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

Journal of biosciences

Ashwin Kelkar²  Raman Sukumar¹  Farhat Habib²  Puli Chandramouli Reddy²  Ishani Sinha¹  Saurabh J Pradhan²  Sanjeev Galande1² 

[1] Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560 012, India$$;Centre of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pashan, Pune 411 008, India$$

关键词: Asian elephant;    comparative genomics;    gene prediction;    transcriptome;   

DOI  :  

来源: Indian Academy of Sciences

【 摘 要 】

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 (Inc)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.

【 授权许可】

Unknown