1
|
Patil GS, Pinto N, Nath R, Goswami M. Decoding the molecular phylogenetics of ornamental catfishes (siluriformes) of North East India using DNA barcoding approach. Mol Biol Rep 2024; 51:528. [PMID: 38637345 DOI: 10.1007/s11033-024-09487-5] [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: 02/01/2024] [Accepted: 03/26/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Catfishes (order Siluriformes) are among the most diverse and widely distributed fish groups in the world. They are not only used for human consumption but are also a major part of the ornamental fish trade. Being a Biodiversity Hotspot, the North Eastern Region of India is home to a diverse population of ornamental fishes. Catfishes contain a humongous number of species; in this study, the authors have tried to elucidate the phylogenetic relationship of some important ornamental catfishes found in North East India using DNA barcodes. METHODS AND RESULTS In this study, we have tried to explore the phylogenetic history of 13 species (41 specimens) of ornamental catfishes spanning 12 genera and 9 families of Siluriformes using DNA barcoding. Pairwise genetic distances using Kimura 2-Parameter (K2P) were calculated at intra-specific and inter-specific levels. A Neighbor-Joining tree was constructed to understand the phylogenetic relationship among the nine different catfish families. All the specimens under this study clustered with their respective species under the same family and formed three sub-clades. However, Olyra longicaudata, belonging to the Bagridae family, did not cluster with other species from the same family. In this study, the authors have suggested a revision of the classification of O. longicaudata back to its original family, Olyridae. CONCLUSIONS In this study, the maximum intraspecific genetic distance of 0.03 and the minimum interspecific genetic distance of 0.14 were observed among the species. Therefore, it is evident that there is a barcoding gap among the species, which helped in the correct identification of the species. Thus, DNA barcoding helped complement the phenetic approach and also revealed a different phylogenetic relationship among the catfishes belonging to the Bagridae family.
Collapse
Affiliation(s)
- Grishma S Patil
- ICAR-Central Institute of Fisheries Education, Mumbai, India
- Mangalore University, Mangaluru, Karnataka, India
| | - Nevil Pinto
- ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - Rupak Nath
- St. Anthony's College, Shillong, Meghalaya, India
| | - Mukunda Goswami
- ICAR-Central Institute of Fisheries Education, Mumbai, India.
| |
Collapse
|
2
|
Yang Q, Liu S, He C, Cowie RH, Yu X, Hayes KA. Invisible apple snail invasions: importance of continued vigilance and rigorous taxonomic assessments. PEST MANAGEMENT SCIENCE 2019; 75:1277-1286. [PMID: 30324686 DOI: 10.1002/ps.5241] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/21/2018] [Accepted: 10/11/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Due to the similarities of overall shell morphology among apple snail species and considerable variability within species, substantial taxonomic confusion has plagued the accurate identification of Pomacea species. Many invasive apple snails have been mistakenly identified as P. canaliculata since their introduction to Asia around 1980. In 2008, three other introduced species in addition to P. canaliculata were recognized. In 2013, a fifth, previously unrecognized lineage was reported from China, indicating that despite the taxonomic clarity brought by previous work, continued surveys and taxonomic research are necessary to prevent additional introductions and continued spread, as well as to develop effective management strategies. RESULTS Phylogenetic analysis of mitochondrial COI sequences confirmed the presence of a widespread unidentified Pomacea lineage in China. All sequences from samples of this newly documented lineage were recovered in a monophyletic clade delineated from closely related species; however, different DNA barcoding methods yielded inconsistent species boundaries. Additionally, nuclear EF1α sequences indicated incomplete lineage sorting or recent hybridization of the unidentified lineage with the other two established species. CONCLUSION Barcoding is a valuable tool for species discovery, and a powerful approach for delineating introduced species. However, determining the identity of the newly discovered invasive lineage in China will require an integrated taxonomic approach incorporating individuals from the native range, and examination of natural history collections at museums around the world. To manage and prevent additional spread of already established species, and to stop the introduction of new taxa, continued monitoring and rigorous taxonomic assessments must be undertaken. © 2018 Society of Chemical Industry.
Collapse
Affiliation(s)
- Qianqian Yang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Suwen Liu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Chao He
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Robert H Cowie
- Pacific Biosciences Research Center, University of Hawaii, Honolulu, HI, USA
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Kenneth A Hayes
- Pacific Biosciences Research Center, University of Hawaii, Honolulu, HI, USA
- Bernice Pauahi Bishop Museum, Honolulu, HI, USA
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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
| |
Collapse
|
6
|
Hubert N, Kadarusman, Wibowo A, Busson F, Caruso D, Sulandari S, Nafiqoh N, Pouyaud L, Rüber L, Avarre JC, Herder F, Hanner R, Keith P, Hadiaty RK. DNA Barcoding Indonesian freshwater fishes: challenges and prospects. ACTA ACUST UNITED AC 2015. [DOI: 10.1515/dna-2015-0018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractWith 1172 native species, the Indonesian ichthyofauna is among the world’s most speciose. Despite that the inventory of the Indonesian ichthyofauna started during the eighteen century, the numerous species descriptions during the last decades highlight that the taxonomic knowledge is still fragmentary. Meanwhile, the fast increase of anthropogenic perturbations during the last decades is posing serious threats to Indonesian biodiversity. Indonesia, however, is one of the major sources of export for the international ornamental trade and home of several species of high value in aquaculture. The development of new tools for species identification is urgently needed to improve the sustainability of the exploitation of the Indonesian ichthyofauna. With the aim to build comprehensive DNA barcode libraries, the co-authors have started a collective effort to DNA barcode all Indonesian freshwater fishes. The aims of this review are: (1) to produce an overview of the ichthyological researches conducted so far in Indonesia, (2) to present an updated checklist of the freshwater fishes reported to date from Indonesia’s inland waters, (3) to highlight the challenges associated with its conservation and management, (4) to present the benefits of developing comprehensive DNA barcode reference libraries for the conservation of the Indonesian ichthyofauna.
Collapse
|
7
|
Dong W, Liu H, Xu C, Zuo Y, Chen Z, Zhou S. A chloroplast genomic strategy for designing taxon specific DNA mini-barcodes: a case study on ginsengs. BMC Genet 2014; 15:138. [PMID: 25526752 PMCID: PMC4293818 DOI: 10.1186/s12863-014-0138-z] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 11/26/2014] [Indexed: 01/20/2023] Open
Abstract
Background Universal conventional DNA barcodes will become more and more popular in biological material identifications. However, in many cases such as processed medicines or canned food, the universal conventional barcodes are unnecessary and/or inapplicable due to DNA degradation. DNA mini-barcode is a solution for such specific purposes. Here we exemplify how to develop the best mini-barcodes for specific taxa using the ginseng genus (Panax) as an example. Results The chloroplast genome of P. notoginseng was sequenced. The genome was compared with that of P. ginseng. Regions of the highest variability were sought out. The shortest lengths which had the same discrimination powers of conventional lengths were considered the best mini-barcodes. The results showed that the chloroplast genome of P. notoginseng is 156,387 bp. There are only 464 (0.30%) substitutions between the two genomes. The intron of rps16 and two regions of the coding gene ycf1, ycf1a and ycf1b, evolved the quickest and served as candidate regions. The mini-barcodes of Panax turned out to be 60 bp for ycf1a at a discrimination power of 91.67%, 100 bp for ycf1b at 100%, and 280 bp for rps16 at 83.33%. Conclusions The strategy by searching the whole chloroplast genomes, identifying the most variable regions, shortening the focal regions for mini-barcodes are believed to be efficient in developing taxon-specific DNA mini-barcodes. The best DNA mini-barcodes are guaranteed to be found following this strategy. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0138-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Wenpan Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China.
| | - Han Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China.
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China.
| | - Yunjuan Zuo
- Shanghai Chenshan Plant Science Research Center, the Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
| | - Zhongjian Chen
- Institute of Sanqi Research, Wenshan College, Wenshan, 663000, Yunnan, China.
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China.
| |
Collapse
|