A whole-genome shotgun assembly for genome characterization of the common ice plant (Mesembryanthemum crystallinum L.)

Abstract

Abstract The common ice plant (Mesembryanthemum crystallinum L.) is an annual herb belonging to the genus Mesembryanthemum family of the family Aizoaceae. Here, we performed shotgun genome paired-end sequencing using the Illumina platform to determine the genome sequence of the ice plants. A draft genome was generated with a total length of 286 Mb corresponding to 79.2% of the estimated genome size (361 Mb), consisting of 49,782 contigs. It encompassed 93.49% of the genes of terrestrial higher plants, 99.5% of the ice plant transcriptome, and 100% of known DNA sequences. In addition, 110.9 Mb (38.8%) of repetitive sequences and untranslated regions, 971 tRNA, and 100 miRNA loci were identified, and their effects on stress tolerance and photosynthesis were investigated. Overall, 35,702 protein-coding regions were identified in the genome, of which 56.05–82.59% were annotated and used in domain searches and gene ontology (GO) analyses. The functional characterization using ice plant draft genome is a fundamental result. It can be helpful to elucidate the mechanism of growth promotion and reversible conversion of the photosynthetic type from C3 to CAM in the presence of NaCl. Further, these data could be used in the creation of novel, extremely salt-tolerant crops.