Leighton Pritchard Phytothreats: WP4

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April 21, 2016

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Leighton Pritchard Phytothreats: WP4

Predicting risk by analysis of Phytophthora genome evolution

Forest Research

April 21, 2016

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Transcript

2016-04-21 THAPBI PHYTO-THREATS PUBLICLY-AVAILABLE PHYTOPHTHORA GENOME DATA
SOURCES
Taxonomy ID: 4783 66 Assemblies, 20 species 2 new assemblies
since last meeting 118 BioProjects (each with >= 1 assembly) NCBI/RefSeq
10 Genome Portals (various versions) 4 projects: P. capsici, P.
cinnamomi, P. ramorum, P. sojae (and an endornavirus…) Data also at NCBI JGI
Short read archive 68 assembly datasets (some duplication/versioning) ENA
(release 31 current) 14 genomes (duplication of NCBI) 1xP. infestans,
1xP. kernoviae, 1xP. lateralis, 9xP. parasitica, 1xP. ramorum, 1xP. sojae Ensembl Compara All-vs-all synteny comparisons not available (also ) Ensembl Protists downloadable downloadable PhytoPath
STATS
None
Assemblies variable 82 contigs - 250k contigs (median 4500) 36Mbp
- 230Mbp total length (median 48Mbp)
None
None
ANIM
None