MICROARRAY-BASED TRANSCRIPTOME ANALYSIS OF THE GRASS ENDOPHYTES Neotyphodium lolii AND N. coenophialum AND HOST INTERACTION

¹ Plant Biotechnology Centre, Primary Industries Research Victoria, Department of Primary Industries, La Trobe University, Bundoora, Victoria 3086, Australia

Neotyphodium lolii and N. coenophialum are frequent endophytic symbiotic fungi of the temperate pasture grasses, perennial ryegrass (Lolium perenne L.) and tall fescue (Festuca arundinacea Schreb.), respectively. A cDNA spotted microarray interrogating 3,806 Neotyphodium endophyte genes has been generated. This endophyte microarray contains 1,596 and 2,210 features of N. lolii and N. coenophialum origin, respectively. It provides a tool for comparative gene expression studies between endophyte species, as well as a tool for high-throughput parallel gene expression profiling in grass endophytes. Microarray-based gene expression analysis using RNA from in vitro grown N. coenophialum and N. lolii demonstrated its utility in comparative transcriptome analysis of both endophyte species. Additional proof of concept was obtained in using this Neotyphodium chip (EndoChip) to analyse genome-wide gene expression in endophytes grown under different culture conditions, endophytes grown in vitro and in planta, for the gene expression profiling of novel genes based on coordinated expression with genes of known cellular functions and for the transcriptional profiling of the grass-endophyte association.