Ten Plastomes of Crassula (Crassulaceae) and Phylogenetic Implications

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.

Keywords: Crassula; Crassulaceae; DNA barcoding; codon aversion; codon usage; evolutionary rates; phylogeny; plastome.

Figure 1

Annotation map of ten new plastomes from Crassula species. Directed with arrows, genes that are listed inside and outside of the circle are respectively transcribed clockwise and counterclockwise. Different colors represent different functional groups.

Figure 2

Structure comparisons of ten new Crassula plastomes using the mVISTA program. Y-scale represents the percent identity between 50% and 100%. The labels 0 to 10 indicate C. perforata (reference), C. alstonii, C. columella, C. dejecta, C. mesembryanthoides, C. tecta, C. mesembrianthemopsis, C. socialis, C. volkensii, C. expansa subsp. fragilis, and C. deltoidei, respectively.

Figure 3

Sliding-window analysis of the plastomes of 11 Crassula species (window length: 600 bp; step size: 200 bp). x-axis: position of the midpoint of a window; y-axis: π value of each window. Regions with higher π values (π > 0.06886) were considered as HVRs.

Figure 4

Comparisons of LSC, SSC, and IR region borders among plastomes of 11 Crassula species. Blue, orange and green blocks represent the LSC, IR and SSC regions, respectively. Gene boxes represented above the block were transcribed clockwise and those represented below the block were transcribed clockwise. “fra.” is the abbreviation of “fragment”.

Figure 5

The heatmap of overall RSCU values among 7 clades of Crassulaceae species based on 53 concatenated plastid genes (length ≥300 bp). The x-axis: the cluster of different codons; y-axis: the clusters of species.

Figure 6

The ENC value distributions of matK for 7 clades of Crassulaceae. The mean values with standard deviations are labeled.

Figure 7

The PR2 plot of matK of Crassulaceae. Different colors represent different clades. Within the clade Crassula (or genus Crassula), red circles with black edges and cyan edges represent species of subgenus Crassula and Disporocarpa, respectively.

Figure 8

The specific codon aversion motifs of matK, pafI and rpl22 gene for the 11 species of Crassula. The dots marked in different colors represent different species. Codons in red and green were specific for subgenus Crassula and subgenus Disporocarpa, respectively.

Figure 9

Sequence polymorphism among 79 PCGs of 87 Crassulaceae species. (a) Nucleotide diversity (π) and percentages of variable sites (PV). (b) Estimations of nonsynonymous (dN) and synonymous (dS) substitution rates and the dN/dS.

Figure 10

The phylogenetic tree of 87 Crassulaceae species based on ML and BI methods. The maximum likelihood bootstrap (BS) and Bayesian posterior probability (PP) values for each node are indicated; * indicates 100% bootstrap or 1.00 PP.