Research Article | Volume: 10, Issue: 1, January, 2022

The ITS2 DNA sequence analysis in six species of barbin fishes with phylogenetic insights

Sandip Choudhury Briyanka Kashyap Karabi Dutta   

Open Access   

Published:  Jan 07, 2022

DOI: 10.7324/JABB.2021.100108

The internal transcribed spacer 2 (ITS2) nuclear DNA was sequenced for six species of barbin fishes from Assam in the North Eastern region of India. The variations in the sequences were investigated to estimate nucleotide composition, nucleotide diversity, transition-transversion bias, genetic distance, and phylogenetic relationship. From the sequence analysis, it was found that the average G + C content (64.8%) was more than A + T content (35.2%). The nucleotide diversity (Pi) was found to be 0.04737. The number of transition substitutions was more than transversion substitutions and the transition–transversion bias was 1.16. Overall mean genetic distance was found to be 0.050 with a range from 0.005716 (between Puntius sophore and Puntius chola) to 0.084536 (between Pethia gelius and Systomus sarana). The phylograms constructed by neighbor-joining and maximum likelihood methods resulted in a similar topology where the monophyly of the Pethia group was recovered which consists of P. gelius, Pethia ticto, and Pethia conchonius. The two Puntius species (P. sophore and P. chola) were not clustered together and S. sarana remained a distinct taxon. The results of the present study partially validated the utility of the ITS2 DNA sequence in genetic diversity and phylogenetic studies in the barbin fishes.

Keyword:     ITS2 nuclear DNA barbin fishes genetic distance phylogenetic relationship


Choudhury S, Kashyap B, Dutta K. The ITS2 DNA sequence analysis in six species of barbin fishes with phylogenetic insights. J Appl Biol Biotech. 2022; 10(01):62–67.

Copyright: Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike license.

HTML Full Text


1. Coleman AW. ITS2 is a double-edged tool for eukaryote evolutionary comparisons. Trends Genet 2003;19:370-5.

2. Schultz J, Müller T, Achtziger M, Seibel PN, Dandekar T, Wolf M. The internal transcribed spacer 2 database-a web server for (not only) low level phylogenetic analyses. Nucleic Acids Res 2006;34(suppl_2):704-7.

3. Porter CH, Collins FH. Species-diagnostic differences in a ribosomal DNA internal transcribed spacer from the sibling species Anopheles freeborni and Anopheles hermsi (Diptera: Culicidae). Am J Trop Med Hyg 1991;45:271-9.

4. Talwar PK, Jhingran AG. Inland fishes of India and adjacent countries. Oxford and IBH, New Delhi, India, vol. II, 1991.

5. Hora SL, Mukherji DD. Notes on fishes in the Indian Museum (xxiii). On a collection of fishes S. Shan states, Burma. Rec Indian Museum 1934;36:353-70.

6. Smith HM. The fresh-water fishes of Siam, or Thailand. Bulletin of U.S. National Museum i-xi, Washington, USA. 1945.

7. Myers GS. Preface to any future classification of the cyprinid fishes of the genus Barbus. Stanford Ichthyol Bull 1960;7:212-5.

8. Kullander SO, Fang F. Two new species of Puntius from Northern Myanmar (Teleostei: Cyprinidae). Copeia 2005;2005:290-302.

9. Kottelat M. Nomenclature of the genera Barbodes, Cyclocheilichthys, Rasbora and Chonerhinos (Teleostei: Cyprinidae and Tetraodontidae), with comments on the definition of the first reviser. Raffles Bull Zoo 1999;47:591-600.

10. Pethiyagoda R, Meegaskumbura M, Maduwage K. A synopsis of the South Asian fishes referred to Puntius (Pisces: Cyprinidae). Ichthyol Explor Freshwaters 2012;23:69-95.

11. Ren Q, Mayden RL. Comparative phylogenetics of the Asian genus "Puntius" and relatives (Cypriniformes; Cyprinidae): explorations into the potential impacts of taxon and character sampling. I3 Biodiversity 2019;3:1-19.

12. Jayaram KC. The freshwater fishes of the Indian region. Narendra Publishing House, New Delhi, India, 1999.

13. Vishwanath W. Fishes of North East India: a field guide to species identification. Manipur University, Imphal, India, 2002.

14. Frose R, Pauly D. FishBase. World Wide Web electronic publication. 2010. Available via Version (11/2010)

15. Sambrook J, Fritsch EF, Maniatis T. Molecular cloning: a laboratory manual. 2nd edition, Cold Spring Harbor laboratory press, New York, NY, 1989.

16. Sambrook J, Russell DW. Molecular cloning: a laboratory manual. 3rd edition, Cold Spring Harbor laboratory press, New York, NY, 2001.

17. Carlos F, Barbas III, Dennis RB, Jamie KS, Gregg JS. Quantitation of DNA and RNA. Cold Spring Harbor laboratory press, New York, NY, 2007.

18. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999;41:95-8.

19. McGinnis S, Madden TL. BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 2004;32(suppl_2):W20-5.

20. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007;23:2947-8.

21. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16:111-20.

22. Felsenstein J. PHYLIP ver. 3.69. University of Washington, Seattle, WA, 2009.

23. Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009;25:1451-2.

24. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30(12):2725-9.

25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783-91.

26. Page RDM. TreeView version 1.6. 6. University of Glasgow, Glasgow, UK, 2001.

27. Presa P, Pardo BG, Martínez P, Bernatchez L. Phylogeographic congruence between mtDNA and rDNA ITS markers in brown trout. Mol Biol Evol 2002;19:2161-75.

28. He M, Huang L, Shi J, Jiang Y. Variability of ribosomal DNA ITS- 2 and its utility in detecting genetic relatedness of pearl oyster. Mar Biotechnol 2005;7:40-5.

29. Marinho MAT, Junqueira ACM, Azeredo-Espin AML. Evaluation of the internal transcribed spacer 2 (ITS2) as a molecular marker for phylogenetic inference using sequence and secondary structure information in blow flies (Diptera: Calliphoridae). Genetica 2011;139:1189-207.

30. Orti G, Bell MA, Reimchen TE, Meyer A. Global survey of mitochondrial DNA sequences in the three spine stickleback: evidence for recent migrations. Evolution 1994;48:608-22.

31. Ashoktaru B, Ali S, Sati J, Sivaraman GK. Phylogenetic analysis of fishes of the subfamily Schizothoracinae (Teleostei: Cyprinidae) from Indian Himalayas using cytochrome b gene. Indian J Fish 2012;59:43-7.

32. Shantakumar M, Vishwanath W. Inter-relationship of Puntius Hamilton-Buchanan (Cyprinidae: cyprininae) found in Manipur, India. Zoo's Print J 2006;21:2279-83.

33. Pallavi, Goswami M, Nautiyal P, Malakar AK, Nagpure NS. Genetic divergence and molecular phylogenetics of Puntius spp. based on the mitochondrial cytochrome b gene. Mitochondrial DNA 2012;23: 77-483.

34. Saroniya RK, Nagpure NS, Saksena DN, Basdeo K, Ravindra K, Mahender S, et al. Phylogenetic analysis of some Puntius species based on 18S rDNA. Eur J Biotechnol Biosci 2016;4:42-7.

35. Gupta D, Dwivedi AK, Tripathi M. Taxonomic validation of five fish species of subfamily Barbinae from the Ganga river system of northern India using traditional and truss analyses. PLoS One 2018;13:1-21.

36. Yazdani MF, Aliabadian M, Khalijah DS, Seifali M. Molecular phylogeny of the Puntius (Hamilton, 1822) based on nuclear gene RAG2. Prog Biol Sci 2012;2:66-75.

37. Mayden RL, Chen WJ, Bart HL, Doosey MH, Simons AM, Tang KL, et al. Reconstructing the phylogenetic relationships of the earth's most diverse clade of freshwater fishes - order Cypriniformes (Actinopterygii: Ostariophysi): a case study using multiple nuclear loci and the mitochondrial genome. Mol Phylogenet Evol 2009;51:500-14.

Article Metrics

0 Absract views 7 PDF Downloads 7 Total views

Related Search

By author names

    Warning: Cannot modify header information - headers already sent by (output started at /home/jabonlin/public_html/jab_php/header.php:1) in /home/jabonlin/public_html/jab_php/articlemodule/searchArticles.php on line 1162
    Choudhury S [PubMed] [Google Scholar ]
    Kashyap B [PubMed] [Google Scholar ]
    Dutta K [PubMed] [Google Scholar ]

    Warning: Invalid argument supplied for foreach() in /home/jabonlin/public_html/jab_php/abstract.php on line 819

Citiaion Alert By Google Scholar

Name Required
Email Required Invalid Email Address

Comment required

Notice: Undefined variable: dbq35 in /home/jabonlin/public_html/jab_php/abstract.php on line 942

Warning: mysqli_num_rows() expects parameter 1 to be mysqli_result, null given in /home/jabonlin/public_html/jab_php/articlemodule/database.php on line 379
Similar Articles