Molecular characterization based on cytochrome C oxidase I gene of the family Channidae from different riverine systems of Odisha, India

Sanmitra Roy; Preetkalyan Purohit; Murchhana Mohapatra; Sameer Sura; Dilraj Puvala; Akshya Kumar Mishra; Jaya Kishor Seth

doi:10.17017/j.fish.750

Sanmitra Roy Post Graduate Department of Zoology, Berhampur University, Berhampur, Odisha 760007, India
Preetkalyan Purohit Post Graduate Department of Zoology, Berhampur University, Berhampur, Odisha 760007, India
Murchhana Mohapatra Post Graduate Department of Zoology, Berhampur University, Berhampur, Odisha 760007, India
Sameer Sura Post Graduate Department of Zoology, Berhampur University, Berhampur, Odisha 760007, India; Department of Zoology, Rajendra University, Prajna Vihar, Balangir, Odisha 767002, India
Dilraj Puvala Post Graduate Department of Zoology, Berhampur University, Berhampur, Odisha 760007, India; Government College, Dayananda Vihar, Landiguda, Koraput, Odisha 764021, India
Akshya Kumar Mishra Department of Zoology, Rajendra University, Prajna Vihar, Balangir, Odisha 767002, India
Jaya Kishor Seth Post Graduate Department of Zoology, Berhampur University, Berhampur, Odisha 760007, India

DOI: https://doi.org/10.17017/j.fish.750

Keywords: biogeography, channids, Odisha, phylogeny, Teleostei

Abstract

This study focuses on four Channa species from the northern part of the Eastern Ghats in India: Channa punctata (Bloch, 1793); Channa striata (Bloch, 1793); Channa marulius (Hamilton, 1822) and Channa gachua (Hamilton, 1822). The aim is to determine whether their molecular divergence aligns with their morphological distinctiveness. The molecular analysis based on mitochondrial COI gene sequences revealed distinct clusters for each species and genus, with K2P distances ranging from 17.28 – 27.96%. Notably, C. marulius was positioned in a distinct clade separate from the C. punctata, C. striata, and C. gachua groups. Channa gachua clustered with Channa rara and Channa kelaartii, suggesting a close evolutionary relationship. Channa punctata and C. striata also clustered together, reinforcing their status as sister species. Species delimitation using the Assemble Species by Automatic Partitioning method identified 10 partitions, with the most reliable delimitation showing a clear separation of Channa species of Odisha. These findings align with recent analyses and confirm that the molecular divergence among the four species is consistent with their morphological differences. The study underscores the importance of molecular methods in resolving taxonomic ambiguities and understanding species diversity. It provides a foundational molecular database for Channa species, supporting future research on genetic divergence and contributing to conservation and aquaculture efforts.

References

Adamson EA, Britz R (2018) The snakehead fish Channa aurolineata is a valid species (Teleostei: Channidae) distinct from Channa marulius. Zootaxa 4514(4): 542–552.

Ahmed MS, Dina SR, Nahar L, Islam NN, Al Reza H (2018) Molecular characterization of Channa species from Bangladesh based on cytochrome c oxidase subunit I (COI) gene. FishTaxa 3(4): 87–93.

Arisuryanti T, Firdaus NU, Hakim L (2020) Genetic characterization of striped snakehead (Channa striata Bloch, 1793) from Arut River, Central Kalimantan inferred from COI mitochondrial gene. In AIP conference proceedings Vol. 2260, No. 1. AIP Publishing.

Barman AS, Singh M, Singh SK, Saha H, Singh YJ, ... Pandey PK (2018) DNA barcoding of freshwater fishes of Indo-Myanmar biodiversity hotspot. Scientific Reports 8: 8579.

Britz R, Tan HH, Rüber L (2024) Four new species of Channa from Myanmar (Teleostei, Labyrinthici, Channidae). Raffles Bulletin of Zoology 72: 1–25.

Conte-Grand C, Britz R, Dahanukar N, Raghavan R, Pethiyagoda R, ... Rüber L (2017) Barcoding snakeheads (Teleostei, Channidae) revisited: discovering greater species diversity and resolving perpetuated taxonomic confusions. PLoS One 12(9): e0184017.

DWR (2021) Annual Report 2019–2020. Department of Water Resources, Government of Odisha, Odisha, India.

Ekanayake H, Perera N, Ukuwela KD, Walpita CN, Kodithuwakku SP, Perera SJ (2021) Cryptic species diversity and molecular diagnosis of Channa orientalis; an endemic freshwater fish of Sri Lanka. Mitochondrial DNA Part A 32(3): 77–84.

Fricke R, Eschmeyer WN, van der Laan R (2024) Eschmeyer's catalog of fishes: genera, species, references. Electronic version. Accessed 28 August 2024.

Froese R, Pauly D (2024) FishBase. World wide web electronic publication. www.fishbase.org, version (02/2024). Electronic version. Accessed on 28 August 2024.

Hall TA (1999) BioEdit: A user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symposium Series 41: 95–98.

Jayaram KC (2010) The freshwater fishes of the Indian region, 2nd ed. Narendra Publishing House, New Delhi.

Kamran M, Yaqub A, Malkani N, Anjum KM, Awan MN, Paknejad H (2020) Identification and phylogenetic analysis of Channa species from riverine system of Pakistan using COI gene as a DNA barcoding marker. Journal of Bioresource Management 7(2): 88–98.

Katsura Y, Stanley CE, Jr Kumar S, Nei M (2017) The reliability and stability of an inferred phylogenetic tree from empirical data. Molecular Biology and Evolution 34(3): 718–723.

Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111–120.

Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution 35: 1547–1549.

Lakra WS, Goswami M, Gopalakrishnan A, Singh DP, Singh A, Nagpure NS (2010) Genetic relatedness among fish species of genus Channa using mitochondrial DNA genes. Biochemical Systematics and Ecology 38(6): 1212–1219.

Li X, Musikasinthorn P, Kumazawa Y (2006) Molecular phylogenetic analyses of snakeheads (Perciformes: Channidae) using mitochondrial DNA sequences. Ichthyological Research 53: 148–159.

Liu H, Luo Q, Ou M, Zhu X, Zhao J, Chen K (2020) High-density genetic linkage map and QTL fine mapping of growth and sex in snakehead (Channa argus). Aquaculture 519: 734760.

Mishra SS, Das A, Barman RP (2013) Notes on some snakehead fishes of India with an aid to their identification. Records of the Zoological Survey of India(Part-2) 113: 145–152.

Miyan K, Afzal Khan M, Khan S (2014) Stock structure delineation using variation in otolith chemistry of snakehead, Channa punctata (Bloch, 1793), from three Indian rivers. Journal of Applied Ichthyology 30(5): 881–886.

Mogalekar HS, Canciyal J (2018) Freshwater fishes of Orissa, India. Journal of Fisheries 6(1): 587–598.

Musikasinthorn P (2000) Channa aurantimaculata, a new channid fish from Assam (Brahmaputra River basin), India, with designation of a neotype for C. amphibeus (McClelland, 1845). Ichthyological Research 47(1): 27–37.

Nagalakshmi K, Annam PK, Venkateshwarlu G, Pathakota GB, Lakra WS (2016) Mislabeling in Indian seafood: An investigation using DNA barcoding. Food Control 59: 196–200.

Praveenraj J, Knight JD, Kiruba-Sankar R, Halalludin B, Raymond JJ, Thakur VR (2018) Channa royi (Teleostei: Channidae): a new species of snakehead from Andaman Islands, India. Indian Journal of Fisheries 64(4): 1–4.

Puillandre N, Brouillet S, Achaz G (2021) ASAP: Assemble species by automatic partitioning. Molecular Ecology Resources 21: 609–620.

Rüber L, Tan HH, Britz R (2019) Snakehead (Teleostei: Channidae) diversity and the Eastern Himalaya biodiversity hotspot. Journal of Zoological Systematics and Evolutionary Research 58(1): 356–386.

Serrao NR, Steinke D, Hanner RH (2014) Calibrating channid diversity with DNA barcodes: expanding taxonomic coverage to enable identification of potential and established invasive species. PLoS ONE 9(6): e99546.

Seth JK, Barik TK (2021) DNA barcoding of the family: Leiognathidae in the water of Bay of Bengal, Odisha coast, India based on 16s rRNA and COI gene sequences. Thalassas: an International Journal of Marine Sciences 37(2): 831–840.

Seth JK, Roy S, Sura S, Puvala P, Mishra SS, Mohapatra A (2023) Description of a new species of the genus Awaous Valenciennes, 1837 (Gobiiformes: Oxudercidae) from the middle stretch of the Mahanadi River, Odisha, India, with comments on the Awaous species from India. Journal of Fish Biology 104(3): 548–563.

Setyaningrum N, Lestari W, Nuryanto A (2022) Exploitation of striped snakehead (Channa striata) in Sempor Reservoir, Central Java, Indonesia: a proposed conservation strategy. Biodiversitas: Journal of Biological Diversity 23(7): 3584–3592.

Talwar PK, Jhingran AG (1991) Inland fishes of India and adjacent countries. Oxford and IBH Publishing Co. 2: 1158.

van der Laan R, Fricke R (2024) Eschmeyer’s catalog of fishes: family-group names. Electronic version. Accessed 28 August 2024.

Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD (2005) DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society B: Biological Sciences 360(1462): 1847–1857.

Yan S, Lai G, Li L, Xiao H, Zhao M, Wang M (2016) DNA barcoding reveals mislabeling of imported fish products in Nansha new port of Guangzhou, Guangdong province, China. Food Chemistry 202: 116–119.

Zhu SR, Fu JJ, Wang Q, Li JL (2013) Identification of Channa species using the partial cytochrome C oxidase subunit I (COI) gene as a DNA barcoding marker. Biochemical Systematics and Ecology 51: 117–122.