Location: Crop Improvement and Protection ResearchTitle: Genome sequence and architecture of the tobacco downy mildew pathogen, Peronospora tabacina) Author
Submitted to: Molecular Plant-Microbe Interactions
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/12/2015
Publication Date: 7/21/2015
Citation: Derevnina, L., Chin-Wo-Reyes, S., Martin, F.N., Wood, K., Froenicke, L., Spring, O., Michelmore, R. 2015. Genome sequence and architecture of the tobacco downy mildew pathogen, Peronospora tabacina. Molecular Plant-Microbe Interactions. doi: 10.1094/MPMI-05-15-0112-R. Interpretive Summary: This manuscript describes the characterization of the nuclear genome of the obligate pathogen, Peronospora tabacina, which causes blue mold or downy mildew of tobacco (Nicotiana tabacum) and is an economically important disease occurring frequently in tobacco growing regions worldwide. The nuclear genomes of two isolates were sequenced using next generation sequencing technologies and characterized for genes associated with pathogenicity. Comparisons were made with the genomes of related pathogens in the genus Phytophthora and Pythium. The mitochondrial genomes of these isolates were also characterized and evaluated for their use as markers for population studies.
Technical Abstract: Peronospora tabacina is an obligate biotrophic oomycete that causes blue mold or downy mildew of tobacco (Nicotiana tabacum), an economically important disease occurring frequently in tobacco growing regions worldwide. We have sequenced and characterized the genomes of two P. tabacina isolates 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 isolates 968-J2 and 968-S26 respectively, with an estimated genome size of 68 Mb. The mitochondrial genome has a similar size (~43 kb) and structure to those of other oomycetes, plus several minor unique features. Repetitive elements, primarily retrotransposons, make up ~22% of the nuclear genome. Approximately 18 K protein coding gene models were predicted. 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, with ~57% located in variable gene-sparse regions of the genome. Aligning the P. tabacina genome to Hyaloperonospora arabidopsidis and Phytophthora spp. revealed a high level of synteny. Blocks of synteny show gene inversions and instances of 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.