Functional annotation and transcript expression analysis of RNA-Seq data (via NGS) from white kelampayan (Neolamarckia cadamba) using bioinformatics approach

• Main Author: Lim, Leong Rui
• Format: Final Year Project Report
• Language: English; English
• Published: Universiti Malaysia Sarawak, (UNIMAS) 2015
• Subjects: SB Plant culture
• Online Access: http://ir.unimas.my/id/eprint/10847/1/Lim.pdf; http://ir.unimas.my/id/eprint/10847/4/Lim%20Leong%20ft.pdf; http://ir.unimas.my/id/eprint/10847/

White kelampayan (Neolamarckia cadamba) is an indigenous tree species under Rubiaceae family. It has a high economic value due to its fast growing properties. However, an understanding on genetics study of kelampayan still remains scarce. Objectives of this study were to define functional annotation and analyse transcripts expression level of the RNA-Seq data from the white kelampayan. In this study, there were 66,468 transcripts expressed via sequence reads assembly. Out of the total expressed transcripts, 29,495 transcripts were annotated and mapped with the gene ontology (GO) terms by using bioinformatics approaches such as the CLC Genomics Workbench 7.5, Blast2GO® and WEGO tool. Differential expression of transcripts was studied and certain candidate genes involving in wood formation, stress response and plant defence were identified. In this study, out of 66,468 transcripts, the number of up-regulated transcripts was higher than the number of down-regulated transcripts, showing more transcripts expressed in the developing xylem tissues. In gene ontology analysis, the biological processes showed the highest distribution of annotated transcripts. Besides, cinnamoyl-dehydrogenase, cinnamoyl 4-hydroxylase, cellulose synthase, enzyme antioxidant, heat shock protein, aquaporin, and genes involved in plant defense were annotated and discussed in this study. This study provides another useful genomic reference for future research on the tree species.