Leighton Pritchard Phytothreats: WP4

Predicting risk by analysis of Phytophthora genome evolution

Transcript

1. 2016-04-21 THAPBI PHYTO-THREATS PUBLICLY-AVAILABLE PHYTOPHTHORA GENOME DATA
2. SOURCES
3. Taxonomy ID: 4783 66 Assemblies, 20 species 2 new assemblies since last meeting 118 BioProjects (each with >= 1 assembly) NCBI/RefSeq
4. 10 Genome Portals (various versions) 4 projects: P. capsici, P. cinnamomi, P. ramorum, P. sojae (and an endornavirus…) Data also at NCBI JGI
5. Short read archive 68 assembly datasets (some duplication/versioning) ENA
6. (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
7. STATS
9. Assemblies variable 82 contigs - 250k contigs (median 4500) 36Mbp - 230Mbp total length (median 48Mbp)
12. ANIM