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Modeel S, Negi RK, Sharma M, Dolkar P, Yadav S, Siwach S, Yadav P, Negi T. A comprehensive DNA barcoding of Indian freshwater fishes of the Indus River system, Beas. Sci Rep 2024; 14:2763. [PMID: 38307873 PMCID: PMC10837433 DOI: 10.1038/s41598-024-52519-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/19/2024] [Indexed: 02/04/2024] Open
Abstract
The Beas River is one of the important rivers of the Indus River system located in Himachal Pradesh, India, that harbors a diverse range of freshwater fish species. The present study employed COI gene to investigate the ichthyofaunal diversity of river Beas. Through the sequencing of 203 specimens from Beas River, we identified 43 species, belonging to 31 genera, 16 families, and 10 orders. To analyze the genetic divergence and phylogeny of identified species, 485 sequences of Indian origin were retrieved from BOLD, resulting in a dataset of 688 sequences. Our findings consistently revealed a hierarchical increase in the mean K2P genetic divergence within species (0.80%), genus (9.06%), and families (15.35%). Automated Barcode Gap discovery, Neighbour Joining, and Bayesian inference consensus tree methodologies were employed to determine the putative species and their phylogeny, successfully delimiting most of the species with only a few exceptions. The results unveiled six species exhibiting high intra-species divergence (> 2%), suggesting the presence of sibling species and falsely identified sequences on online databases. The present study established the first DNA barcoding-based inventory of freshwater fish species in the Beas River providing comprehensive insights into economically exploited endangered and vulnerable species. In order to ensure the sustainable use of aquatic resources in the Beas River, we recommend the implementation of species measures to protect biodiversity and genetic resources.
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Affiliation(s)
- Sonakshi Modeel
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India
| | - Ram Krishan Negi
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India.
| | - Monika Sharma
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India
| | - Padma Dolkar
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India
| | - Sheetal Yadav
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India
| | - Sneha Siwach
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India
| | - Pankaj Yadav
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India
| | - Tarana Negi
- Department of Zoology, Govt. College Dujana, District Jhajjar, Beri, Haryana, India
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Karamat S, Ashraf N, Akhtar T, Rahim F, Shafi N, Khalid S, Shahid B, Khawaja S, Rahim J, Majeed Z, Lateef Z, Mehmood M. CO1-Based DNA barcoding for assessing diversity of Pteropus giganteus from the state of Azad Jammu Kashmir, Pakistan. BRAZ J BIOL 2021; 81:584-591. [PMID: 32785466 DOI: 10.1590/1519-6984.226466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 02/21/2020] [Indexed: 11/22/2022] Open
Abstract
The flying fox (Pteropus giganteus) also familiar with the name of the greater Indian fruit Bat belongs to the order Chiroptera and family Pteropodidae. Current research emphasis on the DNA barcoding of P. giganteus in Azad Jammu Kashmir. Bat sequences were amplified and PCR products were sequenced and examined by bioinformatics software. Congeneric and conspecific, nucleotide composition and K2P nucleotide deviation, haplotype diversity and the number of haplotypes were estimated. The analysis showed that all of the five studied samples of P. giganteus had low G contents (G 19.8%) than C (27.8%), A (25.1%) and T (27.3%) contents. The calculated haplotype diversity was 0.60% and the mean intraspecific K2P distance was 0.001% having a high number of transitional substitutions. The study suggested that P. giganteus (R=0.00) do not deviate from the neutral evolution. It was determined from the conclusion that this mtDNA gene is a better marker for identification of Bat species than nuclear genes due to its distinctive characteristics and may serve as a landmark for the identification of interconnected species at the molecular level and in the determination of population genetics.
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Affiliation(s)
- Sana Karamat
- University of Azad Jammu and Kashmir, Department of Zoology, Muzaffarabad, Pakistan
| | - Nasra Ashraf
- University of Azad Jammu and Kashmir, Department of Zoology, Muzaffarabad, Pakistan
| | - Tasleem Akhtar
- University of Azad Jammu and Kashmir, Department of Zoology, Muzaffarabad, Pakistan
| | - Faisal Rahim
- Department of Agriculture Azad Jammu and Kashmir, Directorate of Agriculture Research, Muzaffarabad, Pakistan
| | - Nuzhat Shafi
- University of Azad Jammu and Kashmir, Department of Zoology, Muzaffarabad, Pakistan
| | - Saba Khalid
- University of Azad Jammu and Kashmir, Department of Zoology, Muzaffarabad, Pakistan
| | - Benish Shahid
- University of Azad Jammu and Kashmir, Department of Zoology, Muzaffarabad, Pakistan
| | - Sundas Khawaja
- University of Azad Jammu and Kashmir, Department of Biotechnology, Muzaffarabad, Pakistan
| | - Junaid Rahim
- University of Poonch Rawalakot, Faculty of Agriculture, Department of Entomology, Shamsabad, Rawalakot, Azad Jammu and Kashmir, Pakistan
| | - Zahid Majeed
- University of Azad Jammu and Kashmir, Department of Biotechnology, Muzaffarabad, Pakistan
| | - Zahid Lateef
- University of Azad Jammu and Kashmir, Department of Zoology, Muzaffarabad, Pakistan
| | - Majid Mehmood
- University of Poonch Rawalakot, Department of Zoology, Shamsabad, Rawalakot, Azad Jammu and Kashmir, Pakistan
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Akhtar T, Ali G, Shafi N, Akhtar W, Khan AH, Latif Z, Wali A, Ain-ul-Batool S, Khan AR, Mumtaz S, Altaf SI, Khawaja S, Sadia, Khalid M, Rehman FU, Javid Q. Sequencing and Characterization of Mitochondrial Protein-Coding Genes for Schizothorax niger (Cypriniformes: Cyprinidae) with Phylogenetic Consideration. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5980135. [PMID: 33490246 PMCID: PMC7787735 DOI: 10.1155/2020/5980135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/29/2020] [Accepted: 11/18/2020] [Indexed: 01/05/2023]
Abstract
The present study was conducted to get more information about the genome and locate the taxonomic position of Schizothorax niger in Schizothoracinae through mitochondrial 13 protein-coding genes (PCGs). These PCGs for S. niger were found to be 11409 bps in length ranging from 165 (ATPase 8) to 1824 bps (NADH dehydrogenase subunit 5) and encode 3801 amino acids. In these PCGs, 4 genes overlap on the similar strands, while one shown on the opposite one: ATPase 6+8 and NADH dehydrogenase subunit 4+4L overlap by 7 nucleotides. Similarly, ND5-ND6 overlap by 4 nucleotides, while ATP6 and COIII overlap by 1 nucleotide. Similarly, four commonly used amino acids in S. niger were Leu (15.6 %), Ile (10.12 %), Thr (8.12 %), and Ala (8.7 %). The results presented that COII, COIII, NDI, ND4L, and Cytb had substantial amino acid conservation as compared to the COI gene. Through phylogenetic analysis, it was observed that S. niger is closely linked with S. progastus, S. labiatus, S. plagiostomus, and S. nepalensis with high bootstrap values. The present study provided more genomic data to know the diversity of the mitochondrial genome and its molecular evolution in Schizothoracinae.
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Affiliation(s)
- Tasleem Akhtar
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Ghazanfar Ali
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Nuzhat Shafi
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Wasim Akhtar
- Department of Botany, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Abdul Hameed Khan
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Zahid Latif
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Abdul Wali
- Faculty of Life Sciences & Informatics, BUITEMS, 87100 Quetta, Pakistan
| | - Syeda Ain-ul-Batool
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Abdul Rehman Khan
- Department of Chemistry, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Sadia Mumtaz
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Syed Iftikhar Altaf
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Sundus Khawaja
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Sadia
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Madiha Khalid
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
- Department of Biotechnology, Women University Bagh, Pakistan
| | - Fazal Ur Rehman
- Department of Microbiology, University of Balochistan, Quetta 87300, Pakistan
| | - Qudir Javid
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
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Ma Q, He K, Wang X, Jiang J, Zhang X, Song Z. Better Resolution for Cytochrome b than Cytochrome c Oxidase Subunit I to Identify Schizothorax Species (Teleostei: Cyprinidae) from the Tibetan Plateau and Its Adjacent Area. DNA Cell Biol 2020; 39:579-598. [PMID: 32069124 DOI: 10.1089/dna.2019.5031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Schizothorax is one of the most diverse groups of schizothoracine fish. Many species within this genus possess highly similar morphological characters and are very difficult to be identified accurately only based on morphology. The present study aims to test the effectiveness of mitochondrial cytochrome c oxidase subunit I (COI) gene and cytochrome b (Cytb) gene for discriminating the Schizothorax fish. A total of 185 individuals of 11 species for COI gene and 264 individuals of 23 species for Cytb gene were used for analyzing, respectively. According to the genetic distances, only one species based on COI gene and five species based on Cytb gene had "barcoding gaps," respectively. The tree-based analysis displayed that four species based on COI gene and six species based on Cytb gene clustered monophyletic group with strong support, respectively. The optimal threshold value of Schizothorax is 0.005 based on COI gene and 0.008 based on Cytb gene. The results of genetic similarity tests performed through online BLAST showed that 108 of 185 similarity searches succeeded in identifying conspecific sequences based on COI gene and 199 of 264 succeeded in identifying conspecific sequences based on Cytb gene. Considering greater interspecific genetic distance in Kimura 2-parameter (K2P) analysis and many clades with higher supporting values in tree-based analysis, we suggest that Cytb gene has better resolution in discrimination of Schizothorax species than COI gene. However, there are still many confused clustering relationships based on molecular data currently available. Incomplete lineage sorting, the existence of possible cryptic species and problematic morphological identification, etc. might have greatly weakened the resolution of Cytb gene in discrimination of Schizothorax species.
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Affiliation(s)
- Qingzhan Ma
- College of Life Sciences, Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Kun He
- College of Life Sciences, Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaodong Wang
- College of Life Sciences, Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiuyue Zhang
- College of Life Sciences, Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhaobin Song
- College of Life Sciences, Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China.,College of Life Sciences, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Ayesha UR, Shafi N, Akhtar T, Zareen A, Ayub H. DNA barcoding of cyprinids ( Labeo rohita, Catla catla and Cirrhinus mrigala), mitochondrial CO1-based study. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1547132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Ume Rubab Ayesha
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Nuzhat Shafi
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Tasleem Akhtar
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Atiya Zareen
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Huma Ayub
- Department of Wildlife & Fisheries, Government of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
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