Two structurally different oomycete MAMPs induce distinctive plant immune responses.

Plants recognize a variety of external signals and induce appropriate mechanisms to increase their tolerance to biotic and abiotic stresses. Precise recognition of attacking pathogens and induction of effective resistance mechanisms are critical functions for plant survival. Some molecular patterns unique to a certain group of microbes (MAMPs, microbe-associated molecular patterns) are sensed by plant cells as non-self molecules via pattern recognition receptors. While a variety of MAMPs of bacterial and fungal origin have been identified, reports on MAMPs of oomycete pathogens are relatively limited. This study aimed to identify unique MAMP elicitors from the oomycete pathogen Phytophthora infestans, the causal agent of potato late blight. Using reactive oxygen species (ROS) production and phytoalexin production in potato as markers for the purification of oomycete elicitors, we identified two structurally different groups of elicitors, namely ceramides and diacylglycerols. P. infestans ceramide (Pi-Cer) elicitors induced ROS production, while diacylglycerol (Pi-DAG) elicitors, containing eicosapentaenoic acid (EPA) as a substructure, induced the formation of phytoalexins in potato. Pi-Cer and Pi-DAG are also contained in the mycelia of another oomycete pathogen Pythium aphanidermatum, indicating that they are MAMPs of oomycetes. When Arabidopsis was treated with Pi-Cer and EPA, partially overlapping but different sets of genes were induced. Furthermore, simultaneous treatment with Pi-Cer and EPA did not have a cumulative effect on induced genes, but rather the expression of some genes induced by EPA was attenuated by the co-treatment with Pi-Cer. These results indicate that plants may combine the signals from simultaneously recognized MAMP elicitors to specifically adapt the defense response to a particular pathogen.

Pathogen-derived 9-methyl sphingoid base is perceived by a lectin receptor kinase in Arabidopsis

In plants, many invading microbial pathogens are recognized by cell-surface pattern recognition receptors (PRRs), inducing defense responses; yet how PRRs perceive pathogen sphingolipids remains unclear. Here, we show that the ceramide Pi-Cer D from a plant pathogenic oomycete Phytophthora infestans triggers defense responses in Arabidopsis. Pi-Cer D is cleaved by an Arabidopsis apoplastic ceramidase, NCER2, and the resulting 9-methyl-branched sphingoid base is recognized by a plasma membrane lectin receptor-like kinase, RDA2. Importantly, 9-methyl-branched sphingoid base, which is unique to microbes, induces plant immune responses by interacting with RDA2. Loss of RDA2 or NCER2 function compromised Arabidopsis resistance against an oomycete pathogen, indicating that these are crucial for defense. We provide new insights that help elucidate the recognition mechanisms of pathogen-derived lipid molecules in plants.

An improved assembly of the Albugo candida Ac2V genome reveals the expansion of the “CCG” class of effectors

Albugo candida is an obligate oomycete pathogen that infects many plants in the Brassicaceae family. We re-sequenced the genome of isolate Ac2V using PacBio long reads and constructed an assembly augmented by Illumina reads. The Ac2VPB genome assembly is 10% larger and more contiguous compared to a previous version. Our annotation of the new assembly, aided by RNASeq information, revealed a 175% expansion (40 to 110) in the CHxC effector class, which we redefined as “CCG” based on motif analysis. This class of effectors consist of arrays of phylogenetically related paralogs residing in gene sparse regions, and shows signatures of positive selection and presence/absence polymorphism. This work provides a resource that allows the dissection of the genomic components underlying A. candida adaptation and particularly the role of CCG effectors in virulence and avirulence on different hosts.

Tightly linked Rps12 and Rps13 genes provide broad-spectrum Phytophthora resistance in soybean

The Phytophtora root and stem rot is a serious disease in soybean. It is caused by the oomycete pathogen Phytophthora sojae. Growing Phytophthora resistant cultivars is the major method of controlling this disease. Resistance is race- or gene-specific; a single gene confers immunity against only a subset of the P. sojae isolates. Unfortunately, rapid evolution of new Phytophthora sojae virulent pathotypes limits the effectiveness of an Rps (“resistance to Phytophthora sojae”) gene to 8–15 years. The current study was designed to investigate the effectiveness of Rps12 against a set of P. sojae isolates using recombinant inbred lines (RILs) that contain recombination break points in the Rps12 region. Our study revealed a unique Rps gene linked to the Rps12 locus. We named this novel gene as Rps13 that confers resistance against P. sojae isolate V13, which is virulent to recombinants that contains Rps12 but lack Rps13. The genetic distance between the two Rps genes is 4 cM. Our study revealed that two tightly linked functional Rps genes with distinct race-specificity provide broad-spectrum resistance in soybean. We report here the molecular markers for incorporating the broad-spectrum Phytophthora resistance conferred by the two Rps genes in commercial soybean cultivars.

Comparative Genomic Analysis Reveals Genetic Variation and Adaptive Evolution in the Pathogenicity-Related Genes of Phytophthora capsici

Phytophthora capsici is an oomycete pathogen responsible for damping off, root rot, fruit rot, and foliar blight in popular vegetable and legume crops. The existence of distinct aggressiveness levels and physiological races among the P. capsici population is a major constraint to developing resistant varieties of host crops. In the present study, we compared the genomes of three P. capsici isolates with different aggressiveness levels to reveal their genomic differences. We obtained genome sequences using short-read and long-read technologies, which yielded an average genome size of 76 Mbp comprising 514 contigs and 15,076 predicted genes. A comparative genomic analysis uncovered the signatures of accelerated evolution, gene family expansions in the pathogenicity-related genes among the three isolates. Resequencing two additional P. capsici isolates enabled the identification of average 1,023,437 SNPs, revealing the frequent accumulation of non-synonymous substitutions in pathogenicity-related gene families. Furthermore, pathogenicity-related gene families, cytoplasmic effectors and ATP binding cassette (ABC) transporters, showed expansion signals in the more aggressive isolates, with a greater number of non-synonymous SNPs. This genomic information explains the plasticity, difference in aggressiveness levels, and genome structural variation among the P. capsici isolates, providing insight into the genomic features related to the evolution and pathogenicity of this oomycete pathogen.

Lytic Polysaccharide Monooxygenases as Chitin-Specific Virulence Factors in Crayfish Plague

The oomycete pathogen Aphanomyces astaci, also known as “crayfish plague”, is an obligate fungal-like parasite of freshwater crustaceans and is considered responsible for the ongoing decline of native European crayfish populations. A. astaci is thought to secrete a wide array of effectors and enzymes that facilitate infection, however their molecular mechanisms have been poorly characterized. Here, we report the identification of AA15 lytic polysaccharide monooxygenases (LPMOs) as a new group of secreted virulence factors in A. astaci. We show that this enzyme family has greatly expanded in A. astaci compared to all other oomycetes, and that it may facilitate infection through oxidative degradation of crystalline chitin, the most abundant polysaccharide found in the crustacean exoskeleton. These findings reveal new roles for LPMOs in animal–pathogen interactions, and could help inform future strategies for the protection of farmed and endangered species.

Pythium myriotylum is recovered most frequently from Pythium soft-rot infected ginger rhizomes in China

Pythium soft rot is a major soil-borne disease of crops such as ginger (Zingiber officinale). Our objective was to identify which Pythium species were associated with Pythium soft-rot of ginger in China, where approximately 20% of global ginger production is from. Oomycetes infecting ginger rhizomes from seven provinces were investigated using two molecular markers, the internal transcribed spacer (ITS) and cytochrome c oxidase subunit II (CoxII). In total, 81 isolates were recovered and approximately 95% of the isolates were identified as Pythium myriotylum and the other isolates were identified as either P. aphanidermatum or P. graminicola. Notably, the P. myriotylum isolates from China did not contain the SNP in the CoxII sequence found previously in the P. myriotylum isolates infecting ginger in Australia. A subset of 36 of the isolates was analyzed repeatedly by temperature-dependent growth, severity of disease on ginger plants and aggressiveness of colonization of ginger rhizome sticks. In the pathogenicity assays, 32/36 of the isolates were able to significantly infect and cause severe disease symptoms on the ginger plants. A range of temperature-dependent growth, disease severity and aggressiveness in colonization was found with a significant moderate positive correlation between growth and aggressiveness of colonization of the ginger sticks. This study identified P. myriotylum as the major oomycete pathogen in China from infected ginger rhizomes and suggests that P. myriotylum should be a key target to control soft rot of ginger disease.

A Diagnostic Guide for Phytophthora capsici infecting vegetable crops

Phytophthora capsici is an oomycete pathogen causing economically important diseases in a wide range of hosts worldwide including cucurbitaceous, solanaceous, and fabaceous crops. All plant parts, crown and roots, or only the fruit may be affected depending on the host, and symptoms can range from wilting to rot and plant death. Considered a hemibiotroph, P. capsici can be cultured in artificial media and maintained in long term storage. In this diagnostic guide, we describe methods to identify P. capsici infection based on disease symptoms and pathogen signs. We also outline methods for molecular identification, pathogen isolation, storage of single-sporangium cultures, and pathogenicity testing.