Identification and analysis of genes expressed in the Ustilago maydis dikaryon: uncovering a novel class of pathogenesis genes

The released genome sequence of Ustilago maydis provided immense insight into this pathogen's genetic structure; however, thorough annotation of the genome requires data from many sources. Information from 4425 expressed sequence tags from the filamentous dikaryon provided an excellent resource for genome annotation. This allowed confirmation and correction of gene models, as well as the documentation of transcript structural features. The depth of coverage provided by the normalized dikaryon cDNA library contributed to the discovery of new candidate pathogenesis genes and enabled the identification of U. maydis antisense and noncoding RNAs. Candidate pathogenesis genes were identified based on their representation in the dikaryon library only or in the dikaryon and diploid cDNA libraries, followed by comparative analysis with the genome sequences of other plant pathogens. Six genes that were conserved only among pathogenic fungi and six genes unique to U. maydis were confirmed to be expressed in planta using reverse-transcriptase PCR. The transcript level of three of these genes varied during the transition from filamentous dikaryotic growth to the formation of the teliospore. This discovery provides representative genes that can be used to begin dissecting the control of gene expression during this transition in pathogenic development. Many of the newly identified U. maydis noncoding RNAs were differentially represented among cDNA libraries, suggesting potential functional roles in different U. maydis cell types. The deletion of one such ncRNA in a solopathogenic strain reduced virulence, revealing a new type of pathogenesis gene in fungi.