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

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Abstract

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.

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Acknowledgements

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).

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    1. Centre of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pashan, Pune, 411 008, India

      Puli Chandramouli Reddy, Ashwin Kelkar, Farhat Habib, Saurabh J. Pradhan & Sanjeev Galande

    2. Centre for Ecological Sciences, Indian Institute of Science, Bangalore, 560 012, India

      Ishani Sinha & Raman Sukumar

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    1. Puli Chandramouli Reddy
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    Corresponding editor: Partha P Majumder

    [Reddy PC, Sinha I, Kelkar A, Habib F, Pradhan SJ, Sukumar R and Galande S 2015 Comparative sequence analyses of genome and transcriptome reveal novel transcripts and variants in the Asian elephant Elephas maximus. J. Biosci.] DOI 10.1007/s12038-015-9580-y

    Supplementary materials pertaining to this article are available on the Journal of Biosciences Website at http://www.ias.ac.in/jbiosci/dec2015/supp/Reddy.pdf

    Raman Sukumar and Sanjeev Galande Shared senior authorship.

    Puli Chandramouli Reddy, Ishani Sinha, Ashwin Kelkar and Farhat Habib contributed equally to this work.

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    Reddy, P.C., Sinha, I., Kelkar, A. et al. Comparative sequence analyses of genome and transcriptome reveal novel transcripts and variants in the Asian elephant Elephas maximus . J Biosci 40, 891–907 (2015). https://doi.org/10.1007/s12038-015-9580-y

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