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Succulent Plant Sequenced with Ion Torrent PGM, Researcher Reports at PAG

By Andrea Anderson

SAN DIEGO (GenomeWeb) – At a Life Technologies industry workshop during the Plant and Animal Genome meeting here yesterday, Monsanto genome analysis center researcher Todd Michael described how he and his colleagues sequenced the genome of white stonecrop, Sedum album, using the Ion Torrent Personal Genome Machine.

During drought conditions, the succulent plant is known for switching from standard C3 photosynthesis, which involves fixing carbon dioxide during the light of day, to a form of photosynthesis known as Crassulacean acid metabolism, which happens at night, Michael explained.

Because plants typically lose less water when fixing CO2 using this photosynthesis-in-the-dark method, researchers reasoned that exploring the genetics behind white stonecrop's ability to flip over to CAM when water is in short supply might help in untangling the roots of this stress response strategy.

To look at the genetic and genomic features behind this adaptation, the group sequenced the 121 million base genome of S. album to roughly 45 times average coverage by doing 20 Ion Torrent PGM sequencing runs over just a few days.

After correcting for errors in the sequence and assembling the genome, the team called genes and annotated the genome via comparisons with the model plant Arabidopsis thaliana.

In addition to this genome sequencing, the researchers did RNA-sequencing on white stonecrop plants — grown under either normal or under drought conditions for 10 days or more — to look for gene expression alterations corresponding to the changeover from C3 to CAM photosynthesis during drought.

A comparison of transcripts in pooled samples from drought-adapted and watered S. album plants collected over two diurnal cycles revealed nearly 1,200 genes with distinct expression patterns in the drought-exposed and watered plants, Michael noted.

Initial analyses of these differentially expressed genes indicates that the expression of many genes gets bumped up under drought conditions, he added, including at least one gene linked to vegetative growth and flowering inhibition in Arabidopsis.

On the other hand, drought appeared to suppress the expression of cell wall-related genes, Michael said, which were more highly expressed in plants grown with enough water to maintain C3 photosynthesis.

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