Table 1.
Characteristics of the three available P. viticola genomes.
| PvitFEM01 | INRA-PV221a | JL-7–2b | |
|---|---|---|---|
| Natural Vitis host | V. vinifera | V. vinifera | V. riparia |
| Geographical origin | Italy | France | China |
| Genome assembly | |||
| Sequencing platform | Illumina | Illumina | Illumina + PacBio |
| Number of scaffolds | 57,890 | 1,883 | 2,165 |
| N50c (kb) | 4.645 | 180.6 | 172.3 |
| Assembly size (Mb) | 83.54 | 74.74 | 101.3 |
| Gene annotation | |||
| Protein coding genes (predicted) | 38,298 | nd | 17,014 |
| Validated transcripts (RNA-Seq) | 18,335 | nd | 11,670 |
| Orthologous groups in Oomycetesd | 6,552 | nd | nd |
| Genome completeness | |||
| Oomycete core genes presente | 81% | na | na |
| CEGMA/BUSCOf | na/87.2% | 95%/na | 97%/90% |
aData retrieved from Dussert et al.21. nd: not determined in the study. na: not applicable.
bData retrieved from Yin et al.22. nd: not determined in the study. na: not applicable.
cN50 is defined as the scaffold size such that 50% of the assembled nucleotides resides on contigs at least this length.
dNumber of orthologous groups found in oomycetes with sequenced genomes and containing at least one protein from P. viticola.
eIn total, 1,299 genes shared by all oomycetes were found, of which 1,054 were present in P. viticola.
fIndicated CEGMA and BUSCO numbers include the counting of partial matches.