Genome Sequence and Architecture of the Tobacco Downy Mildew Pathogen, Peronospora tabacina

Peronospora tabacina is an obligate biotrophic oomycete that causes blue mold or downy mildew of tobacco (Nicotiana tabacum). It is an economically important disease occurring frequently in tobacco growing regions worldwide. We have sequenced and characterized the genomes of two P. tabacina isolates (968-J2 and 968-S26) and mined them for pathogenicity related proteins and effector encoding genes. De novo assembly of the genomes using Illumina reads resulted in 4,016 (63.1 Mb, N₅₀ = 79 kb) and 3,245 (55.3 Mb, N₅₀ = 61 kb) scaffolds for 968-J2 and 968-S26 respectively, with an estimated genome size of 69 Mb. The mitochondrial genome has a similar size (~43 kb) and structure to those of other oomycetes, plus several unique features.  Repetitive elements, primarily retrotransposons, make up ~22% of the nuclear genome.  Approximately 18 k protein coding gene models were predicted ab initio. Mining the secretome revealed ~120 candidate RxLR, ~6 CRN and ~61 WY-domain containing proteins. Candidate RxLR effectors were shown to be predominantly undergoing diversifying selection (average ω > 1.2), with ~57% located in variable gene sparse regions of the genome. Aligning the P. tabacina genome to other Oomycete spp. (Hyaloperonospora arabidopsidis and Phytophthora spp.) revealed a high level of synteny. Blocks of synteny show gene inversions and instances of gene expansion in intergenic regions. Extensive rearrangements of the gene-rich genomic regions do not appear to have occurred during the evolution of these highly variable pathogens. These assemblies provide the basis for studies of virulence in this and other downy mildew pathogens.