand the genome organization of the species and to establish the relationships with other species in respect to genes' organization and evolution in the past. In the present study, we generated end sequences of the BAC clones and analyzed those end sequences within the scaffolds of the draft genome of magur to identify and map the genes bioinformatically for each clone. A total of 36 clones mostly possessing genes were identified and used in probe construction and their subsequent hybridization on the metaphase chromosomes of magur. This study successfully mapped all 36 specific clones on 16 chromosome pairs, out of 25 pairs of magur chromosomes. These clones are now recognized as chromosome-specific makers, which are an aid in individual chromosome identification and fine assembly of the genome sequence, and will ultimately help in developing anchored genes' map on the chromosomes of C. magur for understanding their organization, inheritance of important fishery traits and evolution of magur with respect to channel catfish, zebrafish and other species.
Collapse
Affiliation(s)
- Vishwamitra Singh Baisvar
- ICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, India
| | - Basdeo Kushwaha
- ICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, India
| | - Ravindra Kumar
- ICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, India
- Correspondence:
| | - Murali Sanjeev Kumar
- ICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, India
| | - Mahender Singh
- ICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, India
| | - Anil Rai
- Division of Agricultural Bioinformatics, ICAR—Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi 110012, India
| | - Uttam Kumar Sarkar
- ICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, India
| |
Collapse
|
2
|
Kumar MS, Baisvar VS, Kushwaha B, Kumar R, Singh M, Mishra AK. Thermal stress induces expression of Nuclear protein and Parkin genes in endangered catfish, Clarias magur. Gene 2022; 825:146388. [PMID: 35288199 DOI: 10.1016/j.gene.2022.146388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/18/2022] [Accepted: 02/28/2022] [Indexed: 11/18/2022]
Abstract
Fluctuation in water temperature can create thermal stress, which may impact many aspects of fish life, such as survival, growth, reproduction, disease occurrence etc. The endangered catfish, Clarias magur, has been reported to survive at higher thermal stress, even though the exact mechanism is unknown. The genes coding for Nuclear protein 1 (Nupr1) and Parkin E3 ubiquitin protein ligase (Park2) have been reported to protect cells from stress-induced damage and death. In this study, we characterized both the genes and assessed their quantitative expression in C. magur. Structural features of both the genes were found similar to a related catfish, Ictalurus punctatus, and model fish zebrafish. The genes were fairly conserved in fishes as observed through phylogenetic analysis. The real time expression of the two stress-associated genes were also assessed in brain, kidney, liver and muscle tissues of C. magur exposed to warm (34 °C) and cold (15 °C) water. RT-PCR analysis revealed up-regulation in the relative expression levels of Nupr1 and Park2 genes at both temperatures with maximum positive fold change during stress to cold water, even though the posteriori Dunnett's test after ANOVA revealed that there were significant differences between the control and challenged groups. The study indicated that Nupr1 gene plays role in muscle tissue at both high and low thermal stress, but at high thermal stress in liver, while Park2 plays role in muscle, brain and kidney at low temperature and in liver at high temperature stress in C. magur. The study has generated first-hand information under warm- and cold water, which pave the way to understand the expression response of these genes to thermal vacillations and to establish evolutionary significance in catfishes and other species.
Collapse
Affiliation(s)
- Murali Sanjeev Kumar
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226 002, India
| | - Vishwamitra Singh Baisvar
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226 002, India
| | - Basdeo Kushwaha
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226 002, India
| | - Ravindra Kumar
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226 002, India.
| | - Mahender Singh
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226 002, India
| | - Akhilesh Kumar Mishra
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226 002, India
| |
Collapse
|
3
|
Rashid I, Baisvar VS, Singh M, Kumar R, Srivastava P, Kushwaha B, Pathak AK. Isolation and characterization of hypoxia inducible heme oxygenase 1 (HMOX1) gene in Labeo rohita. Genomics 2020; 112:2327-2333. [PMID: 31923615 DOI: 10.1016/j.ygeno.2020.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/05/2019] [Accepted: 01/06/2020] [Indexed: 11/29/2022]
Abstract
The HMOX1 gene plays role in several biological processes and is also responsive to hypoxia stress. Freshwater carp fish, Labeo rohita, is reported as hypoxia sensitive, but the information of annotated hypoxia genes in public domain is very scanty for this species. Here, an attempt was made to isolate and characterize HMOX1 gene in L. rohita using information from zebrafish. HMOX1 gene was obtained by mapping HMOX1 protein of zebrafish over assembled genome of L. rohita. Aligned region was used for designing primers for HMOX1 amplification. Eight overlapping sets of primers were designed for amplifying ~540 bp long successive overlapping fragments. Splicing of overlapping amplicons generated 3715 bp fragment that was confirmed as HMOX1 gene having full coding region with 6 exons between 184 and 2156 bp positions. HMOX1 characterization is an initiative for L. rohita genes annotation to support the characterization of new genes in the important species.
Collapse
Affiliation(s)
- Iliyas Rashid
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P.O.- Dilkusha, Lucknow, Uttar Pradesh 226 002, India; AMITY Institute of Biotechnology, AMITY University, Uttar Pradesh, Lucknow Campus, Lucknow 226 028, Uttar Pradesh, India.
| | - Vishwamitra Singh Baisvar
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P.O.- Dilkusha, Lucknow, Uttar Pradesh 226 002, India.
| | - Mahender Singh
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P.O.- Dilkusha, Lucknow, Uttar Pradesh 226 002, India.
| | - Ravindra Kumar
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P.O.- Dilkusha, Lucknow, Uttar Pradesh 226 002, India.
| | - Prachi Srivastava
- AMITY Institute of Biotechnology, AMITY University, Uttar Pradesh, Lucknow Campus, Lucknow 226 028, Uttar Pradesh, India.
| | - Basdeo Kushwaha
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P.O.- Dilkusha, Lucknow, Uttar Pradesh 226 002, India.
| | - Ajey Kumar Pathak
- ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, P.O.- Dilkusha, Lucknow, Uttar Pradesh 226 002, India.
| |
Collapse
|
4
|
Kumar R, Baisvar VS, Kushwaha B, Waikhom G, Singh M. Evolutionary analysis of genus Channa based on karyological and 16S rRNA sequence data. J Genet 2019; 98:112. [PMID: 31819022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A wide range of diploid number of chromosomes and the body size of Channa congeners are useful combination of characters for studying the factors controlling the body size. In this study, the karyological information was superimposed on the evolutionary tree generated by 16S rRNA mitochondrial gene sequences. Here, the metaphase chromosome complements stained with Giemsa, AgNO3 and CMA3 were prepared from six snakehead murrel fish species collected from northeast India. The diploid chromosome numbers and the fundamental arms of C. aurantimaculata (2n = 52, NF = 98), C. gachua (2n = 56, NF = 84), C. marulius (2n = 44, NF = 58), C. orientalis (2n = 52, NF = 74), C. punctata (2n = 32, NF = 60) and C. striata (2n = 40, NF = 48) were calculated by the analysis of metaphase chromosome complements. Both methods of nucleolar organizer region (NOR) localization, silver nitrate and chromomycin A3, revealed NOR pairs of 1, 2, 3, 1, 4 and 3 in C. aurantimaculata, C. gachua, C. marulius, C. orientalis, C. punctata and C. striata, respectively. The subject species showed primitive type of asymmetrical chromosomes, except the C. punctata. The variation in 2n for C. orientalis (2n = 52, 78) and C. gachua (2n = 52, 78, 104) of a complete haploid set indicates the possibility of either ploidy change in C. orientalis and C. gachua, if we consider 2n = 52 or the Robertsonian rearrangements in different populations of these two species. The chromosome evolution tree was constructed on 16S rRNA ML-phylogenetic tree using ChromEvol 1.3. The analysis of chromosome evolution explained the loss or gain of chromosome, duplications or semiduplications mechanism. For time scaling the chromosomeevolution, the node age of available 16S rRNA gene of Channa species were estimated, which was also used for estimating the time when chromosomal changes occurred in context of geological time-scale.
Collapse
Affiliation(s)
- Ravindra Kumar
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226 002, India.
| | | | | | | | | |
Collapse
|
5
|
Behera BK, Rout AK, Baisvar VS, Paria P, Singh NS, Ghadei SS, Jana AK, Parida PK, Das BK. The complete mitochondrial genome sequence of Osteobrama belangeri (Cyprinidae) and its comparison with other related Cypriniformes fish species. Mitochondrial DNA B Resour 2019; 4:2330-2331. [PMID: 33365529 PMCID: PMC7687656 DOI: 10.1080/23802359.2019.1624206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 05/17/2019] [Indexed: 11/25/2022] Open
Abstract
The complete mitogenome of Osteobrama belangeri is described using Ion Torrent (PGM sequencer), which was 16,609 bp in size comprising 13 mRNAs, teo rRNA genes, 22 tRNAs, and 926 bp as D-Loop control region, in addition to gene order and organization, being similar to most of the other related Cypriniformes fish mitogenome of NCBI databases. The all 22 tRNAs were packed into a typical clover-leaf structure. In the present study, the mitogenome has 99% similarity to the complete mitogenome sequence of O. belangeri mitogenome details previously and also would be helpful in understanding the phylogenetics, population genetics, and evolution of family Cyprinidae fishes.
Collapse
Affiliation(s)
- Bijay Kumar Behera
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Kolkata, India
| | - Ajaya Kumar Rout
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Kolkata, India
| | | | - Prasenjit Paria
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Kolkata, India
| | | | - Sanjeev Sen Ghadei
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Kolkata, India
| | - Asim Kumar Jana
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Kolkata, India
| | - Pranaya Kumar Parida
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Kolkata, India
| | - Basanta Kumar Das
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Kolkata, India
| |
Collapse
|
6
|
Abstract
Striped snakehead (Channa striata) is a freshwater species of early Miocene period belonging to family Channidae. The genetic variability of the snakehead populations in India was not well known. Present study was undertaken using 149 sequences of control region of mitochondrial DNA from seven geographically distinct populations of Indian water, which resulted in 46 haplotypes with 137 variable nucleotide sites (60 singletons and 77 parsimony informative) and the nucleotide frequencies was: A = 33.0, T = 28.1, G = 15.4, and C = 23.5%. The presence of low-frequency of younger haplotypes with a large number of singletons indicates the absence of dominant haplotype. Hierarchical AMOVA showed highly significant genetic differentiation (FST = 0.56, p < .00) among the populations. The pattern of genetic differentiation was not consistent with geographical distributions. AMOVA identified three genetically heterogeneous clades. The significant finding of Imphal and Chaliyar was that they were found genetically close to each other, but geographically much isolated from each other. The inference of the study suggests that the hypothesis of the single panmictic population of C. striata in Indian waters is rejected.
Collapse
Affiliation(s)
- Vishwamitra Singh Baisvar
- a Molecular Biology and Biotechnology Division , ICAR-National Bureau of Fish Genetic Resources , Lucknow , India
| | - Mahender Singh
- a Molecular Biology and Biotechnology Division , ICAR-National Bureau of Fish Genetic Resources , Lucknow , India
| | - Ravindra Kumar
- a Molecular Biology and Biotechnology Division , ICAR-National Bureau of Fish Genetic Resources , Lucknow , India
| |
Collapse
|
7
|
Baisvar VS, Kumar R, Singh M, Singh AK, Chauhan U, Mishra AK, Kushwaha B. Genetic diversity analyses for population structuring in Channa striata using mitochondrial and microsatellite DNA regions with implication to their conservation in Indian waters. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
8
|
Rout AK, Dehury B, Maharana J, Nayak C, Baisvar VS, Behera BK, Das BK. Deep insights into the mode of ATP-binding mechanism in Zebrafish cyclin-dependent protein kinase-like 1 (zCDKL1): A molecular dynamics approach. J Mol Graph Model 2018; 81:175-183. [PMID: 29574323 DOI: 10.1016/j.jmgm.2018.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/28/2018] [Accepted: 02/02/2018] [Indexed: 12/21/2022]
Abstract
In eukaryotes, the serine/threonine kinases (STKs) belonging to cyclin-dependent protein kinases (CDKs) play significant role in control of cell division and curb transcription in response to several extra and intra-cellular signals indispensable for enzymatic activity. The zebrafish cyclin-dependent protein kinase-like 1 protein (zCDKL1) shares a high degree of sequence and structural similarity with mammalian orthologs and express in brain, ovary, testis, and low levels in other tissues. Regardless of its importance in the developmental process, the structure, function and mode of ATP recognition have not been investigated yet due to lack of experimental data. Henceforth, to gain atomistic insights in to the structural dynamics and mode of ATP binding, a series of computational techniques involving theoretical modeling, docking, molecular dynamics (MD) simulations and MM/PBSA binding free energies were employed. The modeled bi-lobed zCDKL1 shares a high degree of secondary structure topology with human orthologs where ATP prefers to lie in the central cavity of the bi-lobed catalytic domain enclosed by strong hydrogen bonding, electrostatic and hydrophobic contacts. Long range MD simulation portrayed that catalytic domain of zCDKL1 to be highly rigid in nature as compared to the complex (zCDKL1-ATP) form. Comparative analysis with its orthologs revealed that conserved amino acids i.e., Ile10, Gly11, Glu12, Val18, Arg31, Phe80, Glu 130, Cys143 and Asp144 were crucial for ATP binding mechanism, which needs further investigation for legitimacy. MM/PBSA method revealed that van der Waals, electrostatic and polar solvation energy mostly contributes towards negative free energy. The implications of ATP binding mechanism inferred through these structural bioinformatics approaches will help in understanding the catalytic mechanisms of important STKs in eukaryotic system.
Collapse
Affiliation(s)
- Ajaya Kumar Rout
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, West Bengal, India
| | - Budheswar Dehury
- Biomedical Informatics Centre, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India
| | - Jitendra Maharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, 751003, Odisha, India
| | - Chirasmita Nayak
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, 751003, Odisha, India
| | - Vishwamitra Singh Baisvar
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, West Bengal, India
| | - Bijay Kumar Behera
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, West Bengal, India.
| | - Basanta Kumar Das
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, West Bengal, India.
| |
Collapse
|
9
|
Behera BK, Baisvar VS, Rout AK, Pakrashi S, Kumari K, Panda D, Das P, Parida PK, Meena DK, Bhakta D, Das BK, Jena J. The population structure and genetic divergence of Labeo gonius (Hamilton, 1822) analyzed through mitochondrial DNA cytochrome b gene for conservation in Indian waters. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:543-551. [DOI: 10.1080/24701394.2017.1320992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Bijay Kumar Behera
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Vishwamitra Singh Baisvar
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Ajaya Kumar Rout
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Sudip Pakrashi
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Kavita Kumari
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Debabrata Panda
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Pronob Das
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Pranaya Kumar Parida
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Dharmendra Kumar Meena
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - D. Bhakta
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Basanta Kumar Das
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Joykrushna Jena
- Fisheries Division – Indian Council of Agricultural Research, New Delhi, India
| |
Collapse
|
10
|
Behera BK, Kunal SP, Baisvar VS, Meena DK, Panda D, Pakrashi S, Paria P, Das P, Debnath D, Parida PK, Das BK, Jena J. Genetic variation in wild and hatchery population of Catla catla (Hamilton, 1822) analyzed through mtDNA cytochrome b region. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:126-131. [DOI: 10.1080/24701394.2016.1253072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Bijay Kumar Behera
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | | | | | | | - Debarata Panda
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Sudip Pakrashi
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Prasenjit Paria
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Pronob Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Dipesh Debnath
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | | | - Basanta Kumar Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | | |
Collapse
|
11
|
Behera BK, Baisvar VS, Kunal SP, Meena DK, Panda D, Pakrashi S, Paria P, Das P, Bhakta D, Debnath D, Roy S, Suresh VR, Jena JK. Population structure and genetic diversity of Indian Major Carp, Labeo rohita (Hamilton, 1822) from three phylo-geographically isolated riverine ecosystems of India as revealed by mtDNA cytochrome b region sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:199-205. [PMID: 28024428 DOI: 10.1080/24701394.2016.1267156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The population structure and genetic diversity of Rohu (Labeo rohita Hamilton, 1822) was studied by analysis of the partial sequences of mitochondrial DNA cytochrome b region. We examined 133 samples collected from six locations in three geographically isolated rivers of India. Analysis of 11 haplotypes showed low haplotype diversity (0.00150), nucleotide diversity (π) (0.02884) and low heterogeneity value (0.00374). Analysis of molecular variance (AMOVA) revealed the genetic diversity of L. rohita within population is very high than between the populations. The Fst scores (-0.07479 to 0.07022) were the indication of low genetic structure of L. rohita populations of three rivers of India. Conspicuously, Farakka-Bharuch population pair Fst score of 0.0000, although the sampling sites are from different rivers. The phylogenetic reconstruction of unique haplotypes revealed sharing of a single central haplotype (Hap_1) by all the six populations with a point mutations ranging from 1-25 nucleotides.
Collapse
Affiliation(s)
- Bijay Kumar Behera
- a Fish Biotechnology Laboratory , ICAR-Central Inland Fisheries Research Institute , Kolkata , India
| | - Vishwamitra Singh Baisvar
- a Fish Biotechnology Laboratory , ICAR-Central Inland Fisheries Research Institute , Kolkata , India
| | | | - Dharmendra Kumar Meena
- a Fish Biotechnology Laboratory , ICAR-Central Inland Fisheries Research Institute , Kolkata , India
| | - Debarata Panda
- a Fish Biotechnology Laboratory , ICAR-Central Inland Fisheries Research Institute , Kolkata , India
| | - Sudip Pakrashi
- a Fish Biotechnology Laboratory , ICAR-Central Inland Fisheries Research Institute , Kolkata , India
| | - Prasenjit Paria
- a Fish Biotechnology Laboratory , ICAR-Central Inland Fisheries Research Institute , Kolkata , India
| | - Pronob Das
- a Fish Biotechnology Laboratory , ICAR-Central Inland Fisheries Research Institute , Kolkata , India
| | - Dibakar Bhakta
- b ICAR-Central Inland Fisheries Research Institute, Regional Center , Guwahati , India
| | - Dipesh Debnath
- b ICAR-Central Inland Fisheries Research Institute, Regional Center , Guwahati , India
| | - Suvra Roy
- a Fish Biotechnology Laboratory , ICAR-Central Inland Fisheries Research Institute , Kolkata , India
| | - V R Suresh
- a Fish Biotechnology Laboratory , ICAR-Central Inland Fisheries Research Institute , Kolkata , India
| | - J K Jena
- d Fisheries Division- Indian Council of Agricultural Research , New Delhi , India
| |
Collapse
|
12
|
Behera BK, Baisvar VS, Kumari K, Rout AK, Pakrashi S, Paria P, Das A, Rao AR, Rai A. The complete mitochondrial genome of the Asian stinging catfish , Heteropneustes fossilis (Siluriformes, Heteropneustidae) and its comparison with other related fish species. Mitochondrial DNA B Resour 2016; 1:804-805. [PMID: 33473634 PMCID: PMC7799967 DOI: 10.1080/23802359.2016.1219628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The complete mitogenome of Heteropneustes fossilis is described using Ion Torrent (PGM sequencer), which showed it was 16,489 bp in size comprising 13 mRNAs, 22 tRNAs, 2 rRNA genes, and 858 bp as D-Loop control region, along with gene order and organization, being similar to most of the other related Siluriformes fish mitogenome of NCBI databases. The 20 RNAs were packed into a typical cloverleaf structure. The mitogenome in the present study has 99% similarity to the complete mitogenome sequence of H. fossilis mitogenome reported earlier and also would be helpful in understanding the population genetics, phylogenetics, and evolution of catfishes.
Collapse
Affiliation(s)
- Bijay Kumar Behera
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India
| | - Vishwamitra Singh Baisvar
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India
| | - Kavita Kumari
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India
| | - Ajaya Kumar Rout
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India
| | - Sudip Pakrashi
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India
| | - Prasenjet Paria
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India
| | - Abhishek Das
- Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India
| | - A R Rao
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| |
Collapse
|
13
|
Singh AK, Kumar R, Mishra AK, Singh M, Baisvar VS, Chauhan UK, Kushwaha B, Nagpure NS. Authentication of five Barilius species from Indian waters using DNA barcoding. Genetika 2016; 52:943-950. [PMID: 29368907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Authentic identification of fish species is essential for conserving them as a valuable genetic resource in our environment. DNA barcoding of living beings has become an important and ultimate tool for establishing their molecular identity. Among cyprinids, Barilius is an important genus having nearly 23 species in Indian region whose morphological identification is often difficult due to minute differences in their features. Five species collected from Indian waters and primarily identified as Opsarius bakeri (syn. Barilius bakeri), B. gatensis, B. vagra, B. bendelisis and B. ngawa were authenticated by their DNA barcoding based on mitochondrial COI gene sequences. Five individuals of each species were taken for barcode preparation by COI gene sequencing which yielded one barcode for B. ngawa, two barcodes each for O. bakeri, B. gatensis, B. bendelisis and three barcodes for B. vagra. The order of inter and intra-specific variation was estimated to know a preliminary status of variation prevailing in these cold stream fish species significant for evolution and conservation of these valued species of our ichthyofauna. Average variation within genera was found to be 13.6% with intra-specific variation ranging from 0.0% (B. ngawa) to 0.6% (B. gatensis). These distance data are in the same order found by various researchers globally using COI barcode sequences in different fish species. Phylogenetic relatedness among Barilius species and some other cyprinids validate their status of individual species as established by conventional taxonomy.
Collapse
|
14
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
15
|
Behera BK, Baisvar VS, Kumari K, Rout AK, Pakrashi S, Paria P, Rao AR, Rai A. The complete mitochondrial genome of the Anabas testudineus (Perciformes, Anabantidae) and its comparison with other related fish species. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:161-162. [PMID: 26709978 DOI: 10.3109/19401736.2015.1115490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In the present study, the complete mitochondrial genome sequence of Anabas testudineusis reported using PGM sequencer (Ion Torrent, Life Technologies, La Jolla, CA). The complete mitogenome of climbing perch, A. testudineusis obtained by the de novo sequences assembly of genomic reads using the Torrent Mapping Alignment Program (TMAP), which is 16 603 bp in length. The mitogenome of A. testudineus composed of 13 protein- coding genes, two rRNA, and 22 tRNAs. Here, 20 tRNAs genes showed typical clover leaf model, and D-Loop as the control region along with gene order and organization, being closely similar to Osphronemidae and most of other Perciformes fish mitogenomes of NCBI databases. The mitogenome in the present study has 99% similarity to the complete mitogenome sequence of earlier reported A. testudineus. The phylogenetic analysis of Anabantidae depicted that their mitogenomes are closely related to each other. The complete mitogenome sequence of A. testudineus would be helpful in understanding the population genetics, phylogenetics, and evolution of Anabantidae.
Collapse
Affiliation(s)
- Bijay Kumar Behera
- a Fish Biotechnology Laboratory , ICAR - Central Inland Fisheries Research Institute , Barrackpore , Kolkata , West Bengal , India
| | - Vishwamitra Singh Baisvar
- a Fish Biotechnology Laboratory , ICAR - Central Inland Fisheries Research Institute , Barrackpore , Kolkata , West Bengal , India
| | - Kavita Kumari
- a Fish Biotechnology Laboratory , ICAR - Central Inland Fisheries Research Institute , Barrackpore , Kolkata , West Bengal , India
| | - Ajaya Kumar Rout
- a Fish Biotechnology Laboratory , ICAR - Central Inland Fisheries Research Institute , Barrackpore , Kolkata , West Bengal , India
| | - Sudip Pakrashi
- a Fish Biotechnology Laboratory , ICAR - Central Inland Fisheries Research Institute , Barrackpore , Kolkata , West Bengal , India
| | - Prasenjet Paria
- a Fish Biotechnology Laboratory , ICAR - Central Inland Fisheries Research Institute , Barrackpore , Kolkata , West Bengal , India
| | - A R Rao
- b ICAR - Indian Agricultural Statistics Research Institute , New Delhi , India
| | - Anil Rai
- b ICAR - Indian Agricultural Statistics Research Institute , New Delhi , India
| |
Collapse
|
16
|
Behera BK, Kumari K, Baisvar VS, Rout AK, Pakrashi S, Paria P, Jena JK. Complete mitochondrial genome sequence of Indian medium carp, Labeo gonius (Hamilton, 1822) and its comparison with other related carp species. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:7-8. [PMID: 26710185 DOI: 10.3109/19401736.2015.1106517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In the present study, the complete mitochondrial genome sequence of Labeo gonius is reported using PGM sequencer (Ion Torrent). The complete mitogenome of L. gonius is obtained by the de novo sequences assembly of genomic reads using the Torrent Mapping Alignment Program (TMAP) which is 16 614 bp in length. The mitogenome of L. gonius comprised of 13 protein-coding genes, 22 tRNAs, 2 rRNA genes, and D-loop as control region along with gene order and organization, being similar to most of other fish mitogenomes of NCBI databases. The mitogenome in the present study has 99% similarity to the complete mitogenome sequence of Labeo fimbriatus, as reported earlier. The phylogenetic analysis of Cypriniformes depicted that their mitogenomes are closely related to each other. The complete mitogenome sequence of L. gonius would be helpful in understanding the population genetics, phylogenetics, and evolution of Indian Carps.
Collapse
Affiliation(s)
- Bijay Kumar Behera
- a Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute , Barrackpore , West Bengal , Kolkata , India , and
| | - Kavita Kumari
- a Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute , Barrackpore , West Bengal , Kolkata , India , and
| | - Vishwamitra Singh Baisvar
- a Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute , Barrackpore , West Bengal , Kolkata , India , and
| | - Ajaya Kumar Rout
- a Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute , Barrackpore , West Bengal , Kolkata , India , and
| | - Sudip Pakrashi
- a Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute , Barrackpore , West Bengal , Kolkata , India , and
| | - Prasenjet Paria
- a Fish Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute , Barrackpore , West Bengal , Kolkata , India , and
| | - J K Jena
- b ICAR-National Bureau of Fish Genetics Resources , Lucknow , Uttar Pradesh , India
| |
Collapse
|
17
|
Singh AK, Kumar R, Singh M, Mishra AK, Chauhan UK, Baisvar VS, Verma R, Nagpure NS, Kushwaha B. Mitochondrial 16S rRNA gene-based evolutionary divergence and molecular phylogeny of Barilius spp. Mitochondrial DNA 2013; 26:41-7. [PMID: 23883181 DOI: 10.3109/19401736.2013.815168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Barilius is an important genus of fish family Cyprinidae, which comprises 22 species from Indian region. This study aimed to characterize five commonly occurring Bariline species, for example, Barilius bakeri. Barilius gatensis. Barilius vagra. Barilius bendelisis and Barilius tileo, across the country using partial mitochondrial 16 S rRNA gene, to estimate the order of inter- and intra-species divergence among these species and to establish phylogenetic and evolutionary relationships. The average inter-specific divergence was estimated as 7.10%. Intra-specific divergence of 0.20% and 0.10% was observed in B. gatensis and B. bendelisis that exhibited three and two haplotypes with 0.70 and 0.60 haplotype diversities, respectively. The NJ and MP phylogenetic trees were constructed using 16 S rRNA sequences along with sequences of the other five Indian cyprinid species retrieved from NCBI. Phylogenetic trees revealed five discrete branches each as a distinct species of the genus and exhibited identical phylogenetic relationship with other cyprinids. The study provided adequate information to distinguish the five Barilius species and indicated the suitability of 16S rRNA gene sequences in genetic divergence and phylogenetic studies.
Collapse
Affiliation(s)
- Ajay Kumar Singh
- National Bureau of Fish Genetic Resources , Lucknow, Uttar Pradesh , India and
| | | | | | | | | | | | | | | | | |
Collapse
|