Ancestral chromosome karyotype construction and large-scale analysis of CAM biosynthesis genes in ice plant and representative plants

Caryophyllales is one of the evolutionary branches of core eudicots, comprising numerous economically important species. However, comprehensive investigations into the genomic evolution of Caryophyllales remain scarce. Recently, we conducted de novo genome sequencing, yielding a high-quality genome assembly of ice plant, a typical representative of Caryophyllales. Here, we reconstructed the ancestral karyotype of Caryophyllales plants through a comparison of genomic data. Our analysis unveiled that the most recent common ancestor of Caryophyllales harbored a karyotype comprised of nine chromosomes. Subsequent analysis elucidated the evolutionary trajectory of ancestral chromosomes of Caryophyllales. Additionally, the ice plant characterized by its facultative adoption of Crassulacean acid metabolism (CAM) and C3 photosynthesis, epitomizes a halophytic species renowned for its salt tolerance resilience. In pursuit of understanding CAM biosynthesis mechanisms in ice plant, this investigation employed bioinformatic methodologies to identify 23 candidate genes. A comprehensive analysis was then performed on these genes. The findings showed that 23 identified genes within ice plant are categorized into six distinct gene families, namely CA, PEPC, MDH, PPDK, PEPCK, and ME. Based on the evolutionary tree and gene domain analysis, the identified genes were further subdivided into several distinct subfamilies. Furthermore, an extensive exploration ensued into the phylogenetic relationships among 11,148 CAM-related genes from an array of 287 species possessing well-annotated plant genomes, thereby encompassing major taxonomic groups within the plant kingdom. Consequently, this study furnishes a valuable reference for understanding both the evolutionary dynamics of chromosome karyotypes within Caryophyllales and the intricate network of CAM biosynthesis genes across diverse plant species.