Transcriptome and Genome Assemblies of the Common Ice Plant, a Halophytic, Facultative Crassulacean Acid Metabolism (CAM) Species

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. The optimized, cleansed transcriptome assembly was comprised of 24,204 transcripts with a mean transcript length of 1,513 bp of which approximately 78% of the transcripts were full-length. Two generate a draft assembly of the ice plant genome, two different genome sequencing platforms, Illumina and Pacbio, were use to generate 95.5 and 33.8 gigabases resulting in 254X and 90X coverage depths, respectively. A two-step assembly process was performed.  Primary assemblies were created using ABySS, Sparseassembler, SGA and SOAPdenovo2 for Illumina reads and SMRTanalysis was used for Pac Bio reads. The resulting assemblies were compared against a scaffold created from Illumina mate-pair reads. The annotation of the draft genome assembly will be perfected using the de novo transcriptome assembly results. Complete transcriptome and genome assemblies enable the creation of comprehensive genomics ‘parts list’ resources for comparative CAM genomics efforts and biodesign projects aimed at introducing the improved water-use efficiency of CAM and salinity tolerance into crop plants.