Omics applications in plant-microorganism interactions: A view from plant genomics

Abstract

The advent of next generation sequencing has opened up the possibility to carry out detailed molecular genetic analysis on non-model species. Here we present strategies to carry out RNAseq analysis in Agave tequilana which for the first time have permitted the identification and characterization of genes involved in fructan metabolism and flowering time in Agave species. Based on in silico data, expression patterns for individual genes could be determined and later confirmed by qRT-PCR and cDNA´s of genes of interest were cloned and functionally characterized in heterologous systems such as Pichia pastoris and Arabidopsis thaliana. We also present data obtained by RNAseq analysis of the C. lindemuthianum – P. vulgaris pathosystem. Using strains of C. lindemuthianum expressing the green fluorescent protein, the infection process can easily be followed. RNAseq was carried out at different time points during the initial stages of infection by C. lindemuthianum on P. vulgaris cultivar BAT93 using virulent or non-virulent races of C. lindemuthianum (Race 1088 and Race 256 respectively). Differentially expressed genes specific to compatible and non-compatible reactions could therefore be identified.