Complete Mitochondrial Genome Sequence from an Endangered Indian Snake, Python Molurus Molurus (Serpentes, Pythonidae)

Overview

Journal Mol Biol Rep

Specialty Molecular Biology

Date 2012 Feb 15

PMID 22331485

Citations 4

Authors

Bhawna Dubey

P R Meganathan

Ikramul Haque

Affiliations

Soon will be listed here.

Abstract

This paper reports the complete mitochondrial genome sequence of an endangered Indian snake, Python molurus molurus (Indian Rock Python). A typical snake mitochondrial (mt) genome of 17258 bp length comprising of 37 genes including the 13 protein coding genes, 22 tRNA genes, and 2 ribosomal RNA genes along with duplicate control regions is described herein. The P. molurus molurus mt. genome is relatively similar to other snake mt. genomes with respect to gene arrangement, composition, tRNA structures and skews of AT/GC bases. The nucleotide composition of the genome shows that there are more A-C % than T-G% on the positive strand as revealed by positive AT and CG skews. Comparison of individual protein coding genes, with other snake genomes suggests that ATP8 and NADH3 genes have high divergence rates. Codon usage analysis reveals a preference of NNC codons over NNG codons in the mt. genome of P. molurus. Also, the synonymous and non-synonymous substitution rates (ka/ks) suggest that most of the protein coding genes are under purifying selection pressure. The phylogenetic analyses involving the concatenated 13 protein coding genes of P. molurus molurus conformed to the previously established snake phylogeny.

Citing Articles

The complete mitochondrial genome study and phylogenetic analysis of Asiatic Water Snake () using 'Next-Generation Sequencing' technology.

Mitra I, D D, Roy S, Haque I Mitochondrial DNA B Resour. 2022; 7(11):1939-1941.

PMID: 36386021 PMC: 9662045. DOI: 10.1080/23802359.2022.2139157.

Cytonuclear discordance in the Florida Everglades invasive Burmese python (s) population reveals possible hybridization with the Indian python ().

Hunter M, Johnson N, Smith B, Davis M, Butterfield J, Snow R Ecol Evol. 2018; 8(17):9034-9047.

PMID: 30271564 PMC: 6157680. DOI: 10.1002/ece3.4423.

Mitochondrial DNA Sequence and Lack of Response to Anoxia in the Annual Killifish Austrofundulus limnaeus.

Wagner J, Herrejon Chavez F, Podrabsky J Front Physiol. 2016; 7:379.

PMID: 27630577 PMC: 5005410. DOI: 10.3389/fphys.2016.00379.

Concerted Evolution of Duplicate Control Regions in the Mitochondria of Species of the Flatfish Family Bothidae (Teleostei: Pleuronectiformes).

Li D, Shi W, Munroe T, Gong L, Kong X PLoS One. 2015; 10(8):e0134580.

PMID: 26237419 PMC: 4523187. DOI: 10.1371/journal.pone.0134580.

References

Dubey B, Meganathan P, Haque I . DNA mini-barcoding: an approach for forensic identification of some endangered Indian snake species. Forensic Sci Int Genet. 2010; 5(3):181-4. DOI: 10.1016/j.fsigen.2010.03.001. View

Hassanin A, Leger N, Deutsch J . Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of metazoa, and consequences for phylogenetic inferences. Syst Biol. 2005; 54(2):277-98. DOI: 10.1080/10635150590947843. View

Oliveira D, Raychoudhury R, Lavrov D, Werren J . Rapidly evolving mitochondrial genome and directional selection in mitochondrial genes in the parasitic wasp nasonia (hymenoptera: pteromalidae). Mol Biol Evol. 2008; 25(10):2167-80. PMC: 2727384. DOI: 10.1093/molbev/msn159. View

Barnes W . PCR amplification of up to 35-kb DNA with high fidelity and high yield from lambda bacteriophage templates. Proc Natl Acad Sci U S A. 1994; 91(6):2216-20. PMC: 43341. DOI: 10.1073/pnas.91.6.2216. View

Boore J . Complete mitochondrial genome sequence of Urechis caupo, a representative of the phylum Echiura. BMC Genomics. 2004; 5:67. PMC: 521484. DOI: 10.1186/1471-2164-5-67. View

Meganathan P, Dubey B, Batzer M, Ray D, Haque I . Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia. Gene. 2011; 478(1-2):35-41. DOI: 10.1016/j.gene.2011.01.012. View

Heise P, Maxson L, Dowling H, Hedges S . Higher-level snake phylogeny inferred from mitochondrial DNA sequences of 12S rRNA and 16S rRNA genes. Mol Biol Evol. 1995; 12(2):259-65. DOI: 10.1093/oxfordjournals.molbev.a040202. View

Arnason U, Johnsson E . The complete mitochondrial DNA sequence of the harbor seal, Phoca vitulina. J Mol Evol. 1992; 34(6):493-505. DOI: 10.1007/BF00160463. View

Thompson J, Gibson T, Plewniak F, Jeanmougin F, Higgins D . The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1998; 25(24):4876-82. PMC: 147148. DOI: 10.1093/nar/25.24.4876. View

10.

Kelly C, Barker N, Villet M . Phylogenetics of advanced snakes (Caenophidia) based on four mitochondrial genes. Syst Biol. 2003; 52(4):439-59. DOI: 10.1080/10635150390218132. View

11.

Yan J, Li H, Zhou K . Evolution of the mitochondrial genome in snakes: gene rearrangements and phylogenetic relationships. BMC Genomics. 2008; 9:569. PMC: 2632649. DOI: 10.1186/1471-2164-9-569. View

12.

Ojala D, Montoya J, Attardi G . tRNA punctuation model of RNA processing in human mitochondria. Nature. 1981; 290(5806):470-4. DOI: 10.1038/290470a0. View

13.

Jia W, Higgs P . Codon usage in mitochondrial genomes: distinguishing context-dependent mutation from translational selection. Mol Biol Evol. 2007; 25(2):339-51. DOI: 10.1093/molbev/msm259. View

14.

Ryder O . Conservation genomics: applying whole genome studies to species conservation efforts. Cytogenet Genome Res. 2004; 108(1-3):6-15. DOI: 10.1159/000080796. View

15.

Janke A, Erpenbeck D, Nilsson M, Arnason U . The mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): implications for amniote phylogeny. Proc Biol Sci. 2001; 268(1467):623-31. PMC: 1088649. DOI: 10.1098/rspb.2000.1402. View

16.

Man Z, Yishu W, Peng Y, Xiaobing W . Crocodilian phylogeny inferred from twelve mitochondrial protein-coding genes, with new complete mitochondrial genomic sequences for Crocodylus acutus and Crocodylus novaeguineae. Mol Phylogenet Evol. 2011; 60(1):62-7. DOI: 10.1016/j.ympev.2011.03.029. View

17.

Hurst L . The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet. 2002; 18(9):486. DOI: 10.1016/s0168-9525(02)02722-1. View

18.

Perna N, Kocher T . Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol. 1995; 41(3):353-8. DOI: 10.1007/BF00186547. View

19.

Douglas D, Gower D . Snake mitochondrial genomes: phylogenetic relationships and implications of extended taxon sampling for interpretations of mitogenomic evolution. BMC Genomics. 2010; 11:14. PMC: 2820454. DOI: 10.1186/1471-2164-11-14. View

20.

Meganathan P, Dubey B, Jogayya K, Whitaker N, Haque I . A novel multiplex PCR assay for the identification of Indian crocodiles. Mol Ecol Resour. 2011; 10(4):744-7. DOI: 10.1111/j.1755-0998.2010.02834.x. View