Genome Sequencing of the Common Ice Plant (Mesembryanthemum crystallinum L.)

The common ice plant (Mesembryanthemum crystallinum L., Azoaceae, Caryophylalles) 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 (WUE), and salinity tolerance in plants, a high-quality, annotated genome assembly was generated for ice plant using two different genome sequencing platform, Illumina and PacBio, and obtained in a depth of coverage of 254X and 90X, respectively. We assembled the reads in three steps: 1) assemble with SMRT analysis for PacBio reads, 2) polish assembled contigs with Illumina reads, and 3) scaffolding with BioNano whole genome mapping. The resulting assembly generated the longest scaffolds of 24,930,053 bp, an N50 of 7,276,308 bp, the number of contigs was 575, and the total genome size was 379,583,752 bp. The assembly was used for gene annotation, which resulted in a total of 21,437 gene loci expressing 25,522 transcripts. This draft genome assembly identified key genes essential for the operation of CAM and the adaptation to salinity and water-deficit stress. Identification of genome assembly creates a rich genetics ‘parts list’ resource for ongoing ice plant genome annotation, comparative CAM genomics efforts, and biodesign projects aimed at introducing the improved WUE of CAM and salinity and drought tolerance into crop plants.