LAUSR

Simple Summary Plastids are semi-autonomous plant organelles which play critical roles in photosynthesis, stress response, and storage. The plastid genomes (plastomes) in angiosperms are relatively conserved in quadripartite structure, but variable in size, gene content, and evolutionary rates of genes. The genus Crassula L. is the second-largest genus in the family Crassulaceae J.St.-Hil, that significantly contributes to the diversity of Crassulaceae. However, few studies have focused on the evolution of plastomes within Crassula. In the present study, we sequenced ten plastomes of Crassula: C. alstonii Marloth, C. columella Marloth & Schönland, C. dejecta Jacq., C. deltoidei Thunb., C. expansa subsp. fragilis (Baker) Toelken, C. mesembrianthemopsis Dinter, C. mesembryanthoides (Haw.) D.Dietr., C. socialis Schönland, C. tecta Thunb., and C. volkensii Engl. Through comparative studies, we found Crassula plastomes have unique codon usage and aversion patterns within Crassulaceae. In addition, genomic features, evolutionary rates, and phylogenetic implications were analyzed using plastome data. Our findings will not only reveal new insights into the plastome evolution of Crassulaceae, but also provide potential molecular markers for DNA barcoding. Abstract The genus Crassula is the second-largest genus in the family Crassulaceae, with about 200 species. As an acknowledged super-barcode, plastomes have been extensively utilized for plant evolutionary studies. Here, we first report 10 new plastomes of Crassula. We further focused on the structural characterizations, codon usage, aversion patterns, and evolutionary rates of plastomes. The IR junction patterns—IRb had 110 bp expansion to rps19—were conservative among Crassula species. Interestingly, we found the codon usage patterns of matK gene in Crassula species are unique among Crassulaceae species with elevated ENC values. Furthermore, subgenus Crassula species have specific GC-biases in the matK gene. In addition, the codon aversion motifs from matK, pafI, and rpl22 contained phylogenetic implications within Crassula. The evolutionary rates analyses indicated all plastid genes of Crassulaceae were under the purifying selection. Among plastid genes, ycf1 and ycf2 were the most rapidly evolving genes, whereas psaC was the most conserved gene. Additionally, our phylogenetic analyses strongly supported that Crassula is sister to all other Crassulaceae species. Our findings will be useful for further evolutionary studies within the Crassula and Crassulaceae.