The genome sequence of Plasmopara viticola has been obtained from isolate INRA-PV221. This isolate was collected in 2009 from a grapevine leaf lesion in a vineyard in the Bordeaux region (Blanquefort, France).

Dussert et al. (2016) Draft genome sequence of Plasmopara viticola, the grapevine downy mildew pathogen. Genome Announcements 4(5):e00987-16. doi: 10.1128/genomeA.00987-16

Dussert et al. High quality assembly of the grapevine downy mildew (Plasmopara viticola) genome reveals lineage-specific and fast-evolving genes potentially involved in host adaptation. (bioRxiv: )

 

First assembly version using short-reads (Dussert et al. 2016)

The first draft genome of P. viticola was published by INRA in 2016. A paired-end and two mate-pair libraries (3 and 8-kb inserts) were sequenced. The final assembly included 1,886 scaffolds (maximum size: 763.2 kb), for a total assembly size of 74.8 Mb.

 

New reference genome using long reads at deep coverage (Dussert et al bioRxiv)

We sequenced the INRA-PV221 isolate using PacBio long reads on a RS II sequencer with the P6-C4 chemistry at the GeT-PlaGe facility (Toulouse, France). This sequencing produced 2.6 million reads (mean size: 8,072 bp, total data: 21.2 Gb), corresponding to a mean genome coverage of 185X.

This long-read data allowed us to obtain a new assembly of 92.94 Mb with high continuity (358 scaffolds, N50 of 706.5 kb, max. scaffold size of 2.85 Mb) due a better resolution of repeat regions.

The assembly also showed a high level of gene completeness (95.7% using BUSCO with the Alveolata-Stramenopiles dataset), and notably recovered 1,592 genes coding for secreted proteins and potentially involved in plant-pathogen interactions. Compared to the previous short-read draft, it represented a 70% increase of detected secreted proteins.

 

Genbank accession: TBA

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