In particular cases, selected populations on a partially resistant cultivar had values for latent period, uredinium area, and sporulation no different from those of a susceptible host—pathogen combination. Our results suggest the variation to overcome quantitative host resistance exists in extant populations of P. In addition, because more of the variation in latent period for populations of P. Home Phytopathology Vol. Jeffrey S. Lehman Corresponding author: J. Gregory Shaner Search for more papers by this author. Affiliations Authors and Affiliations Jeffrey S.
Lehman Gregory Shaner. Add to favorites Download Citations Track Citations. Metrics Downloaded 27 times. Triticum aestivum. Modelling interaction dynamics between two foliar pathogens in wheat: a multi-scale approach. Chapter Rapid and multiregional adaptation to host partial resistance in a plant pathogenic oomycete: Evidence from European populations of Plasmopara viticola, the causal agent of grapevine downy mildew.
Diversity, specificity and impacts on field epidemics of QTLs involved in components of quantitative resistance in the wheat leaf rust pathosystem. Research on P. However, no investigations have probed this economically important plant pathogen, or other SBFS species, at the genome level. Unlike most other functional groupings of plant pathogens such as biotrophs, hemibiotrophs, and necrotrophs, SBFS fungi neither invade living host cells nor actively absorb nutrients from them, but attach to plant surfaces and subsist primarily on tissue leachates These specialized fungi also differ from free-living saprophytes and symbionts in that they generally colonize living plants but confer no benefits to their hosts.
The genetic and biochemical nature of the adaptations that enable survival in this unique niche has not been elucidated, although high-throughput sequencing and genome analysis have yielded deep insights into a wide range of traits in many other fungal pathogens and symbionts 17 , 18 , Here, we describe the genome sequence of P.
Two main questions were addressed in this work: 1 what genomic features underpin the adaptation of SBFS pathogens to their epicuticular niche? The genome of P. An By calculating the sequencing depth with a frequency distribution of base oligomers in usable reads Supplementary Fig. S1 21 , the genome size of P.
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Only ambiguous positions constituting three gaps were detected in the modified assembly with an average GC content of Among these predicted proteins, 7, S2 , and 5, However, the weak correlation 0. Therefore, we believe that P. Additionally, only nine rDNA tandem repeat units in P. Overall, the genome of P. A genome-based maximum-likelihood ML tree was constructed using the amino acid sequences of single-copy orthologous genes extracted from 12 fungi Fig.
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In this phylogram, P. However, estimation of their divergence time reveals that they split from a common ancestor about million years Myr ago, meaning that the two fungi are actually rather distantly related.
This result strengthens findings of previous research suggesting that P. Such a long-term separate evolution appears to have been accompanied by substantial differentiation. For example, P. In addition, far fewer orphan genes lacking homology to other sequences in the dataset 17 were found in P.
This difference is noteworthy because some researchers proposed that such genes allow organisms to adapt to constantly changing ecological conditions Based on above analysis, we conclude that the genome of P. The numbers on the branches of the phylogenetic tree correspond to acquired left, black , lost right, red , and inferred ancestral oval gene families along each lineage by comparison with the putative pan-proteome. For each species, the number of gene families, orphan genes, and the total gene number are indicated on the right.
The black arrows represent the divergence time of each two lineages with Myr used to abbreviate million years. The numbers of genes without mark , gene families Fam and orphan genes Orp are indicated in separate areas for P. The Dollo parsimony principle treated the 1, gene families from Z.
As a result, we could begin to discern which kinds of genes these two fungi have lost over the course of evolution by means of COG annotation. The result indicates that P. Similarly, species-specific genes including orphans and new family genes in P. Although only Further research is needed to elucidate the functions of these three categories of genes in understanding the ecological adaptations of P. Secreted proteins are essential for fungi, especially for parasites and symbionts that participate in complex biochemical interaction with plants.
These proteins include mainly lyases and hydrolases, which attack plant cell walls or degrade other complex carbon or nitrogen sources for nourishment e. In silico prediction identified secreted proteins in P.
The Phytopathogen - Dimensions
Moreover, their proportion in the total gene number of P. Diminution of the total secretome and its highly active genes accords with the fact of minimal biochemical interaction e. The boxes on the left represent the life style of the selected organisms. The colored bars representing the secondary metabolic enzymes are identified by the key at the top. For both host-penetrating pathogens and saprophytes, secreted peptidases are essential in degrading plant tissues or other organic matter. For pathogens, these peptidases also block activation of host defenses. Proteolytic enzymes in the secretome of P.
Although the secreted zinc-metallopeptidase and subtilisin were once reported to serve as virulence factors by degrading hydroxyproline-rich glycoproteins HRGPs , an important structural component within plant cell walls 30 , 31 , 32 , the fact that none of these seven proteinase-coding genes were up-regulated in vivo and five were expressed at very low levels Fig. For the heatmaps, two columns represent different treatments, i.
Enzymes catalyzing the first five steps have been detected in the P. RPKM, reads per kilobase per million mapped reads. The numbers of small secreted proteins SSPs , which are generally considered to be candidate effectors, ranged from 12 in P. All the classical plant pathogens except Ustilago maydis possessed the largest numbers of SSPs, successively followed by symbionts and free-living saprophytes, while P. As the effectors of classical plant pathogenic fungi are commonly cysteine-rich, functionally unknown and lacking in homology to proteins of other species 29 , we further filtered the SSPs of P.
Taken together, only one SSP produced by P.
In addition, nearly all the SSP-coding genes of P. These results confirm that P.
Plant cell walls, which act as initial protective barriers against pathogen attack, are commonly composed of three classes of polysaccharides: cellulose, hemicellulose and pectin Accordingly, plant-pathogenic fungi evolved an array of plant cell wall degrading enzymes PCWDEs such as cellulase, hemicellulase and pectinase to depolymerize those components. Cutinase is also classed with the PCDWEs here because it plays a vital role in breaking down the plant cuticle, the outermost defense layer against pathogenic fungi The remaining saprophytic and symbiotic fungi were intermediate in the number of putative PCWDEs, indicating that they, despite non-aggressive lifestyles, still retain some cell wall-degrading abilities to decompose plant debris After manually eliminating the false positives, P.
Compared with other plant pathogens and even some nonpathogenic species, P. We then compared P. For P.
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More complex hydrolases are required for degrading hemicelluloses that consist of three major types of amorphous structures: xylan, galactomannan and xyloglucan. In contrast, Z. Consequently, P.