Rapid interrogation of a small plant genome Sedum album using the Ion Torrent (PGM)

Sedum album (White stonecrop) is a small temperate succulent plant with a small genome similar to that of Arabidopsis (142 Mb), and the ability to switch from C₃ photosynthesis to Crassulacean acid metabolism (CAM) to fix carbon dioxide (CO₂). S. album is a facultative CAM plant in that under normal conditions of water and temperature CO₂ is fixed during the daytime (light) through C₃ photosynthesis. In contrast, under conditions of limiting water and high temperatures S. album switches to CAM photosynthesis and restricts CO₂ fixation to the nighttime (dark) to reduce water loss. S. album is an ideal system to understand the mechanisms controlling stress induced C₃-CAM switching, but there are currently no genomic resources available in this species. The advent of bench top sequencers such as the Ion Torrent Personal Genome Machine (PGM) make it possible to identify significant biological/genomics questions and directly test them in a mater of weeks. In order to understand the mechanism of C₃-CAM switching, the S. album genome and transcriptome was sequenced on the Ion PGM. The rapid runtime of the Ion PGM facilitates DNA and library optimization within a mater of days. For instance, in several runs it was possible to establish the level of chloroplast contamination in the DNA sample and confirm the genome size estimate, which enabled determination to move the project forward. The results of S. album genome and transcriptome de novo assembly from Ion PGM data will be discussed.