Genome sequence of Plasmopara viticola and insight into the pathogenic mechanism

Ling Yin,Ian Dry,Junjie Qu,Yali Zhang,Xinlong Li,Yunhe An,Jiang Lu,Huijuan Wu

doi:10.1038/srep46553

Abstract

Plasmopara viticola causes downy mildew disease of grapevine which is one of the most devastating diseases of viticulture worldwide. Here we report a 101.3 Mb whole genome sequence of P. viticola isolate ‘JL-7-2’ obtained by a combination of Illumina and PacBio sequencing technologies. The P. viticola genome contains 17,014 putative protein-coding genes and has ~26% repetitive sequences. A total of 1,301 putative secreted proteins, including 100 putative RXLR effectors and 90 CRN effectors were identified in this genome. In the secretome, 261 potential pathogenicity genes and 95 carbohydrate-active enzymes were predicted. Transcriptional analysis revealed that most of the RXLR effectors, pathogenicity genes and carbohydrate-active enzymes were significantly up-regulated during infection. Comparative genomic analysis revealed that P. viticola evolved independently from the Arabidopsis downy mildew pathogen Hyaloperonospora arabidopsidis. The availability of the P. viticola genome provides a valuable resource not only for comparative genomic analysis and evolutionary studies among oomycetes, but also enhance our knowledge on the mechanism of interactions between this biotrophic pathogen and its host.

Highlights

Plasmopara viticola causes downy mildew disease of grapevine which is one of the most devastating diseases of viticulture worldwide
The P. viticola isolate ‘JL-7-2’ was selected for genome sequencing because it is the most virulent strain, based on pathogenicity analysis, of the grapevine downy mildew isolates collected throughout the Chinese continent[8]
To further assess the quality of this genome assembly, the N length versus the N number from N10 to N100 was plotted and this indicated that 90% of the assembled genome was covered by 714 scaffolds, whilst the remaining 10% of the genome assembly is highly fragmented in 1,456 scaffolds (Supplementary Fig. S1)

Summary

Introduction

Plasmopara viticola causes downy mildew disease of grapevine which is one of the most devastating diseases of viticulture worldwide. Comparative genomic analysis revealed that P. viticola evolved independently from the Arabidopsis downy mildew pathogen Hyaloperonospora arabidopsidis. Plasmopara viticola is a strictly obligate biotrophic organism since its survival depends on living host cells and cannot be propagated on artificial media[3] This pathogen is native to North America and was accidentally introduced into Europe via infected cuttings at the end of the 19th century[4]. Next-generation sequencing technology and bioinformatics analysis packages have greatly facilitated studies on the genomes and transcriptomes of plant pathogens, including oomycetes. Genome sequences have been published for several oomycete species including the biotrophic downy mildews Hyaloperonospora arabidopsidis[18], Plasmopara halstedii[19] and Pseudoperonospora cubensis[20], the white rusts www.nature.com/scientificreports/. Estimated genome size Number of scaffolds (>500 bp) Scaffold N50 size (kb) Longest scaffold (kb) GC content of whole genome (%) GC content in exons (%) Number of gene models Average gene length (bp) % Repeats Gene density (no. of genes per Mb) Mean number of exons per gene Mean exon length (bp) Mean intron length (bp)

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Results

Conclusion