1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Systems biology analysis of rice transcriptome: key genes responsive to salinity stress
Paper ID : 1289-ICB10
Authors:
Mozhde Hamidizade *1, Yaser Biniaz2, Fateme Amiri3, S. Mohsen Taghavi1, Ali Moghadam3
1Department of Plant Protection, School of Agriculture, Shiraz University
2Plant Virology Research Center, Shiraz University, Shiraz, Iran
3Institute of Biotechnology, Shiraz University, Shiraz, Iran
Abstract:
Salt stress is one of the main abiotic stresses limiting rice production. Better understanding of the tolerance mechanisms is a significant subject in agribiotechnology in rice. In this study, transcriptome data were obtained from a European Bioinformatics Institute (EBI) database. CLC Genomics Workbench software was used for data processing. Reference genome and also rice annotation were retrieved from NCBI. To plot the protein-protein interactions and network construction, the String database was used and Cytoscape software was applied for visualizing the interaction networks. The iTAK database was used for transcription factor analysis. Hub genes were identified using Cytoscape software, with the highest number of interactions belonging to the OsJ_02628 gene with an unknown role and a score of 628. Due to the importance of hub genes, their function was evaluated. The most important of these were nucleotide linkers (Os08t0117100-01), similar to ATP-dependent RNA helicase (Os03t0827700-01), helix domains such as tetratricopeptide containing the protein (Os07t0590600-00), and the precursor (Os0000-02). In the results of ontological analysis, the highest number in biological process was related to ribonucleoprotein complex subunit organization and localization, in molecular function to transporter activity and membrane and also in cellular component to plant-type cell wall and membrane. Thus, transcription, kinase activity along with transmitters were introduced as the most important enriched groups in this study. In the TFs analysis, it was defined that the number and type of families at different time points, are almost the same. Hence, the highest numbers belonged to bHLH and WRKY families. Plants overexpressing OsWRKY45-2 have significantly lower survival rates under salinity due to the suppression of SNAC1, DREB1B, NCED4 and Rab16D genes, indicating that OsWRKY45-2 might be a transcriptional repressor of these genes [1]. These results provided valuable information for future research of crops improvement exposed to abiotic stresses.
Keywords:
Transcriptome, Systems Biology, Gene Ontology, Transcription factor, Abiotic stress
Status : Paper Accepted (Poster Presentation)