Phylogenetic analysis of the king cobra, Ophiophagus hannah in Thailand based on mitochondrial DNA sequences

Suntrarachun, Sunutcha; Chanhome, Lawan; Sumontha, Montri

doi:10.5372/1905-7415.0802.289

Abstract

Background: Snakes possess adaptive characteristics of morphology that may result in incorrect reconstruction of phylogeny. Molecular approaches have become the major source of new information for advancing our understanding of evolutionary, genetic relationships, and species identification.

Objective: We studied DNA sequences of Ophiophagus hannah in different parts of Thailand and compared them with those of O. hannah from other countries.

Materials and Methods: We studied the mitochondrial NADH dehydrogenase subunit 2 (ND2) and control region (CR) sequences of 12 individuals O. hannah from different localities across Thailand. Phylogenetic analysis of DNA sequences were compared to the published sequences of O. hannah deposited in NCBI GenBank database from other countries.

Results: O. hannah could be categorized into 2 Clades, 5 haplotypes, and 4 localities based on 43 different nucleotide positions from the 736 bp of ND2 and 673 bp of CR. Clade A was haplotype A from southern Thailand. Clade B consisted of haplotypes B, C, D, and E. Haplotype B and C came from northern Thailand. Haplotype D came from western Thailand, while haplotype E was O. hannah from central Thailand. The DNA sequences of Clade B were similar to the sequences of O. hannah in Myanmar and southern China that are already deposited in NCBI GenBank database.

Conclusion: We found a different genotype of O. hannah from southern Thailand and suggest that this may be a new species of O. hannah.

References

1. Chanhome L, Cox MJ, Wilde H, Jintakoon P, Chaiyabutr N, Sitprija V. Venomous snakebite in Thailand. I: Medically important snakes. Mil Med. 1998; 163: 310-7.10.1093/milmed/163.5.310
Search in Google Scholar Back to article
2. He YY, Lee WH, Zhang Y. Cloning and purification of α-neurotoxins from king cobra (Ophiophagus hannah). Toxicon. 2004; 44:295-303.10.1016/j.toxicon.2004.06.00315302536
Open DOI Search in Google Scholar Back to article
3. Wong KL, Wang J, But PPH., Shaw PC. Application of cytochrome b DNA sequences for the authentication of endangered snake species. Forensic Sci Inter. 2004; 139:49-55.10.1016/j.forsciint.2003.09.01514687773
Open DOI Search in Google Scholar Back to article
4. Ferri G, Alu M, Corradini B, Licata M, Beduschi G. Species identification through DNA “barcodes”. Genet Test Mol Biomarkers. 2009; 13:421-6.10.1089/gtmb.2008.014419405876
Open DOI Search in Google Scholar Back to article
5. Pook CE, McEwing R. Mitochondrial DNA sequences from dried snake venom: a DNA barcoding approach to the identification of venom samples. Toxicon. 2005; 46:711-5.10.1016/j.toxicon.2005.07.00516157361
Open DOI Search in Google Scholar Back to article
6. Rastogi G, Dharne MS, Walujkar S, Kumar A, Patole MS, Shouche YS. Species identification and authentication of tissues of animal origin using mitochondrial and nuclear markers. Meat Sci. 2007; 76:666-74.10.1016/j.meatsci.2007.02.00622061243
Open DOI Search in Google Scholar Back to article
7. Arif IA, Khan HA, Al Sadoon M, Shobrak M. Limited efficiency of universal mini-barcode primers for DNA amplification from desert reptiles, birds, and mammals. Genet Mol Res. 2011; 10:3559-64.10.4238/2011.October.31.322057991
Open DOI Search in Google Scholar Back to article
8. Singh CS, Gaur A, Sreenivas A, Singh L. Species identification from dried snake venom. J Forensic Sci. 2012; 57:826-8.10.1111/j.1556-4029.2011.02049.x22268640
Open DOI Search in Google Scholar Back to article
9. Meusnier I, Singer GAC, Landry J-F, Hickey DA., Hebert PDN, Hajibabaei M. A universal DNA minibarcode for biodiversity analysis. BMC Genomics. 2008; 9:214-7.10.1186/1471-2164-9-214239664218474098
Open DOI Search in Google Scholar Back to article
10. Khan HA, Arif IA, Al Homaidan AA, Al Farhan AH. Application of 16S rRNA, cytochrome b and control region sequences for understanding the phylogenetic relationships in Oryx species. Genet Mol Res. 2008; 7:1392-7.10.4238/vol7-4gmr51419224456
Open DOI Search in Google Scholar Back to article
11. Linacre A, Tobe SS. An overview to the investigative approach to species testing in wildlife forensic science. Investig Genet. 2011; 2:1-9.10.1186/2041-2223-2-2303269121232099
Open DOI Search in Google Scholar Back to article
12. Ashton KG, de Queiroz A. Molecular systematics of the western rattlesnake, Crotalus viridis (Viperidae), with comments on the utility of the D-loop in phylogenetics studies of snakes. Mol Phylogenet Evol. 2001; 21:176-89.10.1006/mpev.2001.101311697914
Open DOI Search in Google Scholar Back to article
13. Nian C, Xiao-Ping L. Sequencing and analysis of the complete mitochondrial genome of the King Cobra, Ophiophagus hannah (Serpents: Elapidae). Yi Chuan. 2010; 32:719-25.10.3724/SP.J.1005.2010.00719
Search in Google Scholar Back to article
14. Wuster W, Peppin L, Pook CE, Walker DE. A nesting of vipers: phylogeny and historical biogeography of the Viperidae (Squamata: Serpentes). Mol Phylogenet Evol. 2008; 49:445-59.10.1016/j.ympev.2008.08.01918804544
Open DOI Search in Google Scholar Back to article
15. Lertwatcharasarakul P, Thongtip N, Boonnontae S, Wajjwalku W, Mahasawankul S, Angkawanish T, et al. Haplotypes of Asian elephant (Elephas maximus) in Thailand based on cytochrome b gene. Kamphaengsaen Acad J. 2003; 1:33-9.
Search in Google Scholar Back to article
16. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol. 2007; 24:1596-9.10.1093/molbev/msm09217488738
Search in Google Scholar Back to article
17. Dubey B, Meganathan PR, Haque I. DNA minibarcoding: An approach for forensic identification of some endangered Indian snake species. Forensic Sci. Int. Genet. 2011; 5:181-4.10.1016/j.fsigen.2010.03.00120457097
Open DOI Search in Google Scholar Back to article
18. Nicolas V, Schaeffer B, Missoup AD, Kennis J, Colyn M, Denys C, et al. Assessment of three mitochondrial genes (16S, Cytb, CO1) for identifying species in the Praomyini tribe (Rodentia: Muridae). PLoS One. 2012; 7:e36586.10.1371/journal.pone.0036586334491222574186
Search in Google Scholar Back to article
19. Powell RL, Reyes SR, Lannutti DI. Molecular barcoding, DNA from snake venom, and toxinological research: considerations and concerns. Toxicon. 2006; 48:1095-7.10.1016/j.toxicon.2006.07.03516965799
Open DOI Search in Google Scholar Back to article
20. Slowinski J, Keogh JS. Phylogenetic relationships of elapid snakes based on cytochrome b mtDNA sequences. Mol Phylogenet Evol. 2000; 15:157-64.10.1006/mpev.1999.072510764543
Open DOI Search in Google Scholar Back to article
21. Amer SAM, Shobrak M. The efficiency of mitochondrial DNA markers in constructing genetic relationship among Oryx species. Afr J Biotechnol. 2011; 10: 4581-5.
Search in Google Scholar Back to article
22. Meenakshi K, Suraj T, Bhagwati SS, Sujith VG, Santhoshkumar K, Sanil G. Molecular resolution of four Fejervarya species from western Ghats (India) with their intrageneric phylogeny based on COI, Cyt B, 12S and 16S rRNA genes. Asian J Exp Biol Sci. 2010; 1:782-6.
Search in Google Scholar Back to article
23. Barker FK, Benesh MK, Vandergon AJ, Lanyon SM. Contrasting evolutionary dynamics and information content of the avian mitochondrial control region and ND2 gene. PLoS One. 2012; 7:e46403.10.1371/journal.pone.0046403346532623071562
Search in Google Scholar Back to article
24. Huang S, He S, Peng Z, Zhao K, Zhao E. Molecular phylogeography of endangered sharp-snouted pitviper (Deinagkistrodon acutus; Reptilia, Viperidae) in Mainland China. Mol Phylogenet Evol. 2007; 44: 942-52.10.1016/j.ympev.2007.05.01917643319
Open DOI Search in Google Scholar Back to article
25. Pyron RA, Burbrink FT, Colli GR, de Oca AN, Vitt LJ, Kuczynski CA, et al. The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees. Mol Phylogenet Evol. 2010; 58: 329-42. 10.1016/j.ympev.2010.11.00621074626
Open DOI Search in Google Scholar Back to article

Phylogenetic analysis of the king cobra, Ophiophagus hannah in Thailand based on mitochondrial DNA sequences

Abstract

Paradigm

My account