Insights into the Host Specificity of a New Oomycete Root Pathogen, P1: Whole Genome Sequencing and Comparative Analysis Reveals Contracted Regulation of Metabolism, Protein Families, and Distinct Pathogenicity Repertoire.

P1 Stanghellini, Mohammadi, Förster, and Adaskaveg is an oomycete root pathogen that has recently been characterized. It only attacks plant species belonging to family, causing root necrosis, stunting, and yield loss. Since P1 is limited in its host range, this prompted us to sequence its whole genome and compare it to those of broad host range spp. such as and var. . A genomic DNA library was constructed with a total of 374 million reads. The sequencing data were assembled using SOAPdenovo2, yielding a total genome size of 50.3 Mb contained in 5434 scaffolds, N50 of 30.2 Kb, 61.2% G+C content, and 13,232 putative protein-coding genes. P1 had 175 species-specific gene families, which is slightly below the normal average. Like , P1 genome did not encode any classical RxLR effectors or cutinases, suggesting a significant difference in virulence mechanisms compared to other oomycetes. P1 had a much smaller proportions of the YxSL sequence motif in both secreted and non-secreted proteins, relative to other species. Similarly, P1 had the fewest (CRN) effectors of all the species. There were 633 proteins predicted to be secreted in the P1 genome, which is, again, slightly below average among genomes. P1 had only one cadherin gene with calcium ion-binding LDRE and DxND motifs, compared to having four copies. P1 had a reduced number of proteins falling under carbohydrate binding module and hydrolytic enzymes. P1 had a reduced complement of cellulase and pectinase genes in contrast to and was deficient in xylan degrading enzymes. The contraction in ABC transporter families in P1 is suggested to be the result of a lack of diversity in nutrient uptake and therefore host range.