Transcriptomics

Biography

Biography: Saurabh Chaudhary

Abstract

Sea buckthorn (Hippophae rhamnoides L.) is well known for its immense medicinal, nutritional and ecological value, and also for its ability to grow in extreme environments. We used next generation Illumina sequencing to gain a comprehensive view of the seabuckthorn transcriptome. A total of 86,253,874 high quality short reads were assembled using different assembly tools and parameters. The use of short read assembler ABySS with an additive k-mer approach followed by TGICL suite was found most promising for de novo transcriptome assembly. Finally, 88,297 transcripts (>100 bp) were generated representing 53 Mb transcriptome. The average transcript length and N50 length remained 610 bp and 1,193 bp, respectively and 91% of the short reads uniquely mapped back to the seabuckthorn transcriptome. Further, 41,340 (46.8%) transcripts showed significant similarity with the sequences present in nr protein databases of NCBI (E-value <1E-06). Assembled transcripts were also screened for the presence of transcription factors and simple sequence repeats. Next, DeepSAGE, a tag based approach was also followed to identify differentially expressed genes under cold and freeze stress. In all, 11,922 differentially expressed genes (DEGs) were identified including 6,539 up regulated and 5,383 down regulated genes. Gene ontology and KEGG pathway analysis was performed to assign gene ontology term to DEGs and ascertain their biological functions. Expression of selected 22 DEGs was validated using qRT-PCR.A combination of de novo transcriptome assembly and DeepSAGE analysis proved to be a powerful method for transcriptome analysis and identifying abiotic stress responsive genes in seabuckthorn.