1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
A Meta-Analysis of Comparative Transcriptomic Data Reveals a Set of Genes Involved in the lignin synthesis in Nicotiana tabacum
Paper ID : 1291-ICB10
Authors:
Maryam Rashidifar *1, hosein Askari1, Ali Moghadam2
1Associate Prof., Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
2Institute of Biotechnology, Shiraz University, Shiraz, Iran
Abstract:
Lignin is the second component of plant biomass and provides mechanical strength to tree trunks and confers impermeability to vascular tissues. It is mainly involved in defense mechanisms against biotic and abiotic stresses [1]. This study was designed to explore the gene expression regulatory networks of this pathway in tobacco under drought stress conditions. We retrieved four datasets from different gene expression studies on tobacco in drought stress conditions from Gene Expression Omnibus. Preprocessed reads were aligned to the reference genome with Hisat2. HTSeq was used to count the number of reads mapped to each gene [2,3]. The meta-analysis approach evaluated differentially expressed genes by the combined data (P-value ≤ 0.05). In addition, based on the R Package Weighted Gene Co-Expression Network Analysis (WGCNA), we identified some modules related to the lignin biosynthesis pathway. The gene network analysis also identified several hub genes such as FAS1and PPC2.51 which may play crucial roles in the lignin biosynthesis pathway. The previous study represents that FLAs are cell wall structural glycoproteins that mediate cellulose deposition and cell wall development and they are abundant in the xylem [5]. It is also shown PP2C signaling cascade provides land plants with a hormone-modulated, resulting in a tolerance strategy allowing them to support tissues built of cells with thicker cell walls. In the present study, we identified several hub genes. The results showed that these hub genes may have vital roles in regulation of lignin biosynthesis [6]. The current findings provide an overall insight into lignin biosynthesis and can expand the potential for engineering genome-scale pathways and systems metabolic engineering to alter the production of lignin by plants.
Keywords:
Phenylpropanoid pathway; RNA-seq data; Meta-analysis; co-expression; WGCNA
Status : Paper Accepted (Poster Presentation)