Background: The genus Sanicula comprises ca. 45 taxa, widely distributed from East Asia to North America, which is a taxonomically difficult genus with high medicinal value in Apiaceae. The systematic classification of the genus has been controversial for a long time due to varied characters in key morphological traits. China is one of the most important distributed centers, with ca. 18 species and two varieties. At present, chloroplast genomes are generally considered to be conservative and play an important role in evolutionary relationship study. To investigate the plastome evolution and phylogenetic relationships of Chinese Sanicula, we comprehensively analyzed the structural characteristics of 13 Chinese Sanicula chloroplasts and reconstructed their phylogenetic relationships. Results: In present study, four newly complete chloroplast genome of Sanicula taxa by using Illumina sequencing were reported, with the typical quadripartite structure and 155,396–155,757 bp in size. They encoded 126 genes, including 86 protein-coding genes, 32 tRNA genes and 8 rRNA genes. Genome structure, distributions of SDRs and SSRs, gene content, among Sanicula taxa, were similar. The nineteen intergenic spacers regions, including atpH-atpI, ndhC-trnM, petB-petD, petD-rpoA, petN-psbM, psaJ-rpl33, rbcL-accD, rpoB-trnC, rps16-trnQ, trnE-psbD, trnF-ndhJ, trnH-psbA, trnN-ndhF, trnS-psbZ, trnS-trnR, trnT-trnF, trnV-rps12, ycf3-trnS and ycf4-cemA, and one coding region (ycf1 gene) were the most variable. Results of maximum likelihood analysis based on 79 unique coding genes of 13 Chinese Sanicula samples and two Eryngium (Apiaceae-Saniculoideae) species as outgroup taxa revealed that they divided into four subclades belonged to two clades, and one subclade was consistent with previously traditional Sanicula section of its system. The current classification based on morphology at sect. Sanicla and Sect. Tuberculatae in Chinese Sanicula was not supported by analysis of cp genome phylogeny. Conclusions: The chloroplast genome structure of Sanicula was similar to other angiosperms and possessed the typical quadripartite structure with the conserved genome arrangement and gene features. However, their size varied owing to expansion/contraction of IR/SC boundaries. The variation of non-coding regions was larger than coding regions of the chloroplast genome. Phylogenetic analysis within these Chinese Sanicula were determined using the 79 unique coding genes. These results could provide important data for systematic, phylogenomic and evolutionary research in the genus for the future studies.

Based on critical observations on herbarium specimens (including type material) and living plants in the wild, we demonstrate that Sanicula lamelligera (Apiaceae) is highly variable in character of basal leaves, branches of inflorescences, and character of fruits. We therefore accept some previous synonyms of this species, including S. ichangensis, S. lamelligera var. wakayamensis, S. orthacantha var. longispina, S. satsumana, and S. yunnanensis, and further reduce S. orthacantha var. pumila, and S. pengshuiensis to its synonymy. Lectotypification is proposed for S. lamelligera var. wakayamensis and S. orthacantha var. pumila.

Through field observations of living plants and the analysis of herbarium collections, including type material, it is demonstrated that Sanicula rugulosa can be distinguished from S. subgiraldii by several morphological characteristics, including the presence of slightly tripartite basal leaves (vs. deeply ternate leaves), umbellules that typically contain 5–7 flowers (vs. 4–11), 3–8 staminate flowers (vs. 2–3), generally three fertile flowers (vs. 1–3) and a consistently black stylopodium (vs. a whitish or pale green one). Furthermore, S. astrantiifolia and S. hanyuanensis are not essentially different morphologically from S. rugulosa and we, therefore, propose to treat them as synonyms in this study.

The genus Hydrocotyle Tourn. ex L. is a key group for further study on the evolution of Apiales, comprising around 170 species globally. Previous studies mainly focused on separate sections and provided much information about this genus, but its infrageneric relationships are still confusing. In addition, the genetic basis of its adaptive evolution remains poorly understood. To investigate the phylogeny and evolution of the genus, we selected ten representative species covering two of three diversity distribution centers and exhibiting rich morphology diversity. Comparative plastome analysis was conducted to clarify the structural character of Hydrocotyle plastomes. Positive selection analyses were implemented to assess the evolution of the genus. Phylogenetic inferences with protein-coding sequences (CDS) of Hydrocotyle and 17 related species were also performed. Plastomes within Hydrocotyle were generally conservative in structure, gene order, and size. A total of 14 regions (rps16-trnK, trnQ-rps16, atpI-atpH, trnC-petN-psbM, ycf3-trnS, accD-psaI-ycf4, petA-psbJ, rps12-rpl20, rpl16 intron, rps3-rpl16 intron, rps9-rpl22, ndhF-rpl32, ndhA intron, and ycf1a) were recognized as hotspot regions within the genus, which suggested to be promising DNA barcodes for global phylogenetic analysis of Hydrocotyle. The ycf15 gene was suggested to be a protein-coding gene for Hydrocotyle species, and it could be used as a DNA barcode to identify Hydrocotyle. In phylogenetic analysis, three monophyletic clades (Clade I, II, III) were identified with evidence of rapid radiation speciation within Clade I. The selective pressure analysis detected that six CDS genes (ycf1b, matK, atpF, accD, rps14, and psbB) of Hydrocotyle species were under positive selection. Within the genus, the last four genes were conservative, suggesting a relation to the unique evolution of the genus in Apiales. Seven genes (atpE, matK, psbH, ycf1a, ycf1b, rpoA, and ycf2) were detected to be under some degree of positive selection in different taxa within the genus Hydrocotyle, indicating their role in the adaptive evolution of species. Our study offers new insights into the phylogeny and adaptive evolution of Hydrocotyle. The plastome sequences could significantly enhance phylogenetic resolution and provide genomic resources and potential DNA markers useful for future studies of the genus.

Based on observations of living plants in the field and examination of herbarium specimens (including type materials), we demonstrate that Sanicula serrata var. serrata (Apiaceae) differs from S. potaninii by having single fruit bearing squamose spines – occasionally tuberculate-spiculate or apically prickly – whereas S. potaninii usually bears three fruits with densely uncinate spines. This morphological distinction is further supported by differences in their biogeographic distributions. In addition, S. tienmuensis, S. elongata, S. tienmuensis var. pauciflora, and S. langaoensis are found to be conspecific with S. serrata, while S. serrata var. uncinata is conspecific with S. potaninii; we therefore reduce these taxa to synonymy accordingly. Lectotypifications are proposed for S. elongata and S. tienmuensis var. pauciflora.

In the present study, we examined the morphological variations within Sanicula caerulescens and determined the identity of S. oviformis through observations of herbarium specimens (including type material) and field studies of plants in their type locality. Our findings revealed that S. oviformis, originally described from Nanchuan County in southern Chongqing, is conspecific with S. caerulescens. This species is mainly distributed in Chongqing, Guizhou, western Hunan, Sichuan and north-eastern Yunnan in China, as well as in Hà Giang in Vietnam. Key morphological characters of leaves, inflorescences and fruits confirm this synonymy. Based on these findings, we propose reducing S. oviformis to a synonym of S. caerulescens. Additionally, the geographical distribution of S. caerulescens is clarified.