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Title: Identification and analysis of regulatory elements and associated transcription factors of costunolide biosynthetic pathway genes in Saussurea lappa
Researcher: Thakur, Vasundhara
Guide(s): Kashmir Singh
Keywords: Costunolide
Saussurea lappa
Secondary metabolite
Transcription factors
University: Panjab University
Completed Date: 2020
Abstract: The PhD work included the comparative analysis of root and leaf tissue transcriptomes (three replicates each) to study the costunolide pathway genes and the related TFs in Saussurea lappa. Various bioinformatics tools were employed to study the transcriptomic data, revealing about 162,539 assembled unigenes. These were functionally annotated, classified and used in tissue-specific differential expression analysis studies. The differentially expressed costunolide pathway genes and putative TF transcripts were identified and annotated. Putative transcription factors were identified using PlantTFDB and TF-gene co-expression network was generated followed by clustering using module based analysis to observe their coordinated behavior. Further, the analysis of key regulatory genes i.e. diphosphomevalonate decarboxylase (SlDPD) and costunolide synthase (SlCOS) involved in the costunolide biosynthesis was performed and their promoter region were cloned using genome walking technique to study the existing cis-regulatory elements. Bioinformatics tools were employed to predict the cis regulatory elements, leading to the identification of bHLH, Dof and WRKY family of TFs as the interacting partners of SlDPD gene, and MYB family of TFs as an interacting partner of SlCOS gene. The transcripts of TF families were identified and annotated using various in silico tools to reveal potential candidates that could be interacting with the genes of interest. Yeast one-hybrid technique was appointed to identify the interacting TFs and revealed SlbHLH, SlDof and SlWRKY TFs interacting with SlDPD gene promoters and SlMYB TF intecating with SlCOS gene promoter. RT-PCR was performed to obtain the comparative gene and TF candidates expression patterns. newline
Pagination: iv, 206p.
Appears in Departments:Department of Biotechnology

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01_title.pdfAttached File5.06 kBAdobe PDFView/Open
02_certificate.pdf630.21 kBAdobe PDFView/Open
03_acknowledgement.pdf272.3 kBAdobe PDFView/Open
04_content.pdf168 kBAdobe PDFView/Open
05_abbrevations.pdf148.1 kBAdobe PDFView/Open
06_chapter1.pdf723.82 kBAdobe PDFView/Open
07_chapter2.pdf1.03 MBAdobe PDFView/Open
08_chapter3.pdf1.32 MBAdobe PDFView/Open
09_chapter4.pdf7.32 MBAdobe PDFView/Open
10_chapter5.pdf521.63 kBAdobe PDFView/Open
11_summary.pdf378.37 kBAdobe PDFView/Open
12_references.pdf688.83 kBAdobe PDFView/Open
13_appendices.pdf1.26 MBAdobe PDFView/Open
80_recommendation.pdf378.37 kBAdobe PDFView/Open

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