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Lam TTH, Dinh QM, Truong VTB, Truong NT, Tran NS, Nguyen THD. The use of mtCOI gene sequences in identifying Butis species in the Southwest of Vietnam. Heliyon 2023; 9:e20139. [PMID: 37809956 PMCID: PMC10559908 DOI: 10.1016/j.heliyon.2023.e20139] [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: 02/11/2022] [Revised: 09/06/2023] [Accepted: 09/12/2023] [Indexed: 10/10/2023] Open
Abstract
Butis genus is characterised by their small body size and morphological variability, allowing them to adapt to different habitats. This paper analyses the mitochondrial cytochrome C oxidase subunit I gene sequences and morphology of Butis for identification purposes and to understand genetic relationships. The morphological characteristics of Butis koilomatodon differed obviously from Butis humeralis and Butis butis. After classification based on morphology, the total deoxyribonucleic acid of fish samples was isolated, and the mitochondrial cytochrome C oxidase subunit I genes were successfully amplified using the polymerase chain reaction method. At approximately 617bp, the obtained mitochondrial cytochrome C oxidase subunit I gene sequences were highly similar to the reference sequences on Genbank (85.90-100%). The phylogenetic graphic was divided into five distinct groups, where B. koilomatodon was grouped in one group; and B. humeralis and B. butis were grouped together. The results suggest that B. humeralis was an entirely different species from B. butis, with a mean genetic divergence of up to 14%. However, further studies using a combination of other types of deoxyribonucleic acid barcoding together with morphological features should be undertaken to confirm these findings.
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Affiliation(s)
- Tran Thi Huyen Lam
- 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
| | - Van Thi Bich Truong
- Institute of Food and Biotechnology, Can Tho University, Xuan Khanh Ward, Ninh Kieu District, Can Tho, 900000, Viet Nam
| | - Ngon Trong Truong
- Institute of Food and Biotechnology, Can Tho University, Xuan Khanh Ward, Ninh Kieu District, Can Tho, 900000, Viet Nam
| | - Nam Sy Tran
- Department of Environmental Sciences, College of Environment and Natural Resources, Can Tho University, 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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Canoglu H, Aksu I, Turan D, Bektas Y. DNA barcoding of the genus Alburnoides Jeitteles, 1861 (Actinopterygii, Cyprinidae) from Anatolia, Turkey. ZOOSYST EVOL 2023. [DOI: 10.3897/zse.99.94333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
The present study investigated the ability of DNA barcoding to reliably identify the endemic freshwater species in Turkey, known as biodiversity hotspots. The barcode region (652 bp) of the mitochondrial cytochrome c oxidase subunit I (COI) was used to barcode 153 individuals from 13 morphologically identified species of the genus Alburnoides. Based on the Kimura two-parameter (K2P) evolution model, the average interspecific distance (0.0595) was 31-fold higher than the average intraspecific distance (0.0019). There was a clear-cut barcode gap (0.0158–0.0187) between maximum intraspecific distance (A. tzanevi and A. velioglui) and minimum nearest-neighbour distance (A. freyhofi and A. kurui) for Anatolian Alburnoides species and a common genetic threshold of 0.0158 sequence divergence was defined for species delimitation. The multiple species delimitation methods (ABGD, ASAP, GMYC and bPTP) revealed a total of 11 molecular operational taxonomic units (MOTUs) for 13 morphospecies. Neighbour-joining (NJ), Maximum Likelihood (ML) and Bayesian Inference (BI) tree analysis indicated that all haplotypes were clustered into two major clades, which corresponded to eleven Alburnoides species clusters, with strong bootstrap support. Furthermore, all the specimens clustered in concurrence with the morpho-taxonomic status of the species, except for two species (A. coskuncelebii and A. emineae) that were morphologically differentiated, but showed overlap in variation for COI-based DNA barcode data with other species. Overall, present results identified that COI-based DNA barcoding is effective for species identification and cataloguing of genus Alburnoides in Turkey.
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Awas M, Ahmed I, Ahmad SM, Al-Anazi KM, Farah MA, Bhat B. Integrative approach for validation of six important fish species inhabiting River Poonch of north-west Himalayan region (India). Front Genet 2023; 13:1047436. [PMID: 36726718 PMCID: PMC9886096 DOI: 10.3389/fgene.2022.1047436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 11/29/2022] [Indexed: 01/06/2023] Open
Abstract
Traditionally, species of fish are identified based on morphological characteristics. Although these taxonomic descriptions are essential, there are cases where the morphological characters distinguishing these species show marginal differences. For instance, in the Poonch River in the Himalayas, there are 21 species, out of which some are morphologically similar, and the taxonomic distinction between these species is unclear. Therefore, in this study, we used sequences from two mitochondrial genes, Cytochrome b (Cyt b) and a larger ribosomal subunit (16S rRNA), as well as the morphological analysis to address any taxonomic ambiguities among the six fish species. Maximum Likelihood results revealed that all the species were clustered according to their families and genera. The phenotypic analysis also supported this statement, as all the species of different genera like Schizothorax, Tor, Garra, Traqilabeo, and Glyptothorax are grouped in their particular cluster, it shows that species of a separate class share a mutual morphological characteristic. While genetic analyses of these species suggest nucleotide diversity (p) and haplotype diversity, with Hd values as 0.644 for Cyt b and 0.899 for 16S rRNA, confirming the rich genetic diversity in the river. Overall, we recommend that the integrative approach in delimiting the fish species is more effective than the individual one and can be used to rapidly diagnose a species and understand the evolutionary relationship between the species.
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Affiliation(s)
- Mohd Awas
- Fish Nutrition Laboratory, Department of Zoology, University of Kashmir, Srinagar, India
| | - Imtiaz Ahmed
- Fish Nutrition Laboratory, Department of Zoology, University of Kashmir, Srinagar, India,*Correspondence: Imtiaz Ahmed, ; Syed Mudasir Ahmad,
| | - Syed Mudasir Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, India,*Correspondence: Imtiaz Ahmed, ; Syed Mudasir Ahmad,
| | | | - Mohammad Abul Farah
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Basharat Bhat
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, India
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Habib KA, Neogi AK, Rahman M, Oh J, Lee YH, Kim CG. DNA barcoding of brackish and marine water fishes and shellfishes of Sundarbans, the world's largest mangrove ecosystem. PLoS One 2021; 16:e0255110. [PMID: 34339426 PMCID: PMC8328341 DOI: 10.1371/journal.pone.0255110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/09/2021] [Indexed: 11/18/2022] Open
Abstract
The present study aims to apply a DNA barcoding tool through amplifying two mitochondrial candidate genes i.e., COI and 16S rRNA for accurate identification of fish, aquatic molluscs and crustaceans of Sundarbans mangrove wetland, to build a reference library of fish and shellfishes of this unique ecosystems. A total of 185 mitochondrial COI barcode sequences and 59 partial sequences of the 16S rRNA gene were obtained from 120 genera, 65 families and 21 orders of fish, crustaceans and molluscs. The collected samples were first identified by examining morphometric characteristics and then assessed by DNA barcoding. The COI and 16S rRNA sequences of fishes and crustaceans were clearly discriminated among genera in their phylogenies. The average Kimura two-parameter (K2P) distances of COI barcode sequences within species, genera, and families of fishes are 1.57±0.06%, 15.16±0.23%, and 17.79±0.02%, respectively, and for 16S rRNA sequences, these values are 1.74±.8%, 0.97±.8%, and 4.29±1.3%, respectively. The minimum and maximum K2P distance based divergences in COI sequences of fishes are 0.19% and 36.27%, respectively. In crustaceans, the K2P distances within genera, families, and orders are 1.4±0.03%, 17.73±0.15%, and 22.81±0.02%, respectively and the minimum and maximum divergences are 0.2% and 33.93%, respectively. Additionally, the present study resolves the misidentification of the mud crab species of the Sundarbans as Scylla olivacea which was previously stated as Scylla serrata. In case of molluscs, values of interspecific divergence ranges from 17.43% to 66.3% in the barcoded species. The present study describes the development of a molecular and morphometric cross-referenced inventory of fish and shellfish of the Sundarbans. This inventory will be useful in future biodiversity studies and in forming future conservation plan.
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Affiliation(s)
- Kazi Ahsan Habib
- Faculty of Fisheries, Department of Fisheries Biology and Genetics, Aquaculture and Marine Science, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
- Department of Fisheries Biology and Genetics, Aquatic Bioresource Research Lab, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
- * E-mail: ,
| | - Amit Kumer Neogi
- Department of Fisheries Biology and Genetics, Aquatic Bioresource Research Lab, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
| | - Muntasir Rahman
- Department of Biological Science, Wayne State University, Detroit, Michigan, United States of America
| | - Jina Oh
- Marine Biology and Biological Oceanography Division, Korea Institute of Ocean Science and Technology (KIOST), Busan, Korea
| | - Youn-Ho Lee
- Marine Biology and Biological Oceanography Division, Korea Institute of Ocean Science and Technology (KIOST), Busan, Korea
| | - Choong-Gon Kim
- Marine Biology and Biological Oceanography Division, Korea Institute of Ocean Science and Technology (KIOST), Busan, Korea
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Székely C, Ghosh S, Borzák R, Goswami U, Molnár K, Cech G. The occurrence of known Myxobolus and Thelohanellus species (Myxozoa, Myxosporea) from Indian major carps with the description of Myxobolus bandyopadhyayi n. sp. in West Bengal. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2021; 16:18-25. [PMID: 34381686 PMCID: PMC8334371 DOI: 10.1016/j.ijppaw.2021.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 11/29/2022]
Abstract
Myxosporean infection of Indian major carps (rohu, Labeo rohita; catla, Gibelion catla; mrigal, Cirrhinus mrigala) was examined from two fish farms and two fish markets in West Bengal, India. One Thelohanellus and four Myxobolus species were detected from the fins and scales of the investigated species. Comprehensive morphological and molecular biological studies revealed four already known species, Thelohanellus caudatus from the fins of rohu, Myxobolus dermiscalis from the scales of rohu, Myxobolus chakravartyi from the fins of catla, and Myxobolus rewensis from the fins of mrigal. This study complemented the species description of M. chakravartyi and M. rewensis with the missing molecular data. Moreover, based on morphometrics and ssrDNA sequence data, a new species was documented from the scales of rohu, and named Myxobolus bandyopadhyayi n. sp. Myxozoan infections were recognised from Indian major carps in West Bengal, India. A new Myxobolus species was discovered from the scales of rohu: Myxobolus bandiopadhyayi n. sp. Redescription of four known Indian Myxobolus and Thelohanellus spp. The first molecular data were obtained on Myxobolus chakravartyi and Myxobolus rewensis. ssrDNA was used to support the morphological identification of taxa.
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Affiliation(s)
- Csaba Székely
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Subarna Ghosh
- Serampore College, Serampore, Hooghly, West Bengal, India
| | - Réka Borzák
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Urvashi Goswami
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Kálmán Molnár
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Gábor Cech
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
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Ngwakum BB, Payne RP, Teske PR, Janson L, Kerwath SE, Samaai T. Hundreds of new DNA barcodes for South African sponges. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1915896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Benedicta B. Ngwakum
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Robyn P. Payne
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Bellville, Cape Town, South Africa
| | - Peter R. Teske
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Liesl Janson
- Department of Forestry, Fisheries and the Environment, Oceans & Coasts Branch, Oceans & Coasts Research, Private Bag X4390, Cape Town, 8001, Western Cape, South Africa
| | - Sven E. Kerwath
- Department of Biological Sciences, University of Cape Town, Private Bag X 3, Rondebosch, Cape Town, 7701, South Africa
- Department of Forestry, Fisheries and the Environment, Fisheries Branch, Fisheries Research, Private Bag X2, Roggebaai, Cape Town, 8012, Western Cape, South Africa
| | - Toufiek Samaai
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Bellville, Cape Town, South Africa
- Department of Forestry, Fisheries and the Environment, Oceans & Coasts Branch, Oceans & Coasts Research, Private Bag X4390, Cape Town, 8001, Western Cape, South Africa
- Department of Biological Sciences, University of Cape Town, Private Bag X 3, Rondebosch, Cape Town, 7701, South Africa
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Kundu S, Chandra K, Tyagi K, Pakrashi A, Kumar V. DNA barcoding of freshwater fishes from Brahmaputra River in Eastern Himalaya biodiversity hotspot. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2411-2419. [PMID: 33365567 PMCID: PMC7710314 DOI: 10.1080/23802359.2019.1637290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The genetic diversity of freshwater fishes is still anonymous in several drainage systems in northeast India. Moreover, the comparative genetic analysis is largely sporadic to judge their actual diversity and true status. We generated 89 DNA barcodes of 40 morphologically identified fishes collected from two major tributaries of Brahmaputra River. The comparative study revealed that most of the species were clearly discriminated by their estimated genetic distances and monophyletic clustering in Bayesian (BA) tree. Considering the genetic divergence (2%) for species discrimination boundary, the high genetic diversity (2.36–10.73%) was detected in 11 species (Macrognathus pancalus, Channa punctata, Puntius terio, Bangana ariza, Garra arupi, Badis badis, Mystus vittatus, Rita rita, Gagata cenia, Mastacembelus armatus, and Danio dangila), which signified the occurrence of concealed genetic diversity in this ecozone. However, the insignificant genetic distances were also noticed in few reportedly valid species: Channa stiktos and C. ornatipinnis (1.43%); Mystus ngasep, M. rufescens, and M. carcio (0.4%); Glyptothorax trilineatus, G. churamanii, and G. verrucosus (0.4%); Botia almorhae, B. histrionica, B. lohachata, and B. rostrata (0–0.4%); Barilius barilia and B. vagra (0.4%); Batasio merianiensis and B. tengana (1.2%); Puntius chola and P. fraseri (0%), Schistura beavani and S. paucireticulata (0%); hence to validate this species, generation of more barcode data was required from their types or topotypes. The present study would help to develop conservation schemes for the native species and collegiate ecosystem, which associated with the livelihoods of millions of ethnic communities in this region.
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Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Avas Pakrashi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
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Rathipriya A, Karal Marx K, Jeyashakila R. Molecular identification and phylogenetic relationship of flying fishes of Tamil Nadu coast for fishery management purposes. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:500-510. [PMID: 30691341 DOI: 10.1080/24701394.2018.1558220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The partial sequences of cytochrome c oxidase subunit I (COI) mitochondrial gene were analysed for developing species specific molecular signatures and phylogenetic relationship among the commercially important flying fishes (Cheilopogon cyanopterus, Cheilopogon furcatus and Hirundichthys coromandelensis) distributed in Tamil Nadu coast. Accurate identification of these species is important for fishery management as its morphological characters are very similar. Since the morphological features are very similar, accurate identification using molecular tools is essential for sustainable utilization and management of these species across their distributional range. The estimated transition/transversion bias (R) is 3.45. The average nucleotide sequences calculated were A = 30.00%, T/U = 26.40%, C = 17.00% and G = 26.60%. Using COI data analysis, the intraspecies genetic distance ranged from 0.00 to 0.05, while it varied from 0.06 to 0.08 for interspecies. Partial sequences of the genes provided sufficient phylogenetic information to distinguish the three flying fishes indicating the usefulness of mtDNA-based approach in species identification.
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Affiliation(s)
- A Rathipriya
- a Tamil Nadu Dr. J. Jayalalithaa Fisheries University , Nagapattinam , India
| | - K Karal Marx
- b Institute of Postgraduate Studies, OMR Campus , Chennai , India
| | - R Jeyashakila
- c Fisheries College and Research Institute , Thoothukudi , India
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Huang J, Wang NN, Zhang Y, Chen HW. Stegana (Oxyphortica) convergens species group (Diptera: Drosophilidae) from the Oriental region, with morphological and molecular evidence. J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1478010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Jia Huang
- Department of Entomology, South China Agricultural University, Guangzhou, China
| | - Nan-Nan Wang
- Department of Entomology, South China Agricultural University, Guangzhou, China
| | - Yuan Zhang
- Department of Entomology, South China Agricultural University, Guangzhou, China
| | - Hong-Wei Chen
- Department of Entomology, South China Agricultural University, Guangzhou, China
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Barman AS, Singh M, Singh SK, Saha H, Singh YJ, Laishram M, Pandey PK. DNA Barcoding of Freshwater Fishes of Indo-Myanmar Biodiversity Hotspot. Sci Rep 2018; 8:8579. [PMID: 29872224 PMCID: PMC5988717 DOI: 10.1038/s41598-018-26976-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/22/2018] [Indexed: 12/22/2022] Open
Abstract
To develop an effective conservation and management strategy, it is required to assess the biodiversity status of an ecosystem, especially when we deal with Indo-Myanmar biodiversity hotspot. Importance of this reaches to an entirely different level as the hotspot represents the area of high endemism which is under continuous threat. Therefore, the need of the present study was conceptualized, dealing with molecular assessment of the fish fauna of Indo-Myanmar region, which covers the Indian states namely, Manipur, Meghalaya, Mizoram, and Nagaland. A total of 363 specimens, representing 109 species were collected and barcoded from the different rivers and their tributaries of the region. The analyses performed in the present study, i.e. Kimura 2-Parameter genetic divergence, Neighbor-Joining, Automated Barcode Gap Discovery and Bayesian Poisson Tree Processes suggest that DNA barcoding is an efficient and reliable tool for species identification. Most of the species were clearly delineated. However, presence of intra-specific and inter-specific genetic distance overlap in few species, revealed the existence of putative cryptic species. A reliable DNA barcode reference library, established in our study provides an adequate knowledge base to the groups of non-taxonomists, researchers, biodiversity managers and policy makers in sketching effective conservation measures for this ecosystem.
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Affiliation(s)
- Anindya Sundar Barman
- College of Fisheries (Central Agricultural University, Imphal), Lembucherra, Tripura (West), 799210, India.
| | - Mamta Singh
- College of Fisheries (Central Agricultural University, Imphal), Lembucherra, Tripura (West), 799210, India
| | - Soibam Khogen Singh
- College of Fisheries (Central Agricultural University, Imphal), Lembucherra, Tripura (West), 799210, India
| | - Himadri Saha
- College of Fisheries (Central Agricultural University, Imphal), Lembucherra, Tripura (West), 799210, India
| | - Yumlembam Jackie Singh
- College of Fisheries (Central Agricultural University, Imphal), Lembucherra, Tripura (West), 799210, India
| | - Martina Laishram
- College of Fisheries (Central Agricultural University, Imphal), Lembucherra, Tripura (West), 799210, India
| | - Pramod Kumar Pandey
- College of Fisheries (Central Agricultural University, Imphal), Lembucherra, Tripura (West), 799210, India
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Bingpeng X, Heshan L, Zhilan Z, Chunguang W, Yanguo W, Jianjun W. DNA barcoding for identification of fish species in the Taiwan Strait. PLoS One 2018; 13:e0198109. [PMID: 29856794 PMCID: PMC5983523 DOI: 10.1371/journal.pone.0198109] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/14/2018] [Indexed: 11/30/2022] Open
Abstract
DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding reference database of fishes in the Taiwan Strait and evaluate the applicability of using the COI gene for the identification of fish at the species level. A total of 284 mitochondrial COI barcode sequences were obtained from 85 genera, 38 families and 12 orders of fishes. The mean length of the sequences was 655 base pairs. The average Kimura two parameter (K2P) distances within species, genera, families, orders and classes were 0.21%, 6.50%, 23.70% and 25.60%, respectively. The mean interspecific distance was 31-fold higher than the mean intraspecific distance. The K2P neighbor-joining trees based on the sequence generally clustered species in accordance with their taxonomic classifications. High efficiency of species identification was demonstrated in the present study by DNA barcoding, and we conclude that COI sequencing can be used to identify fish species.
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Affiliation(s)
- Xing Bingpeng
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Lin Heshan
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Zhang Zhilan
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Wang Chunguang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Wang Yanguo
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
| | - Wang Jianjun
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography State Oceanic Administration, Xiamen, Fujian, China
- * E-mail:
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QAYOOM UBAID, PAWAR RAVINDRAA, MOHITE SWAPNAJAA, SAWANT MILINDS, NIRMALE VIVEKH, PAWAR SHRIKANTP, GOSWAMI MUKUNDA, LAKRA WAZIRS. DNA barcoding of some commonly exploited fishes from the northern Western Ghats, India. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2018. [DOI: 10.56093/ijans.v88i2.79354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The Western Ghats, being very rich in freshwater fish diversity, has recently been confirmed as a globallysignificant centre of diversity and endemism for freshwater species and comprise one of the 34 global biodiversityhotspots. Owing to its extreme ichthyofaunal diversity, the present study was designed to generate cytochromeoxidase I (COI) DNA barcodes for the identification of some commonly exploited fishes from the west-flowingrivers of northern Western Ghats. Twenty-three fish specimens representing 6 families and 10 species were barcodedfrom the major west-flowing rivers of the northern Western Ghats. The obtained barcodes discriminated all thespecies with sufficient barcode gap. The average Kimura two parameter (K2P) values for within species, the genusand family distances were 0.37, 17.74 and 18.51% respectively. The neighbour-joining tree revealed distinct clusterscorresponding to the taxonomic status of the species. Generated barcodes are expected to provide the much-neededbaseline reference for the ichthyofaunal biodiversity of the global biodiversity hotspot.
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Wang ZL, Yang XQ, Wang TZ, Yu X. Assessing the effectiveness of mitochondrial COI and 16S rRNA genes for DNA barcoding of farmland spiders in China. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:695-702. [PMID: 28712321 DOI: 10.1080/24701394.2017.1350949] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
DNA barcoding has been widely used to identify and discover new species in a wide range of taxa. In order to assess the effectiveness of COI (cytochrome C oxidase subunit I) and 16S (16S ribosomal RNA) in the discrimination of spiders, we have generated 289 barcodes for a total of 56 farmland spider species from 14 different families for the first time in China. Our results reveal that the standard barcoding marker COI can be used to distinguish the farmland spiders both in species and family level by NJ tree-based method, despite the absence of a barcode gap between the intra- and inter-specific genetic divergences. 16S has a lower species identification success as compared with COI. However, almost 98% of the species can be correctly distinguished for both COI and 16S when a threshold of 3% nucleotide divergence was used for species discrimination. Our study significantly improves the barcode reference sequence library for Chinese farmland spiders, and will be very useful in pest management and eco-environmental monitoring and protection.
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Affiliation(s)
- Zheng Liang Wang
- a Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences , China Jiliang University , Hangzhou , Zhejiang , People's Republic of China
| | - Xiao Qing Yang
- a Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences , China Jiliang University , Hangzhou , Zhejiang , People's Republic of China
| | - Tian Zhao Wang
- a Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences , China Jiliang University , Hangzhou , Zhejiang , People's Republic of China
| | - Xiaoping Yu
- a Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences , China Jiliang University , Hangzhou , Zhejiang , People's Republic of China
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14
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Dhar B, Ghosh SK. Mini-DNA barcode in identification of the ornamental fish: A case study from Northeast India. Gene 2017; 627:248-254. [PMID: 28652184 DOI: 10.1016/j.gene.2017.06.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 05/28/2017] [Accepted: 06/22/2017] [Indexed: 11/30/2022]
Abstract
The ornamental fishes were exported under the trade names or generic names, thus creating problems in species identification. In this regard, DNA barcoding could effectively elucidate the actual species status. However, the problem arises if the specimen is having taxonomic disputes, falsified by trade/generic names, etc., On the other hand, barcoding the archival museum specimens would be of greater benefit to address such issues as it would create firm, error-free reference database for rapid identification of any species. This can be achieved only by generating short sequences as DNA from chemically preserved are mostly degraded. Here we aimed to identify a short stretch of informative sites within the full-length barcode segment, capable of delineating diverse group of ornamental fish species, commonly traded from NE India. We analyzed 287 full-length barcode sequences from the major fish orders and compared the interspecific K2P distance with nucleotide substitutions patterns and found a strong correlation of interspecies distance with transversions (0.95, p<0.001). We, therefore, proposed a short stretch of 171bp (transversion rich) segment as mini-barcode. The proposed segment was compared with the full-length barcodes and found to delineate the species effectively. Successful PCR amplification and sequencing of the 171bp segment using designed primers for different orders validated it as mini-barcodes for ornamental fishes. Thus, our findings would be helpful in strengthening the global database with the sequence of archived fish species as well as an effective identification tool of the traded ornamental fish species, as a less time consuming, cost effective field-based application.
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Affiliation(s)
- Bishal Dhar
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Sankar Kumar Ghosh
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India; University of Kalyani, Kalyani 741235, West Bengal, India.
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15
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Chakraborty M, Dhar B, Ghosh SK. Design of character-based DNA barcode motif for species identification: A computational approach and its validation in fishes. Mol Ecol Resour 2017; 17:1359-1370. [PMID: 28332322 DOI: 10.1111/1755-0998.12671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 01/26/2017] [Accepted: 03/07/2017] [Indexed: 11/29/2022]
Abstract
The DNA barcodes are generally interpreted using distance-based and character-based methods. The former uses clustering of comparable groups, based on the relative genetic distance, while the latter is based on the presence or absence of discrete nucleotide substitutions. The distance-based approach has a limitation in defining a universal species boundary across the taxa as the rate of mtDNA evolution is not constant throughout the taxa. However, character-based approach more accurately defines this using a unique set of nucleotide characters. The character-based analysis of full-length barcode has some inherent limitations, like sequencing of the full-length barcode, use of a sparse-data matrix and lack of a uniform diagnostic position for each group. A short continuous stretch of a fragment can be used to resolve the limitations. Here, we observe that a 154-bp fragment, from the transversion-rich domain of 1367 COI barcode sequences can successfully delimit species in the three most diverse orders of freshwater fishes. This fragment is used to design species-specific barcode motifs for 109 species by the character-based method, which successfully identifies the correct species using a pattern-matching program. The motifs also correctly identify geographically isolated population of the Cypriniformes species. Further, this region is validated as a species-specific mini-barcode for freshwater fishes by successful PCR amplification and sequencing of the motif (154 bp) using the designed primers. We anticipate that use of such motifs will enhance the diagnostic power of DNA barcode, and the mini-barcode approach will greatly benefit the field-based system of rapid species identification.
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Affiliation(s)
- Mohua Chakraborty
- Department of Biotechnology, Assam University, Silchar, Assam, India
| | - Bishal Dhar
- Department of Biotechnology, Assam University, Silchar, Assam, India
| | - Sankar Kumar Ghosh
- Department of Biotechnology, Assam University, Silchar, Assam, India.,University of Kalyani, Kalyani, West Bengal, India
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16
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Chatterjee N, Dhar B, Bhattarcharya D, Deori S, Doley J, Bam J, Das PJ, Bera AK, Deb SM, Devi NN, Paul R, Malvika S, Ghosh SK. Genetic assessment of leech species from yak (Bos grunniens) in the tract of Northeast India. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:73-81. [PMID: 28290215 DOI: 10.1080/24701394.2016.1238914] [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: 10/20/2022]
Abstract
Yak is an iconic symbol of Tibet and high altitudes of Northeast India. It is highly cherished for milk, meat, and skin. However, yaks suffer drastic change in milk production, weight loss, etc, when infested by parasites. Among them, infestation by leeches is a serious problem in the Himalayan belt of Northeast India. The parasite feeds on blood externally or from body orifices, like nasopharynx, oral, rectum, etc. But there has been limited data about the leech species infesting the yak in that region because of the difficulties in morphological identification due to plasticity of the body, changes in shape, and surface structure and thus, warrants for the molecular characterization of leech. In anticipation, this study would be influential in proper identification of leech species infesting yak track and also helpful in inventorying of leech species in Northeast India. Here, we investigated, through combined approach of molecular markers and morphological parameters for the identification of leech species infesting yak. The DNA sequences of COI barcode fragment, 18S and 28S rDNA, were analyzed for species identification. The generated sequences were subjected to similarity match in global database and analyzed further through Neighbour-Joining, K2P distance based as well as ML approach. Among the three markers, only COI was successful in delineating species whereas the 18S and 28S failed to delineate the species. Our study confirmed the presence of the species from genus Hirudinaria, Haemadipsa, Whitmania, and one species Myxobdella annandalae, which has not been previously reported from this region.
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Affiliation(s)
| | - Bishal Dhar
- a Department of Biotechnology , Assam University , Silchar , India
| | | | - Sourabh Deori
- b ICAR-National Research Centre on Yak , Dirang , Arunachal Pradesh , India
| | - Juwar Doley
- b ICAR-National Research Centre on Yak , Dirang , Arunachal Pradesh , India
| | - Joken Bam
- b ICAR-National Research Centre on Yak , Dirang , Arunachal Pradesh , India
| | - Pranab J Das
- b ICAR-National Research Centre on Yak , Dirang , Arunachal Pradesh , India
| | - Asit K Bera
- b ICAR-National Research Centre on Yak , Dirang , Arunachal Pradesh , India
| | - Sitangshu M Deb
- b ICAR-National Research Centre on Yak , Dirang , Arunachal Pradesh , India
| | | | - Rajesh Paul
- a Department of Biotechnology , Assam University , Silchar , India
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17
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Barman AS, Singh M, Pandey PK. DNA barcoding and genetic diversity analyses of fishes of Kaladan River of Indo-Myanmar biodiversity hotspot. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:367-378. [PMID: 28278695 DOI: 10.1080/24701394.2017.1285290] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Species are considered as a fundamental unit of biodiversity. Therefore, the prerequisite for biodiversity management and conservation is to know the number of species one is dealing with. Consequently, the need of the present study was conceptualized, which dealt with the comprehensive molecular appraisal of Kaladan's Fish fauna. A total of 291 specimens representing 49 species, 28 genera, 11 families, and 4 orders, were collected from 11 sampling stations situated along the main Kaladan River and its four major tributaries, i.e. Tiau, Tuipui, Mat, and Tuichang, flowing in Mizoram state of India (part of Indo-Myanmar biodiversity hotspot) and COI sequences of all the 291 samples were generated. All the analyses conducted in the present study, i.e. K2P genetic divergence, bPTP and Neighbour-Joining suggest that DNA Barcoding is an efficient and reliable tool for species identification and deciding the species boundary. Most of the species of Kaladan showed the clear existence of barcode gap. However, the presence of intra-specific and inter-specific genetic distance overlap in two species revealed the existence of putative sibling species or hidden taxa. This study also revealed the presence of two cryptic species and putative previously unknown species of genus Garra and Schistura. The COI barcode database of Kaladan's fish fauna, established in the present study, may serve as a reference library for accurate identification of fishes and will help ichthyologist, researcher, students, biodiversity managers and policy makers in proper planning with regard to conservation and management of the resources.
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Affiliation(s)
- Anindya Sundar Barman
- a College of Fisheries, Central Agricultural University , Lembucherra , Tripura , India
| | - Mamta Singh
- a College of Fisheries, Central Agricultural University , Lembucherra , Tripura , India
| | - Pramod Kumar Pandey
- a College of Fisheries, Central Agricultural University , Lembucherra , Tripura , India
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18
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Chang CH, Shao KT, Lin HY, Chiu YC, Lee MY, Liu SH, Lin PL. DNA barcodes of the native ray-finned fishes in Taiwan. Mol Ecol Resour 2016; 17:796-805. [DOI: 10.1111/1755-0998.12601] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/19/2016] [Accepted: 09/21/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Chia-Hao Chang
- Biodiversity Research Center; Academia Sinica; 128 Academia Road Sec. 2 Nankang Taipei 115 Taiwan
| | - Kwang-Tsao Shao
- Biodiversity Research Center; Academia Sinica; 128 Academia Road Sec. 2 Nankang Taipei 115 Taiwan
| | - Han-Yang Lin
- Biodiversity Research Center; Academia Sinica; 128 Academia Road Sec. 2 Nankang Taipei 115 Taiwan
| | - Yung-Chieh Chiu
- Department of Aquaculture; National Taiwan Ocean University; Keelung Taiwan
| | - Mao-Ying Lee
- Biodiversity Research Center; Academia Sinica; 128 Academia Road Sec. 2 Nankang Taipei 115 Taiwan
| | - Shih-Hui Liu
- Department of Biology; Saint Louis University; 3507 Laclede Avenue, Macelwane Hall St. Louis MO 63103 USA
| | - Pai-Lei Lin
- Biodiversity Research Center; Academia Sinica; 128 Academia Road Sec. 2 Nankang Taipei 115 Taiwan
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19
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Patil TS, Tamboli AS, Patil SM, Bhosale AR, Govindwar SP, Muley DV. Relative profile analysis of molecular markers for identification and genetic discrimination of loaches (Pisces, Nemacheilidae). C R Biol 2016; 339:364-70. [PMID: 27427438 DOI: 10.1016/j.crvi.2016.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 05/24/2016] [Accepted: 06/03/2016] [Indexed: 11/15/2022]
Abstract
Genus Nemacheilus, Nemachilichthys and Schistura belong to the family Nemacheilidae of the order Cypriniformes. The present investigation was undertaken to observe genetic diversity, phylogenetic relationship and to develop a molecular-based tool for taxonomic identification. For this purpose, four different types of molecular markers were utilized in which 29 random amplified polymorphic DNA (RAPD), 25 inter-simple sequence repeat (ISSR) markers, and 10 amplified fragment length polymorphism (AFLP) marker sets were screened and mitochondrial COI gene was sequenced. This study added COI barcodes for the identification of Nemacheilus anguilla, Nemachilichthys rueppelli and Schistura denisoni. RAPD showed higher polymorphism (100%) than the ISSR (93.75-100%) and AFLP (93.86-98.96%). The polymorphic information content (PIC), heterozygosity, multiplex ratio, and gene diversity was observed highest for AFLP primers, whereas the major allele frequency was observed higher for RAPD (0.5556) and lowest for AFLP (0.1667). The COI region of all individuals was successfully amplified and sequenced, which gave a 100% species resolution.
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20
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Basheer VS, Vineesh N, Bineesh KK, Kumar RG, Mohitha C, Venu S, Kathirvelpandian A, Gopalakrishnan A, Jena JK. Mitochondrial signatures for identification of grouper species from Indian waters. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:451-457. [PMID: 27159687 DOI: 10.3109/19401736.2015.1137899] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Groupers are important commercial fish in many parts of the world. Accurate identification is critical for effective conservation assessment and fisheries management. Genetic barcodes provide a simple and reproducible method for the identification of species even in the absence of taxonomic expertise. The generation of reference barcodes from properly identified specimens is an important first step in this direction. Here, 36 species belonging to the subfamily Epinephelinae (Family: Serranidae) were collected from landings on the west coast of India and Port Blair, Andaman, and partial nucleotide sequence data of the mitochondrial cytochrome C oxidase subunit I (COI) gene was generated. Barcodes for 13 species were developed from Indian waters for the first time. Analysis using the COI gene produced phylogenetic trees in concurrence with other multi-gene studies. Epinephelus fasciatus and E. areolatus were found to be a species complex, as hypothesized in other studies. The DNA barcodes developed in the study can be used for identifying species within Epinehelinae, where taxonomic ambiguity still exists.
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Affiliation(s)
- V S Basheer
- a National Bureau of Fish Genetic Resources, PMFGR Centre , CMFRI Campus, Ernakulam North , Kochi , Kerala , India
| | - N Vineesh
- a National Bureau of Fish Genetic Resources, PMFGR Centre , CMFRI Campus, Ernakulam North , Kochi , Kerala , India
| | - K K Bineesh
- a National Bureau of Fish Genetic Resources, PMFGR Centre , CMFRI Campus, Ernakulam North , Kochi , Kerala , India
| | - Rahul G Kumar
- a National Bureau of Fish Genetic Resources, PMFGR Centre , CMFRI Campus, Ernakulam North , Kochi , Kerala , India
| | - C Mohitha
- a National Bureau of Fish Genetic Resources, PMFGR Centre , CMFRI Campus, Ernakulam North , Kochi , Kerala , India
| | - S Venu
- b Department of Ocean Studies & Marine Biology Brookshabad Campus , Pondicherry University , Junglighat , PortBlair , Andamans , India
| | - A Kathirvelpandian
- a National Bureau of Fish Genetic Resources, PMFGR Centre , CMFRI Campus, Ernakulam North , Kochi , Kerala , India
| | - A Gopalakrishnan
- c Central Marine Fisheries Research Institute , Ernakulam North , Kochi , Kerala , India
| | - J K Jena
- d National Bureau of Fish Genetic Resources , Dilkusha , Lucknow , India
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21
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Bamaniya DC, Pavan-Kumar A, Gireesh-Babu P, Sharma N, Reang D, Krishna G, Lakra WS. DNA barcoding of marine ornamental fishes from India. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3093-7. [DOI: 10.3109/19401736.2014.1003923] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Dhaval C. Bamaniya
- ICAR – Central Institute of Fisheries Education (CIFE), Mumbai, Maharashtra, India
| | - A. Pavan-Kumar
- ICAR – Central Institute of Fisheries Education (CIFE), Mumbai, Maharashtra, India
| | - P. Gireesh-Babu
- ICAR – Central Institute of Fisheries Education (CIFE), Mumbai, Maharashtra, India
| | - Niti Sharma
- ICAR – Central Institute of Fisheries Education (CIFE), Mumbai, Maharashtra, India
| | - Dhalongsaih Reang
- ICAR – Central Institute of Fisheries Education (CIFE), Mumbai, Maharashtra, India
| | - Gopal Krishna
- ICAR – Central Institute of Fisheries Education (CIFE), Mumbai, Maharashtra, India
| | - W. S. Lakra
- ICAR – Central Institute of Fisheries Education (CIFE), Mumbai, Maharashtra, India
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22
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Dhar B, Ghosh SK. Genetic assessment of ornamental fish species from North East India. Gene 2015; 555:382-92. [DOI: 10.1016/j.gene.2014.11.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 11/04/2014] [Accepted: 11/15/2014] [Indexed: 02/07/2023]
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23
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Khedkar GD, Jamdade R, Naik S, David L, Haymer D. DNA barcodes for the fishes of the Narmada, one of India's longest rivers. PLoS One 2014; 9:e101460. [PMID: 24991801 PMCID: PMC4081587 DOI: 10.1371/journal.pone.0101460] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 06/06/2014] [Indexed: 01/12/2023] Open
Abstract
This study describes the species diversity of fishes of the Narmada River in India. A total of 820 fish specimens were collected from 17 sampling locations across the whole river basin. Fish were taxonomically classified into one of 90 possible species based on morphological characters, and then DNA barcoding was employed using COI gene sequences as a supplemental identification method. A total of 314 different COI sequences were generated, and specimens were confirmed to belong to 85 species representing 63 genera, 34 families and 10 orders. Findings of this study include the identification of five putative cryptic or sibling species and 43 species not previously known from the Narmada River basin. Five species are endemic to India and three are introduced species that had not been previously reported to occur in the Narmada River. Conversely, 43 species previously reported to occur in the Narmada were not found. Genetic diversity and distance values were generated for all of the species within genera, families and orders using Kimura's 2 parameter distance model followed by the construction of a Neighbor Joining tree. High resolution clusters generated in NJ trees aided the groupings of species corresponding to their genera and families which are in confirmation to the values generated by Automatic Barcode Gap Discovery bioinformatics platform. This aided to decide a threshold value for the discrimination of species boundary from the Narmada River. This study provides an important validation of the use of DNA barcode sequences for monitoring species diversity and changes within complex ecosystems such as the Narmada River.
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Affiliation(s)
- Gulab Dattarao Khedkar
- Paul Hebert Centre for DNA Barcoding and Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, India
| | - Rahul Jamdade
- Paul Hebert Centre for DNA Barcoding and Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, India
| | - Suresh Naik
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Lior David
- Department of Animal Sciences, R.H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - David Haymer
- Department of Cell and Molecular Biology, University of Hawaii, Honolulu, Hawaii, United States of America
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Han SH, Lee YD, Baek HJ, Oh HS, Noh CH. Genetic Structure and Phylogenetic Relationship of Red Spotted Grouper (Epinephelus akaara) Based on the Haplotypes and Polymorphisms of Mitochondrial COI Gene Sequences. ACTA ACUST UNITED AC 2014. [DOI: 10.5352/jls.2014.24.6.626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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