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

Abstract

The oomycete pathogen Phytophthora cactorum causes crown rot, a major disease of cultivated strawberry. We report the draft genome of P. cactorum isolate 10300, isolated from symptomatic Fragaria x ananassa tissue. Our analysis revealed that there are a large number of genes encoding putative secreted effectors in the genome, including nearly 200 RxLR domain containing effectors, 77 Crinklers (CRN) grouped into 38 families, and numerous apoplastic effectors, such as phytotoxins (PcF proteins) and necrosis inducing proteins. As in other Phytophthora species, the genomic environment of many RxLR and CRN genes differed from core eukaryotic genes, a hallmark of the two-speed genome. We found genes homologous to known Phytophthora infestans avirulence genes including Avr1, Avr3b, Avr4, Avrblb1 and AvrSmira2 indicating effector sequence conservation between Phytophthora species of clade 1a and clade 1c. The reported P. cactorum genome sequence and associated annotations represent a comprehensive resource for avirulence gene discovery in other Phytophthora species from clade 1 and, will facilitate effector informed breeding strategies in other crops.

Genomic Investigation of the Strawberry Pathogen Phytophthora fragariae Indicates Pathogenicity Is Associated With Transcriptional Variation in Three Key Races

“…This was slightly larger than the closely related, well studied species from Clade 7, P. sojae, at 83 Mb ( Table 3; Tyler et al, 2006). The BC-16 assembly contained 266 of 303 eukaryotic Benchmarking Universal Single-Copy Orthologs (BUSCO) genes (Table 4), compared to 270 in P. sojae (Armitage et al, 2018) and so likely represented a similar completeness of the genome as the P. sojae assembly. The P. fragariae genome was shown to be highly repeat rich, with 38% of the assembly identified as repetitive or low complexity, a larger value than the 29% shown for P. sojae (Armitage et al, 2018).…”

“…Gene and effector prediction was performed similarly to a previously described method (Armitage et al, 2018). Firstly, raw RNA-Seq reads of BC-16 from both mycelial samples and the inoculation time course were cleaned with fastq-mcf (Aronesty, 2013).…”

“…RNA-Seq data from P. rubi were aligned to P. rubi assemblies with the same method. Further steps were performed as previously described (Armitage et al, 2018). Additionally, putative apoplastic effectors were identified through the use of ApoplastP (Sperschneider et al, 2018).…”

“…The BC-16 assembly contained 266 of 303 eukaryotic Benchmarking Universal Single-Copy Orthologs (BUSCO) genes (Table 4), compared to 270 in P. sojae (Armitage et al, 2018) and so likely represented a similar completeness of the genome as the P. sojae assembly. The P. fragariae genome was shown to be highly repeat rich, with 38% of the assembly identified as repetitive or low complexity, a larger value than the 29% shown for P. sojae (Armitage et al, 2018). A total of 37,049 genes encoding 37,346 proteins were predicted in the BC-16 assembly, consisting of 20,222 genes predicted by BRAKER1 (Hoff et al, 2016) and 17,131 additional genes added from CodingQuarry (Testa et al, 2015).…”

Genome reconstruction of the non-culturable spinach downy mildew Peronospora effusa by metagenome filtering

“…The effector prediction for the comparative analysis was done in a similar fashion, except the published Phytophthora HMM model for RxLR prediction and a published model for CRN prediction was used [51]. The prediction of effectors using the same model in each species enabled the comparison.…”