Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum

Abstract

22The oomycete pathogen Phytophthora cactorum causes crown rot, a major disease of 23 cultivated strawberry. We report the draft genome of P. cactorum isolate 10300, cultured 24 from symptomatic Fragaria x ananassa tissue. Our analysis revealed that there are a large 25 number of genes encoding putative secreted effectors in the genome, including nearly 200 26 RxLR domain containing effectors, 77 Crinklers (CRN) grouped into 38 families and 27 numerous apoplastic effectors, such as phytotoxins (PcF proteins) and necrosis inducing 28 proteins. As in other Phytophthora species, the genomic environment of many RxLR and CRN 29 genes differed from core eukaryotic genes, a hallmark of the two-speed genome. We found 30 genes homologous to known Phytophthora infestans avirulence genes including Avr1, Avr3b, 31 Avr4, Avrblb1 and AvrSmira2 indicating effector sequence conservation between Phytophthora 32 species of Clade 1A and 1C. The reported P. cactorum genome sequence and associated 33 annotations represent a comprehensive resource for avirulence gene discovery in other 34 Phytophthora species from Clade 1 and will facilitate effector informed breeding strategies in 35 other crops. 36 37 38 39 40 The oomycetes are a diverse class of eukaryotic microorganisms that include pathogens of plants, 41 animals and fungi (Simão et al. 2015). The causal agents of plant diseases are well represented in 42 this phylogenetic class, with over 60% of known oomycetes characterised as plant pathogens 43

Comparative analysis of host-associated variation in Phytophthora cactorum

“…Of the 18 P. cactorum isolates, 13 of these were isolated from strawberry crown tissue exhibiting crown rot symptoms, two from strawberry fruit exhibiting leather rot symptoms and three isolated from symptomatic apple bark. One of the crown rot isolates, 10300, has been previously published by (Armitage et al, 2018). The three isolates of P. idaei were isolated from infected raspberry material.…”

“…Gene models were also augmented with further effector candidates from open reading frames (ORFs) using the methods previously described in (Armitage et al, 2018).…”

“…Genomic resources have recently become available for P. cactorum, with genomes released for isolates from beech, Fagus sylvatica (Grenville-Briggs et al, 2017), Chinese ginseng, Panax notoginseng (Yang et al, 2018) and strawberry, F. x ananassa (Armitage et al, 2018). Phytophthora spp.…”

“…In addition to cytoplasmic effectors, Phytophthora spp. also deploy an arsenal of apoplastic effector proteins during infection, including a large number of hydrolytic enzymes, such as cutinases, glycoside hydrolases (GHs), pectinases, and proteases, which promote their infection and manipulation of the plant immune system (Armitage et al, 2018;Wang, 2018a, 2018b). They also encode members of extracellular phytotoxin families such as the conserved necrosis-inducing proteins (NLPs) and small cysteine-rich (SCR) proteins, for such as PcF (Phytophthora cactorum factor) (Orsomando et al, 2001) and INF1 (Kamoun et al, 1997).…”

“…Orthology analysis identifies gene expansion and contraction associated with phylogenetic lineage. The total set of 157,038 predicted proteins from the 20 sequenced isolates, as well as the proteome of P. cactorum isolate 10300 from (Armitage et al, 2018), were clustered into 22,572 orthogroups. Orthogroups showing a consistent pattern of expansion/contraction by phylogenetic clade were identified (Figure 4).…”