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

Reddy, Puli Chandramouli and Sinha, Ishani and Kelkar, Ashwin and Habib, Farhat and Pradhan, Saurabh J and Sukumar, Raman and Galande, Sanjeev (2015) Comparative sequence analyses of genome and transcriptome reveal novel transcripts and variants in the Asian elephant Elephas maximus. In: JOURNAL OF BIOSCIENCES, 40 (5). pp. 891-907.

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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 similar to 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.

Item Type:	Journal Article
Publication:	JOURNAL OF BIOSCIENCES
Publisher:	INDIAN ACAD SCIENCES
Additional Information:	Copy right for this article belongs to the INDIAN ACAD SCIENCES, C V RAMAN AVENUE, SADASHIVANAGAR, P B #8005, BANGALORE 560 080, INDIA
Keywords:	Asian elephant; comparative genomics; gene prediction; transcriptome
Department/Centre:	Division of Biological Sciences > Centre for Ecological Sciences
Date Deposited:	14 Jan 2016 06:23
Last Modified:	14 Jan 2016 06:23
URI:	http://eprints.iisc.ac.in/id/eprint/53090

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