“Core” RxLR effectors in phytopathogenic oomycetes: A promising way to breeding for durable resistance in plants?

Figures & data

Table 1. “Core” effectors in different groups of plant pathogens

Group	Organism	Identified core effectors	Virulence role	Reference
Oomycete	Plasmopara halstedii	354 [30]	Suppress pattern-triggered immunity and some induce hypersensitive responses	[78]
	Hyaloperonospora arabidopsidis	18 [4]	RXLR29 was shown to suppress pathogen-induced callose deposition	[153]
Bacteria	Ralstonia solanacearum	60–75 [32]	-	[154–156]
	Xanthomonas arboricola	57 [11]	-	[157]
Fungi	Ustilaginoidea virens	193 [18]	UV_1261 suppress host plant hypersensitive responses	[158–160]
	Zymoseptoria tritici	591 [153]	-	[161]
	Ustilago maydis	467 (202)	Pep1 inhibits the activity of the apoplastic maize peroxidase POX12 Cce1 hypothesized to inhibit early plant defense responses in the apoplast Rsp3 has a conserved virulence role of protecting the fungal hyphae from maize antifungal proteins activity. Sta1 a novel core effector with virulence role through host cell-wall modification for disease progression	[27,162–167]
	Colletotrichum orbiculare		necrosis-inducing secreted protein 1 (NIS1), targets conserved immune kinases hence interfering with PTI signaling	[115]

Figure 1. A schematic representation of in silico prediction and validation of putative CREs in oomycetes. The secretome prediction pipeline begins with the removal of proteins without a signal peptide (SP) while retaining those with a transmembrane domain (TM), by use of signalP tool and THMM, respectively. Effector proteins with a TM are discarded after signal peptide cleavage as these proteins are not likely to be retained in the plasma membrane. This is followed by removing effector proteins without the signature RxLR motif using HMMscan tool. Orthology analysis is performed to determine RxLR effectors that are conserved within strains or within species of a pathogen (CREs) using orthology analyses tools like COG, eggNOG or orthofinder. The final output is composed of putative secreted CREs with a SP, RxLR motif and without a TM. This output is further authenticated through in planta expression to ascertain their role in virulence for instance, their role in enhancing/suppressing host immunity, localization in planta using confocal microscopy as well as interacting proteins within host partners

Figure 2. Illustration of phytopathogenic oomycetes with their respective genome sizes (Mb) on the outermost ring. Most of the genomes are Phytophthora spp (p). In terms of genome size, P. infestans and Pseudoperonospora humulis recorded the highest (240Mb) and lowest (40.5Mb) genome sizes, respectively. Counting from the outside, the second ring is the total number of predicted RxLR effectors ranging from 172 in P. parasitica to 563 in P. infestans. The third ring is the total number of putative CREs while the fourth ring is the total number of authentic CREs with Plasmopara halstedii recording a total of 30 CREs. In terms of association between genome size and the number of predicted RxLR effectors in oomycetes, insignificant positive correlation (P = 0,07;R² = 0.51, at 95% confidence level) was recorded (b)

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Data Availability Statement

The authors confirm that the data supporting the findings of this study are available within the article and freely available, under a license allowing re-use by any third party for any lawful purpose. Data shall be findable and fully accessible.