Heterobasidion annosum gene expression during saprotrophic growth on topsoil (organic layer) from mineral soil, drained and undrained peatland forests.. Heterobasidion annosum

Transcript profiles of H. annosum from different tissues and mycelium grown on different substrates and under different stresses were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) H. irregulare genome sequence version 1. One aim of this study was to compare gene expression profiles of H. annosum during saprotrophic growth on topsoil from mineral soil, drained and undrained peatland. Overall design: The Heterobasidion irregulare custom-exon expression array (4 x 72K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) (http://www.nimblegen.com/products/exp/index.html) contained five independent, non-identical, 60-mer probes per gene model coding sequence. For 12,199 of the 12,299 annotated protein-coding gene models probes could be designed. For 19 gene models no probes could be generated and 81 gene models shared all five probes with other gene models. Included in the array were 916 random 60-mer control probes and labelling controls. For 2032 randomly chosen gene models, technical duplicates were included on the array. We performed 12 hybridizations (NimbleGen) with samples derived from H. annosum grown in either liquid Malt Extract Medium (three biological replicates), on Pine-dominated mineral forest topsoil (three biological replicates), on Pine-dominated pristine peatland forest topsoil (three biological replicates) or on Pine-dominated drained peatland forest topsoil (three biological replicates).