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Leighton Pritchard Phytothreats: WP4

Leighton Pritchard Phytothreats: WP4

Predicting risk by analysis of Phytophthora genome evolution

Forest Research

April 21, 2016
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  1. 2016-04-21 THAPBI
    PHYTO-THREATS
    PUBLICLY-AVAILABLE
    PHYTOPHTHORA GENOME DATA

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  2. SOURCES

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  3. Taxonomy ID: 4783
    66 Assemblies, 20 species
    2 new assemblies since last meeting
    118 BioProjects (each with >= 1 assembly)
    NCBI/RefSeq

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  4. 10 Genome Portals (various versions)
    4 projects: P. capsici, P. cinnamomi, P. ramorum, P.
    sojae (and an endornavirus…)
    Data also at NCBI
    JGI

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  5. Short read archive
    68 assembly datasets (some duplication/versioning)
    ENA

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  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

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  7. STATS

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  9. Assemblies variable
    82 contigs - 250k contigs (median 4500)
    36Mbp - 230Mbp total length (median 48Mbp)

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  12. ANIM

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