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

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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