High Quality De Novo Genome Assemblies of the Common Ice Plant (Mesembryanthemum crystallinum L.) - 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 genome assembly was generated for ice plant using two different genome sequencing platform, Illumina and PacBio, and obtained 95,569,388,632 and 33,865,183,009 bases, respectively, resulting in a depth of coverage of 254X and 90X. We assembled the reads in two steps, first with ABySS, SparseAssembler, String Graph Assembler, and SOAPdenovo2 for Illumina and SMRTanalysis for PacBio reads, independently. The resulting assemblies were compared with each assembler result and with the Illumina mate-pair reads used for scaffolding. The scaffold from the PacBio-only assembly generated the longest scaffolds of 11,659,217 bp, N50 & NG50 of 3,255,505 bp, 957 contigs, and a total size is 382.6 Mbp, which is close to the genome size estimate of 390 Mbp for this species. This scaffolding result will be used for BioNano Genomics Irys^® single-molecule next-generation mapping (NGM) to improve the accuracy and completeness of the genome assembly. This high-quality draft genome assembly will enable the identification of all genes required for the operation of CAM and for the adaptation of this halophytic species to salinity stress conditions, comparative CAM genomics efforts, and CAM biodesign projects aimed at introducing the improved WUE of CAM into crop plants.