The pathogenic mechanisms of Tilletia horrida as revealed by comparative and functional genomics

Abstract

Tilletia horrida is a soil-borne, mononucleate basidiomycete fungus with a biotrophic lifestyle that causes rice kernel smut, a disease that is distributed throughout hybrid rice growing areas worldwide. Here we report on the high-quality genome sequence of T. horrida; it is composed of 23.2 Mb that encode 7,729 predicted genes and 6,973 genes supported by RNA-seq. The genome contains few repetitive elements that account for 8.45% of the total. Evolutionarily, T. horrida lies close to the Ustilago fungi, suggesting grass species as potential hosts, but co-linearity was not observed between T. horrida and the barley smut Ustilago hordei. Genes and functions relevant to pathogenicity were presumed. T. horrida possesses a smaller set of carbohydrate-active enzymes and secondary metabolites, which probably reflect the specific characteristics of its infection and biotrophic lifestyle. Genes that encode secreted proteins and enzymes of secondary metabolism, and genes that are represented in the pathogen-host interaction gene database genes, are highly expressed during early infection; this is consistent with their potential roles in pathogenicity. Furthermore, among the 131 candidate pathogen effectors identified according to their expression patterns and functionality, we validated two that trigger leaf cell death in Nicotiana benthamiana. In summary, we have revealed new molecular mechanisms involved in the evolution, biotrophy, and pathogenesis of T. horrida.

Comparative secretome analysis of different smut fungi and identification of plant cell death-inducing secreted proteins from Tilletia horrida

“…Of these, 131 small secreted proteins that were up-regulated at 8 h after inoculation were selected as putative effectors, according to our previous study (Fig. 2) [23].

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“…However, the homolog genes of smut_5844 were not found; we therefore predicted that it is a novel effector in T. horrida . To further select high confidence candidate effectors from among these genes that encode secreted proteins, expression trend clustering analysis of 291 differentially expressed genes ( P ≤ 0.05 and |log 2 fold change| ≥ 1) that encoded secreted proteins was performed at different infection time points, based on our previous transcriptome data [23]. This approach categorized the genes into 23 clustered profiles and enabled the selection of clusters with different sets of characteristics that may relate to different functions (Fig.…”

“…According to genome sequencing, T. horrida encodes 597 secreted proteins, of which 131 are predicted to be effectors [23]. Furthermore, many potential effector genes are arranged in clusters and transcriptome analyses during infection suggest that putative secreted effectors have an essential role in establishing successful infection in T. horrida [23]. No effector genes of T. horrida have been functionally characterized.…”

Comparative transcriptome analysis by Tilletia horrida infection in resistant and susceptible rice (Oryza sativa L.) male sterile lines reveals candidate genes and resistant mechanisms

“…They were provided by the Department of Food Crop Research Institute of Hubei Academy of Agricultural Science. The T. horrida isolate JY-521, a virulent strain with a sequenced the genome, was used for plant inoculations and separating and preserving by the Department of Rice Research Institute of Sichuan Agricultural University [14]. Monoconidial cultures of T. horrida were grown in potato dextrose broth in an incubator at 28℃ for 7 days on a shaker at 150 rpm.…”

“…Over the past two decades, researchers have predominantly focused on the process of pathogen infection, morphological characteristics and evolutionary biology of the pathogen, and mechanism of infection. However, little is known about the molecular mechanisms of resistance to RKS, and no genes or QTL underlying resistance to T. horrida have been reported to data [14,15].…”