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

Abstract

<p>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 <em>Agave tequilana</em> which for the first time have permitted the identification and characterization of genes involved in fructan metabolism and flowering time in <em>Agave</em> 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 <em>Pichia pastoris</em> and <em>Arabidopsis thaliana</em>. We also present data obtained by RNAseq analysis of the <em>C. lindemuthianum</em>–<em>P. vulgaris</em> pathosystem. Using strains of <em>C. lindemuthianum</em> 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 <em>by C. lindemuthianum</em> on <em>P. vulgaris</em> cultivar BAT93 using virulent or non-virulent races of <em>C. lindemuthianum</em> (Race 1088 and Race 256 respectively). Differentially expressed genes specific to compatible and non-compatible reactions could therefore be identified.</p>