Download - Rapid interrogation of a small plant genome Sedum album using the Ion Torrent™ PGM™ System
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Rapid interrogation of a small plant genome Sedum album using the Ion Torrent™ PGM™ System. Dr. Todd P. Michael, Head, The Genome Analysis Center, Monsanto CompanyPAGXX Life Technologies Workshop presentationJanuary 16th, 2012
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Rapid interrogation of a small plant genome Sedum album using the
Ion Torrent (PGM)
Todd P. Michael, Ph.D.Head, The Genome Analysis Center
Monsanto Company
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Sedum albumSmall genome and facultative CAM plant
• Sedum album, white stonecrop– 142 Mb by flow cytometry– 2n = 34– Hart, 1991
• C3-CAM photosynthesis switching– Facultative Crassulacean acid
metabolism (CAM) plant– Under well watered conditions
fixes carbon through C3 photosynthesis (light)
– Under drought, switches to CAM and fixes carbon at night (dark)
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Several types of photosynthesis
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Sedum album switches from C3 to CAM under
drought
• Sedum album grown under 10 days drought switches to CAM metabolism and fixes carbon at night
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Genome and transcriptome analysis on the PGM in under 20
days*
6
Day 1Buy plant
Day 2-3Extract DNA and make ION library
Day 4-820 ION runs
Day 9-10Assemble genome
Day 11-13Extract RNA, sequencing libraries
Day 15-17Extract RNA, sequencing libraries
*in this case the days were non-contiguous
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PGM increasing throughput and read length
7
316
318
100 bp
200 bp
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Sedum album genome assembly, gene calling and
annotation• Error correct raw reads (SAET)
• Remove any remaining adaptors
• Assembly using CLC
• Assembly still fragmented
• Annotate using SNAP and annotate against Arabidopsis
8
avg stDev min max range median L50 (bp) N50 # #Seq #Base
1,205 1,111 501 32,123 31,622 822 1,400 23,085 101,283 121,999,640
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Sedum drought experiment to find C3-CAM switch genes
• Sedum album seedlings were drought treated for 10 days
• Triplicate samples were taken over two diurnal cycles
• Drought and watered samples were pooled for transcriptome analysis
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More genes are upregulated under drought conditions compared to
watered
• 1,183 genes significantly differentially expressed
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Cell wall down regulated under drought
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SaFRIGIDA expressed under drought
• SaFRIGIDA was not expressed in the well watered Sedum (at least not detected)
• SaFRI is highly expressed under drought• High FRI levels in Arabidopsis result in high
levels of FLC and block flowering
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Conclusions
• PGM provides a low cost and robust platform for genome and transcriptome discovery
• Sedum genome is small; Arabidopsis size
• Drought reduces cell wall genes
• FRIGIDA is upregulated suggesting flowering supression
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Acknowledgements
• Monsanto’s Genome Analysis Center– Genome Assembly and Annotation Team– Expression Team
• LIFE Technologies
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