A high-quality grapevine downy mildew genome assembly reveals rapidly evolving and lineage-specific putative host adaptation genes

Abstract

DATA AVAILABILITYRaw reads and genome assemblies have been deposited in GenBank (BioProjects PRJNA329579 for Pl. viticola and PRJNA448661 for Pl. muralis). Genome assemblies, gene annotations and analysis files (e.g. orthology relationships, full tables for GO enrichment analyses, pairwise dN/dS values and branch-site tests) have been deposited in Dataverse (Pl.viticola assembly and annotation: doi.org/10.15454/4NYHD6, Pl. muralis assembly and annotation: doi.org/10.15454/Q1QJYK, analysis files: doi.org/10.15454/8NZ8X9). Links to the data and information about the grapevine downy mildew genome project can be found at ABSTRACT Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high continuity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant-pathogen interactions. Pl. viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeatrich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species.

Sunflower resistance to multiple downy mildew pathotypes revealed by recognition of conserved effectors of the oomycete Plasmopara halstedii

“…To assess the accuracy of our genome assembly, we compared it to genome assemblies of the closest sequenced oomycete Plasmopara viticola, the grapevine downy mildew (Dussert et al ., , ; Mestre et al ., ; Yin et al ., ). We did the same comparisons with the genome published by Sharma et al .…”

A secreted WY-domain-containing protein present in European isolates of the oomycete Plasmopara viticola induces cell death in grapevine and tobacco species

“…We then studied the expression of the WY-domain genes upon infection and in germinated spores. For studying expression upon infection, we used the Illumina RNA-Seq data described in [29], at 48 and 72 hours post-infection. Analysis of expression in germinated spores was performed using the transcriptome described in [24], obtained with Roche 454 GS-FLX Titanium.…”

Genetic structure of Italian population of the grapevine downy mildew agent, Plasmopara viticola

“…However, the presence of two distinct clusters in the population could be a consequence of several reasons, that cannot be completely elucidated in the present study and need further investigation. The availability of genome sequences, opening the way to population genomics (Dussert et al, , ), could be a powerful tool to be employed in this regard. Of particular importance will also be increasing the number of samples per region to obtain an even sample size and gathering of data on genetic variability of P .…”