Analysis and comparison of multiple sugarcane metabolic networks to unravel mechanisms of sugarcane immune system

Abstract

This work plan is an integral part of the FAPESP thematic project entitled "RGAs sugarcane expression profile during infection with various pathogens". The project aimed to create a database of Resistance Gene Analogs (RGAs) in sugarcane from data originating from different new generation sequencing platforms and data from public databases. The results obtained were published in the journal BMC Genomics ("Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype"). In addition, the "Sugarcane Orthologs of Resistance Database (SORD)" database is available for access through the link ttp://amos.esalq.usp.br/sord/. Then, from the understanding that living organisms can have their metabolic networks modeled based on graph theory, an interaction network protein-protein based on the Arabidopsis thaliana model with information obtained from the KEGG, BioGRID, and STRING databases, was built for sugarcane orthologs. This work was published in Frontiers in Plant Pathology, Plant Systems and Synthetic Biology ("Arabidopsis-based dual-layered biological network analysis elucidates fully modulated pathways related to sugarcane resistance on biotrophic pathogen infection"). The method revealed sugarcane metabolism modulation events during the interaction with smut. Furthermore, data on the genomic distribution of RGAs in the sugarcane genome, also inserted into the network, revealed co-expression modules between specific RGAs induced in the resistant variety and sugar metabolism. This new project aims to include a new layer of analysis comparing the molecular events during the sugarcane-Sporisorium scitamineum interaction with data obtained in the context of the thematic project (2016/17545-8) "Genes, Genomes & Transposable Elements contribution to plant-microbe interaction: a sugarcane study case" under the general coordination of Profa. Marie-Anne Van Sluys. Under similar conditions, RNAseq data for infection with other sugarcane pathogens, Leifsonia xyli subsp. xyli and Xanthomonas albilineans, and an endophytic Gluconacetobacter diazotrophicus. The data will be treated similarly as previously described in the published articles and inserted into the network to verify the overlap of differential expression between resistant and susceptible varieties and microorganisms concerning RGAs and the activated metabolic pathways or repressed during the interaction. Furthermore, comparisons through the alignment of networks are expected to show the divergences of the immune system between sugarcane genotypes and infection with different pathogens. (AU)