title: Comparative sequence analyses of genome and transcriptome reveal novel transcripts and variants in the Asian elephant Elephas maximus.
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.
authors.affiliation: Centre of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pashan, Pune 411 008, India.
authors.forename: Puli Chandramouli
authors.initials: PC
authors.lastname: Reddy
authors.forename: Ishani
authors.initials: I
authors.lastname: Sinha
authors.forename: Ashwin
authors.initials: A
authors.lastname: Kelkar
authors.forename: Farhat
authors.initials: F
authors.lastname: Habib
authors.forename: Saurabh J
authors.initials: SJ
authors.lastname: Pradhan
authors.forename: Raman
authors.initials: R
authors.lastname: Sukumar
authors.forename: Sanjeev
authors.initials: S
authors.lastname: Galande
mesh_terms: D000818:Animals; D004606:Elephants / Q000235:genetics*; D015870:Gene Expression; D020869:Gene Expression Profiling; D014644:Genetic Variation; D016678:Genome; D006720:Homozygote; D008214:Lymphocytes / Q000502:physiology; D058977:Molecular Sequence Annotation; D062085:RNA, Long Noncoding; D017421:Sequence Analysis; D059467:Transcriptome
chemical_list: D062085:RNA, Long Noncoding