Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

Abstract

The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.

Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

“…Armillaria species share significant synteny, comprising macro-to microsynteny ( Supplementary Fig. 1), whereas mesosynteny, which is characteristic of certain fungal groups 18 , was not observed. The transposable element (TE) content of Armillaria genomes shows a modest expansion relative to other Agaricales and an even distribution along the scaffolds, suggesting that their genome expansion is not driven by transposon proliferation, as observed in other plant pathogens 17 (Supplementary Figs.…”

“…Plant pathogenic fungi possess diverse gene repertoires for invading host plants and modulating their immune systems [18][19][20] . We catalogued 20 families of putative pathogenesis-related genes to assess whether Armillaria shares expansions of these families with other plant pathogens (Supplementary Table 5).…”

Lignocellulolytic Capability of Endophytic Phyllosticta sp.

“…According to the result, cellulase activity on LFM or LSM were not significant different from day 3 to 10 the activity range between 20-27 U/ml, especially, xylanase activity during cultivation time could be detected at approximately 7-10 U/ml. Due to the low number of cellulolytic and hemi cellulolytic CAZymes (GH6, GH7, GH10, GH11, GH45, GH61, CE1, CE3 and CBM1) present in the Capnodiales order of Dothideomycetes compared to the Hysteriales and Pleosporales order, it has been suggested that the Capnodiales (sooty molds) do not extensively degrade cellulose or that they employ another strategy for degradation [4]. Phyllosticta/Guignardia sp.…”

“…It is a ubiquitous class of fungi whose members span a wide spectrum of lifestyles and host interactions [1][2][3]. Members of the Dothideomycetes can cause disease in every major crop [4]. Approximately 1,300 genera and 19,000 species have been identified either as endophytes, plant pathogens, or as saprophytes degrading plant biomass, thus threatening agriculture and food security throughout the world [5][6][7][8].…”

Population diversity and genomics of the fungal pathogen of canola Leptosphaeria maculans

“…These effectors do not share sequence homology with other effectors and also do not share any conserved motifs (de Guillen et al, 2015). Ohm et al (2012) (Zhang et al, 2013) and Pyrenophora tritici-repentis (Sarma et al, 2005) that all share β-sandwich structures. It is therefore largely unusual to notice sequence similarity amongst genes that are involved in the infection process.…”