Comparative sequence analyses of genome and transcriptome reveal novel transcripts and variants in the Asian elephant Elephas maximus 1,† 2,† 1,† 1,† PULI CHANDRAMOULI REDDY , ISHANI SINHA , ASHWIN KELKAR , FARHAT HABIB , 1 2,‡ 1, ,‡ SAURABH J. PRADHAN , RAMAN SUKUMAR and SANJEEV GALANDE * 1Centre of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pashan, Pune 411 008, India 2Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560 012, India *Corresponding author (Fax, 91-20-25865086; Email,
[email protected]) †These authors contributed equally to the work. ‡Shared senior authorship. 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.