High Quality de novo Assembly of the Common Ice Plant (Mesembryanthemum crystallinum L.) Transcriptome - A Functional Genomics Resource for Crassulacean Acid Metabolism (CAM) and Halophytism

The common ice plant (Mesembryanthemum crystallinum L., Azoaceae, Caryophyllales) is an important halophytic and facultative crassulacean acid metabolism (CAM) model in which CAM can be induced by salinity or water-deficit stress. To improve our understanding of molecular genetic basis of CAM, water-use efficiency, and salinity tolerance in plants, a high-quality, annotated transcriptome assembly was generated for ice plant using RNA isolated from 12 different tissue or organ types and under well-watered, salinity-stressed, and water-deficit stress conditions over both diel and circadian time courses. To maximize the completeness of the transcriptome assembly, multiple transcriptome assemblies were generated using data sets from Sanger expressed sequence tags (27,348 EST reads, 0.017 Gb), Roche 454 pyrosequencing (4.0 M reads, 1.5 Gb), and Illumina Hiseq2000 (2.5 B reads, 254 Gb) short-read DNA sequence data sets. The EvidentialGene pipeline was used to combine these assemblies into an optimized, cleansed transcriptome assembly comprised of 24,204 transcripts with a mean transcript length of 1,513 bp of which approximately 78% of the transcripts were full-length.  The draft assembly contained 95% of ultra-conserved core eukaryotic genes (CEGs) and 552-modeled metabolic reactions as estimated by the PlantSEED resource. Functional annotation of the final assembly identified key genes essential for the operation of CAM and the adaptation to salinity and water-deficit stress. Identification of these genes creates a rich genetics ‘parts list’ resource for ongoing ice plant genome annotation and comparative CAM genomics efforts, and biodesign projects aimed at introducing the improved WUE of CAM and salinity tolerance into crop plants.