Comparative sequence analyses of genome and transcriptome reveal novel transcripts and variants in the Asian elephant Elephas maximus.
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Date
2015-12
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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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Keywords
Asian elephant, comparative genomics, gene prediction, transcriptome
Citation
Reddy Puli Chandramouli, Sinha Ishani, Kelkar Ashwin, Habib Farhat, Pradhan Saurabh J, Sukumar Raman, Galande Sanjeev. Comparative sequence analyses of genome and transcriptome reveal novel transcripts and variants in the Asian elephant Elephas maximus. Journal of Biosciences. 2015 Dec; 40(5):891-907.