Rapid interrogation of a small plant genome Sedum album using the Ion Torrent™ PGM™ System.

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 Company PAGXX Life Technologies Workshop presentation January 16 th , 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 Learn more about the Ion Personal Genome Machine (PGM) Sequencer

Sedum album Small 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)
Learn more about the Ion Personal Genome Machine (PGM) Sequencer

Several types of photosynthesis Learn more about the Ion Personal Genome Machine (PGM) Sequencer

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

Genome and transcriptome analysis on the PGM in under 20 days* Day 1 Buy plant Day 2-3 Extract DNA and make ION library Day 4-8 20 ION runs Day 9-10 Assemble genome Day 11-13 Extract RNA, sequencing libraries Day 15-17 Extract RNA, sequencing libraries *in this case the days were non-contiguous Learn more about the Ion Personal Genome Machine (PGM) Sequencer

PGM increasing throughput and read length 316 318 100 bp 200 bp Learn more about the Ion Personal Genome Machine (PGM) Sequencer

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
Learn more about the Ion Personal Genome Machine (PGM) Sequencer 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

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

More genes are upregulated under drought conditions compared to watered
1,183 genes significantly differentially expressed

Cell wall down regulated under drought Learn more about the Ion Personal Genome Machine (PGM) Sequencer

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

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

Acknowledgements
Monsanto’s Genome Analysis Center
Genome Assembly and Annotation Team
Expression Team
LIFE Technologies

Rapid interrogation of a small plant genome Sedum album using the Ion Torrent™ PGM™ System.

by Life Technologies Corp

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Rapid interrogation of a small plant genome Sedum album using the Ion Torrent™ PGM™ System. Presentation Transcript