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Annotating the cytochrome P450 CYP720B gene family in white spruce

Shaun Jackman
November 23, 2012

Annotating the cytochrome P450 CYP720B gene family in white spruce

Shaun Jackman

November 23, 2012
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  1. 2012-11-23
    Annotating the cytochrome P450
    CYP720B gene family in white spruce
    Shaun Jackman
    http://en.wikipedia.org/wiki/Picea_glauca
    1

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  2. White spruce
    Picea glauca
    http://en.wikipedia.org/wiki/Picea_glauca
    2

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  3. Cytochrome P450
    ✤ Enzymes involved in
    biosynthesis and
    metabolism
    ✤ Catalyze the oxidation of
    organic compounds
    ✤ Contain a heme cofactor
    ✤ Primarily membrane
    bound
    3

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  4. CYP720B gene family
    ✤ Conifer-specific gene family
    ✤ Involved in the biosynthesis of
    diterpene resin acids, important in
    conifer defence against insects and
    fungus
    http://en.wikipedia.org/wiki/Mountain_pine_beetle
    4
    http://en.wikipedia.org/wiki/Resin

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  5. CYP720B in sitka spruce
    Picea sitchensis
    ✤ Twelve CYP720B genes
    identified in sitka spruce
    ✤ Full-length transcript
    sequences available
    ✤ Use these sequences to
    identify orthologs in white
    spruce (Picea glauca)
    http://en.wikipedia.org/wiki/Picea_sitchensis
    Katrin Geisler 5

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  6. White spruce sequencing data
    Picea glauca
    ✤ RNA-seq of eight tissues:
    bark, embryo, flush bud,
    mature needle,
    megagametophyte,
    seedling, xylem
    and young bud
    ✤ Whole genome sequencing
    24 lanes of Illumina HiSeq
    for 64-fold coverage
    6
    Hamberger, Ohnishi et al. (2011) Plant Phys. 157: 1677-1695

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  7. Identify white spruce transcripts
    ✤ Assemble the white spruce RNA-seq data
    usingTrinity (Grabherr et al. 2011)
    (assembled by Mack Yuen)
    ✤ Identify the white spruce CYP720B transcripts by aligning
    the sitka spruce transcripts to the white spruce RNA-seq
    contigs using BWA-SW (Li and Durbin 2010)
    ✤ Cluster the sitka spruce and white spruce transcripts
    using CLC Genomics Workbench
    7

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  8. 8
    White spruce CYP720B transcripts
    Sitka spruce
    White spruce

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  9. Assemble the white spruce genome
    ✤ Assemble the white spruce genome sequence using
    ABySS (Simpson et al. 2009)
    ✤ Assembled 8.4 billion reads using 996 processors on 83
    machines with an aggregate 4 TB of RAM
    ✤ Assembled 18 Gbp in 5 million scaffolds larger than 500
    bp with a scaffold N50 of 6 kbp
    9

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  10. Identify white spruce genes
    ✤ Identify CYP720B genomic contigs by aligning the sitka
    spruce and white spruce transcripts to the white spruce
    genome assembly using BWA-SW
    ✤ Align the sitka spruce and white spruce transcripts to the
    CYP720B genome contigs using gmap (Wu and Watanabe 2005)
    10

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  11. CYP720B4
    11
    ✤ Expressed in both sitka spruce and white spruce
    Sitka spruce
    White spruce

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  12. CYP720B7
    12
    ✤ Expressed only in sitka spruce
    Sitka spruce
    White spruce

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  13. CYP720B15/16/17 related
    13
    ✤ White spruce transcripts align, but no sitka spruce transcripts
    Sitka spruce
    White spruce

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  14. Cytochrome P450 CYP720B Genes
    Sitka spruce
    EST
    White spruce
    RNA-seq
    White spruce
    genome assembly
    CYP720B2 yes yes
    CYP720B4 yes yes
    CYP720B5 yes yes
    CYP720B7 no yes
    CYP720B8 no partial
    CYP720B9 no yes
    CYP720B10 no partial
    CYP720B12 yes yes
    CYP720B15 yes partial
    CYP720B16 no partial
    CYP720B17 no partial 14

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