annotating the cytochrome p450 cyp720b gene family in white spruce
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2012-11-23
Annotating the cytochrome P450 CYP720B gene family in white spruceShaun Jackman
http://en.wikipedia.org/wiki/Picea_glauca
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White sprucePicea glauca
http://en.wikipedia.org/wiki/Picea_glauca 2
Cytochrome P450
✤ Enzymes involved in biosynthesis and metabolism
✤ Catalyze the oxidation of organic compounds
✤ Contain a heme cofactor
✤ Primarily membrane bound
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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
4http://en.wikipedia.org/wiki/Resin
CYP720B in sitka sprucePicea 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
White spruce sequencing dataPicea glauca
✤ RNA-seq of eight tissues:bark, embryo, flush bud, mature needle, megagametophyte, seedling, xylemand young bud
✤ Whole genome sequencing24 lanes of Illumina HiSeq for 64-fold coverage
6Hamberger, Ohnishi et al. (2011) Plant Phys. 157: 1677-1695
Identify white spruce transcripts
✤ Assemble the white spruce RNA-seq datausingTrinity (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
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White spruce CYP720B transcriptsSitka spruceWhite spruce
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
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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)
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CYP720B4
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✤ Expressed in both sitka spruce and white spruce
Sitka spruceWhite spruce
CYP720B7
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✤ Expressed only in sitka spruce
Sitka spruceWhite spruce
CYP720B15/16/17 related
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✤ White spruce transcripts align, but no sitka spruce transcripts
Sitka spruceWhite spruce
Cytochrome P450 CYP720B Genes
Sitka spruceEST
White spruce RNA-seq
White spruce genome assembly
CYP720B2 yes yesCYP720B4 yes yesCYP720B5 yes yesCYP720B7 no yesCYP720B8 no partialCYP720B9 no yesCYP720B10 no partialCYP720B12 yes yesCYP720B15 yes partialCYP720B16 no partialCYP720B17 no partial 14
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