Additional file 1 of Plastid genome and its phylogenetic implications of Asiatic Spiraea (Rosaceae)

Additional file 1: Fig. S1. Sequence identity plots of plastomes of Spiraea by mVISTA. The top line shows the orientation of genes. A cutoff of 70% identity was used for the plots, and the Y-scale represents the percentage identity ranging from 50 to 100%. Fig. S2. Comparison of LSC, IRs, and SSC junction positions among Spiraea plastomes. Fig. S3. Cladogram of the maximum likelihood (ML) phylogenetic tree constructed based on the whole plastid sequences. Node labels represent the bootstrap values (left) and Bayesian posterior probabilities (right), respectively. Fig. S4. Maximum clade-credibility tree of Rosaceae from BEAST with 12 fossil calibration points. The bar at each node indicates age with a 95% height posterior distribution. Red stars represent fossil calibration points (see Table S2). Table S1. The sampling information in this study. Table S2. Fossil calibration points used in this study. Table S3. Plastid genome information of Spiraea. Table S4. List of annotated genes in the plastid genome of Spiraea. Table S5. The value of nonsynonymous (dN), synonymous (dS) substitution rate and dN/dS in each functional gene. Table S6. The likelihood ratio and positively selected codon site tests in this study.

附加文件1：图S1。基于mVISTA绘制的绣线菊属（Spiraea）质体基因组（plastome）序列一致性图谱。图谱顶部线条显示基因的转录方向。本次绘图采用70%的序列一致性作为阈值，Y轴刻度代表序列一致性百分比，取值范围为50%至100%。
图S2。绣线菊属质体基因组中大单拷贝区（Large Single Copy, LSC）、反向重复区（Inverted Repeat, IRs）及小单拷贝区（Small Single Copy, SSC）的边界位点比较。
图S3。基于全质体序列构建的最大似然（maximum likelihood, ML）系统发育树分支图。节点标注分别代表自举值（左侧）和贝叶斯后验概率（右侧）。
图S4。基于BEAST软件构建的蔷薇科（Rosaceae）最大分支置信树，共采用12个化石校准点。每个节点处的标尺代表该节点的分化年龄，其95%最高后验密度区间。红色星号代表化石校准点（详见表S2）。
表S1。本研究的采样信息。
表S2。本研究采用的化石校准点。
表S3。绣线菊属质体基因组信息。
表S4。绣线菊属质体基因组注释基因列表。
表S5。各功能基因的非同义替换率（dN）、同义替换率（dS）及dN/dS比值。
表S6。本研究中的似然比检验及正选择密码子位点分析结果。