Skip to main content

Advertisement

SpringerLink
Log in

Complete mitogenome sequencing of Andaman buffalo: an endangered germplasm of Andaman and Nicobar Islands, India

  • Research Article
  • Published:
Journal of Genetics Aims and scope Submit manuscript

Abstract

Andaman buffalo is an indigenous buffalo of Andaman and Nicobar Islands, India. Over the last decade, it has witnessed a rapid decline in population, necessitating its immediate characterization and conservation. The present study reports the complete mitogenome profile of Andaman buffalo which is 16,359 bp in length and comprised of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs and two ribosomal RNAs. In addition, one \(\hbox {A}\,+\,\hbox {T}\) rich region (D-loop) was also present. A biasness towards A and T base was observed in all the genes. All the PCGs except ND6 were present on heavy strand. Start codons for all the 13 PCGs were ATN codon and abbreviated/truncated stop codons were observed in ND1, ND2, COX3, ND3 and ND4. The phylogenetic analysis revealed that the Andaman buffalo is closely related to buffalo from India and China. The results from this study will help in sketching the conservation plan of the threatened breed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Barłowska J., Szwajkowska M., Litwińczuk Z. and Król J. 2011 Nutritional value and technological suitability of milk from various animal species used for dairy production. Compr. Rev. Food Sci. F. 10, 291–302.

    Article  Google Scholar 

  • Behura S. K., Lobo N. F., Haas B., deBruyn B., Lovin D. D., Shumway M. F. et al. 2011 Complete sequences of mitochondria genomes of Aedes aegypti and Culex quinquefasciatus and comparative analysis of mitochondrial DNA fragments inserted in the nuclear genomes. Insect Biochem. Mol. Biol. 41, 770–777.

    Article  CAS  Google Scholar 

  • Bernt M., Donath A., Jühling F., Externbrink F., Florentz C., Fritzsch G. et al. 2013 MITOS: improved de novo metazoan mitochondrial genome annotation. Mol. Phylogenet. Evol. 69, 313–319.

    Article  Google Scholar 

  • FAO 2000 Water Buffalo: an asset undervalued, pp. 1-6. FAO Regional Office for Asia and the Pacific, Bangkok.

  • Hassanin A., Léger N. and Deutsch J. 2005 Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of Metazoa, and consequences for phylogenetic inferences. Syst. Biol. 54, 277–298.

    Article  Google Scholar 

  • Kierstein G., Vallinoto M., Silva A., Schneider M. P., Iannuzzi L. and Brenig B. 2004 Analysis of mitochondrial D-loop region casts new light on domestic water buffalo (Bubalus bubalis) phylogeny. Mol. Phylogenet. Evol. 30, 308–324.

    Article  CAS  Google Scholar 

  • Kumar S., Stecher G., Li M., Knyaz C. and Tamura K. 2018 MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549.

    Article  CAS  Google Scholar 

  • Kumar S., Nagarajan M., Sandhu J. S., Kumar N., Behl V. and Nishanth G. 2007 Mitochondrial DNA analyses of Indian water buffalo support a distinct genetic origin of river and swamp buffalo. Anim. Genet. 38, 227–232.

    Article  CAS  Google Scholar 

  • Kundu A., Sunder J., Jeyakumar S., Verma S. K., Kundu M. S., De A. K. et al. 2010 Livestock and poultry production policy for Andaman and Nicobar Islands: a scientific perspective. CARI, Port Blair.

    Google Scholar 

  • Lannuzzi L. and Di Meo G. 2009 Water Buffalo. In genome mapping and genomics in domestic animals (ed. N. E. Cockett and C. Kole), vol. 3, pp. 280. Springer-Verlag, Berlin Herdelberg.

  • Lei C. Z., Zhang W., Chen H., Lu F., Liu R. Y., Yang X. Y. et al. 2007 Independent maternal origin of Chinese swamp buffalo (Bubalus bubalis). Anim. Genet. 38, 97–102.

    Article  CAS  Google Scholar 

  • Li H. and Durbin R. 2009 Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760.

    Article  CAS  Google Scholar 

  • Lohse M., Drechsel O., Kahlau S. and Bock R. 2013 Organellargenome DRAW - a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res. 41, W575–W581.

    Article  Google Scholar 

  • Lowe T. M. and Chan P. P. 2016 tRNAscan-SE On-line: search and contextual analysis of transfer RNA genes. Nucleic Acids Res. 44, W54–W57.

    Article  CAS  Google Scholar 

  • Ludwig A., Alderson L., Fandrey E., Lieckfeldt D., Soederlund T. K. and Froelich K. 2013 Tracing the genetic roots of the indigenous White Park Cattle. Anim. Genet. 44, 383–386.

    Article  CAS  Google Scholar 

  • Parma P., Erra-Pujada M., Feligini M., Greppi G. and Enne G. 2004 Water buffalo (Bubalus bubalis): complete nucleotide mitochondrial genome sequence. DNA Seq. 15, 369–373.

    Article  CAS  Google Scholar 

  • Perna N. T. and Kocher T. D. 1995 Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J. Mol. Evol. 41, 353–358.

    Article  CAS  Google Scholar 

  • Rissler L. J. 2016 Union of phylogeography and landscape genetics. Proc. Natl. Acad. Sci. USA 113, 8079–8086.

    Article  CAS  Google Scholar 

  • Santamaria M., Lanave C., Vicario S. and Saccone C. 2007 Variability of the mitochondrial genome in mammals at the inter-species/intra-species boundary. Biol. Chem. 388, 943–946.

    Article  CAS  Google Scholar 

  • Sarvani R. K., Parmar D. R., Tabasum W., Thota N., Sreenivas A. and Gaur A. 2018 Characterization of the complete mitogenome of Indian Mouse Deer, Moschiola indica (Artiodactyla: Tragulidae) and its evolutionary significance. Sci. Rep. 8, 2697.

    Article  Google Scholar 

  • Simon C., Buckley T. R., Frati F., Stewart J. B. and Beckenbach A. T. 2006 Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Annu. Rev. Ecol. Evol. Syst. 37, 545–579.

    Article  Google Scholar 

  • Sunder J., Kundu A., Kundu M. S., Sujatha T. and De A. K. 2018. Farming practices and morphometric characterization of Andaman Local Goat. Indian J. Anim. Res. Article Id: B-3615.

  • Thompson J. D., Higgins D. G. and Gibson T. J. 1994 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680.

    Article  CAS  Google Scholar 

  • Wang S., Chen N., Capodiferro M. R., Zhang T., Lancioni H., Zhang H. et al. 2017 Whole mitogenomes reveal the history of swamp buffalo: initially shaped by glacial periods and eventually modelled by domestication. Sci. Rep. 7, 4708.

    Article  CAS  Google Scholar 

  • Wei S. J., Shi M., Chen X. X., Sharkey M. J., van Achterberg C., Ye G. Y. et al. 2010 New views on strand asymmetry in insect mitochondrial genomes. PLoS One 5, e12708.

    Article  Google Scholar 

  • Yindee M., Vlamings B. H., Wajjwalku W., Techakumphu M., Lohachit C., Sirivaidyapong S. et al. 2010 Y-chromosomal variation confirms independent domestications of swamp and river buffalo. Anim. Genet. 41, 433–435.

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by a grant from Department of Biotechnology, Ministry of Science and Technology, Government of India (grant no. BT/BI/04/066/2004). The Indian Council of Agricultural Research (ICAR), India, also supported the study.

Author information

Authors and Affiliations

  1. Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, 744 101, India

    Arun Kumar De, Perumal Ponraj, A. Kundu & Debasis Bhattacharya

  2. Bioinformatics Centre, ICAR-Central Island Agricultural Research Institute, Port Blair, 744 101, India

    Arun Kumar De

  3. Animal Biotechnology Centre, National Dairy Research Institute, Karnal, 132 001, India

    Dhruba Malakar

  4. GCC Biotech India Pvt. Ltd., Kirtankhola, Joychandipur, 743 377, India

    Ramachandran Muthiyan

Authors
  1. Arun Kumar De
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Perumal Ponraj
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Dhruba Malakar
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ramachandran Muthiyan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. A. Kundu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Debasis Bhattacharya
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Debasis Bhattacharya.

Additional information

Corresponding editor: H. A. Ranganath

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kumar De, A., Ponraj, P., Malakar, D. et al. Complete mitogenome sequencing of Andaman buffalo: an endangered germplasm of Andaman and Nicobar Islands, India. J Genet 98, 97 (2019). https://doi.org/10.1007/s12041-019-1140-z

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s12041-019-1140-z

Keywords

Search

Navigation