Journal of Biosciences

, Volume 40, Issue 5, pp 891–907 | Cite as

Comparative sequence analyses of genome and transcriptome reveal novel transcripts and variants in the Asian elephant Elephas maximus

  • Puli Chandramouli Reddy
  • Ishani Sinha
  • Ashwin Kelkar
  • Farhat Habib
  • Saurabh J. Pradhan
  • Raman Sukumar
  • Sanjeev Galande


The Asian elephant Elephas maximus and the African elephant Loxodonta africana that diverged 5–7 million years ago exhibit differences in their physiology, behaviour and morphology. A comparative genomics approach would be useful and necessary for evolutionary and functional genetic studies of elephants. We performed sequencing of E. maximus and map to L. africana at ~15X coverage. Through comparative sequence analyses, we have identified Asian elephant specific homozygous, non-synonymous single nucleotide variants (SNVs) that map to 1514 protein coding genes, many of which are involved in olfaction. We also present the first report of a high-coverage transcriptome sequence in E. maximus from peripheral blood lymphocytes. We have identified 103 novel protein coding transcripts and 66-long non-coding (lnc)RNAs. We also report the presence of 181 protein domains unique to elephants when compared to other Afrotheria species. Each of these findings can be further investigated to gain a better understanding of functional differences unique to elephant species, as well as those unique to elephantids in comparison with other mammals. This work therefore provides a valuable resource to explore the immense research potential of comparative analyses of transcriptome and genome sequences in the Asian elephant.


Asian elephant comparative genomics gene prediction transcriptome 



This work was supported by grant from the Centre of Excellence in Epigenetics program of the Department of Biotechnology, India, and from IISER Pune to SG. PCR is supported by Postdoctoral Fellowship from the Department of Biotechnology, India. AK is supported by an Early Career Fellowship from the Wellcome Trust-DBT India Alliance. FH is supported by the Centre of Excellence in Epigenetics Program. SJP is supported by Senior Research Fellowship from the Council of Scientific and Industrial Research, India. IS is supported by Centre for Ecological Sciences through grant-in-aid from Ministry of Environment, Forest and Climate Change. RS is a JC Bose National Fellow. Elephant blood sample was obtained with the permission and support of the Karnataka Forest Department (vide permit No. B1/WL/CR-25/2013-14).

Supplementary material

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Copyright information

© Indian Academy of Sciences 2015

Authors and Affiliations

  • Puli Chandramouli Reddy
    • 1
  • Ishani Sinha
    • 2
  • Ashwin Kelkar
    • 1
  • Farhat Habib
    • 1
  • Saurabh J. Pradhan
    • 1
  • Raman Sukumar
    • 2
  • Sanjeev Galande
    • 1
  1. 1.Centre of Excellence in EpigeneticsIndian Institute of Science Education and ResearchPuneIndia
  2. 2.Centre for Ecological SciencesIndian Institute of ScienceBangaloreIndia

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