Faculty
Science
Supervisor Name
Mark Bernards
Keywords
suberin, metabolism, RNAseq, R-statistical-software, genes, WGCNA, potato, modules
Description
Suberin is a heteropolymer comprising a cell wall-bound poly(phenolic) domain (SPPD) covalently linked to a poly(aliphatic) domain (SPAD) that is deposited between the cell wall and plasma membrane (Woolfson 2018). Previous studies have measured phenolic and/or fatty acid compounds in suberized tissues, and for many of these the biosynthesis is known, However, restricting analyses to only those biomolecules that are known does not yield new information about other genes that may be involved. This experiment serves to identify suberin associated gene clusters within Modules, based on an analysis of their expression patterns using Weighted Gene Correlation Network Analysis (WGCNA). Once suberin associated modules are identified, other genes associated with the module may be identified that are essential for the suberization process and mechanism(s) that regulate and coordinate SPPD and SPAD production and assembly. From data output dendrograms of Module Membership (MM) were visualized and the genes assigned to each queried for the presence of suberin-associated genes. In total, 18 distinct modules were generated. Genes involved in the suberin biosynthesis and deposition process were expressed primarily in Modules 1, 2, 3, 4 and 10. More specifically, Module 3 was shown to contain a full set of genes for fatty acid metabolism (i.e., modification of fatty acids for suberin) and aliphatic suberin assembly, while Module 10 contained most of the genes for fatty acid biosynthesis. Phenolic metabolism genes were found across a few modules but predominantly in Modules 1, 2, 3 and 4. Specifically, 184 of the genes were able to match to known suberin functions and separate based on Module specific clusters. Results provide more detail in genes involved in suberin biosynthesis and metabolism.
Acknowledgements
Gratefully acknowledge the support provided by my supervisor Dr. Mark Bernards, and helpful discussions with Dr. Vladimir Zhurov and Dr. Kathlyn Natalie Woolfson.
This work was supported by the WUSRI program which gave me the opportunity and funding to complete this research.
This work was supported by the Biology Department at the University of Western Ontario for providing the resources and materials necessary to produce this experiment.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Document Type
Poster
Included in
Using WGCNA for Comprehensive Understanding of Genes Involved in Suberin Biosynthesis from RNA-seq data Analysis
Suberin is a heteropolymer comprising a cell wall-bound poly(phenolic) domain (SPPD) covalently linked to a poly(aliphatic) domain (SPAD) that is deposited between the cell wall and plasma membrane (Woolfson 2018). Previous studies have measured phenolic and/or fatty acid compounds in suberized tissues, and for many of these the biosynthesis is known, However, restricting analyses to only those biomolecules that are known does not yield new information about other genes that may be involved. This experiment serves to identify suberin associated gene clusters within Modules, based on an analysis of their expression patterns using Weighted Gene Correlation Network Analysis (WGCNA). Once suberin associated modules are identified, other genes associated with the module may be identified that are essential for the suberization process and mechanism(s) that regulate and coordinate SPPD and SPAD production and assembly. From data output dendrograms of Module Membership (MM) were visualized and the genes assigned to each queried for the presence of suberin-associated genes. In total, 18 distinct modules were generated. Genes involved in the suberin biosynthesis and deposition process were expressed primarily in Modules 1, 2, 3, 4 and 10. More specifically, Module 3 was shown to contain a full set of genes for fatty acid metabolism (i.e., modification of fatty acids for suberin) and aliphatic suberin assembly, while Module 10 contained most of the genes for fatty acid biosynthesis. Phenolic metabolism genes were found across a few modules but predominantly in Modules 1, 2, 3 and 4. Specifically, 184 of the genes were able to match to known suberin functions and separate based on Module specific clusters. Results provide more detail in genes involved in suberin biosynthesis and metabolism.