Info • Phytophthora cinnamomi var cinnamomi v1.0


The Phytophthora cinnamomi var. cinnamomi genome was sequenced using the Illumina platform , 454 platform and Sanger sequencing. Each fastq file was QC filtered for artifact/process contamination and subsequently assembled with AllPathsLG release version R41043 (Gnerre et al., 2010).

Summary statistics for the Phytophthora cinnamomi var cinnamomi v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp} 77.97
Sequencing read coverage depth 69.6x
# of contigs 9537
# of scaffolds 1314
# of scaffolds >= 2Kbp 840
Scaffold N50 89
Scaffold L50 (Mbp) 0.26
# of gaps 8223
% of scaffold length in gaps 25.3%
Three largest Scaffolds (Mbp) 1.21, 1.09, 0.99

ESTs Data set # sequences total # mapped to genome % mapped to genome
EstClusters EstClusters2 61542 50305 81.7%
Other RNAseq_assemblies 40282 34236 85.0%

Gene Models FilteredModels1
length (bp) of: average median
gene 1303 907
transcript 1123 788
exon 536 288
intron 166 79
protein length (aa) 348 233
exons per gene 2.10 1
# of gene models 26131


Wayne Reeve Ph.D., Centre for Phytophthora Science and Management, Murdoch University, School of Biological Science, Perth, Australia


The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.