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.

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Summary of presentation: 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......

Summary of presentation: 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. The 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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  • 1. 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
  • 2. 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
  • 3. 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
  • 4. Several types of photosynthesis Learn more about the Ion Personal Genome Machine (PGM) Sequencer
  • 5. 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
    Learn more about the Ion Personal Genome Machine (PGM) Sequencer
  • 6. 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
  • 7. PGM increasing throughput and read length 316 318 100 bp 200 bp Learn more about the Ion Personal Genome Machine (PGM) Sequencer
  • 8. 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
  • 9. 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
    Learn more about the Ion Personal Genome Machine (PGM) Sequencer
  • 10. More genes are upregulated under drought conditions compared to watered
    • 1,183 genes significantly differentially expressed
    Learn more about the Ion Personal Genome Machine (PGM) Sequencer
  • 11. Cell wall down regulated under drought Learn more about the Ion Personal Genome Machine (PGM) Sequencer
  • 12. 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
    Learn more about the Ion Personal Genome Machine (PGM) Sequencer
  • 13. 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
    Learn more about the Ion Personal Genome Machine (PGM) Sequencer
  • 14. Acknowledgements
    • Monsanto’s Genome Analysis Center
      • Genome Assembly and Annotation Team
      • Expression Team
    • LIFE Technologies
    Learn more about the Ion Personal Genome Machine (PGM) Sequencer