Project description:BackgroundThe genus Sanicula L. is a unique perennial herb that holds important medicinal values. Although the previous studies on Sanicula provided us with a good research basis, its taxonomic system and interspecific relationships have not been satisfactorily resolved, especially for those endemic to China. Moreover, the evolutionary history of this genus also remains inadequately understood. The plastid genomes possessing highly conserved structure and limited evolutionary rate have proved to be an effective tool for studying plant phylogeny and evolution.ResultsIn the current study, we newly sequenced and assembled fifteen Sanicula complete plastomes. Combined with two previously reported plastomes, we performed comprehensively plastid phylogenomics analyses to gain novel insights into the evolutionary history of this genus. The comparative results indicated that the seventeen plastomes exhibited a high degree of conservation and similarity in terms of their structure, size, GC content, gene order, IR borders, codon bias patterns and SSRs profiles. Such as all of them displayed a typical quadripartite structure, including a large single copy region (LSC: 85,074-86,197 bp), a small single copy region (SSC: 17,047-17,132 bp) separated by a pair of inverted repeat regions (IRs: 26,176-26,334 bp). And the seventeen plastomes had similar IR boundaries and the adjacent genes were identical. The rps19 gene was located at the junction of the LSC/IRa, the IRa/SSC junction region was located between the trnN gene and ndhF gene, the ycf1 gene appeared in the SSC/IRb junction and the IRb/LSC boundary was located between rpl12 gene and trnH gene. Twelve specific mutation hotspots (atpF, cemA, accD, rpl22, rbcL, matK, ycf1, trnH-psbA, ycf4-cemA, rbcL-accD, trnE-trnT and trnG-trnR) were identified that can serve as potential DNA barcodes for species identification within the genus Sanicula. Furthermore, the plastomes data and Internal Transcribed Spacer (ITS) sequences were performed to reconstruct the phylogeny of Sanicula. Although the tree topologies of them were incongruent, both provided strong evidence supporting the monophyly of Saniculoideae and Apioideae. In addition, the sister groups between Saniculoideae and Apioideae were strongly suggested. The Sanicula species involved in this study were clustered into a clade, and the Eryngium species were also clustered together. However, it was clearly observed that the sections of Sanicula involved in the current study were not respectively recovered as monophyletic group. Molecular dating analysis explored that the origin of this genus was occurred during the late Eocene period, approximately 37.84 Ma (95% HPD: 20.33-52.21 Ma) years ago and the diversification of the genus was occurred in early Miocene 18.38 Ma (95% HPD: 10.68-25.28 Ma).ConclusionThe plastome-based tree and ITS-based tree generated incongruences, which may be attributed to the event of hybridization/introgression, incomplete lineage sorting (ILS) and chloroplast capture. Our study highlighted the power of plastome data to significantly improve the phylogenetic supports and resolutions, and to efficiently explore the evolutionary history of this genus. Molecular dating analysis explored that the diversification of the genus occurred in the early Miocene, which was largely influenced by the prevalence of the East Asian monsoon and the uplift of the Hengduan Mountains (HDM). In summary, our study provides novel insights into the plastome evolution, phylogenetic relationships, taxonomic framework and evolution of genus Sanicula.

Project description:BackgroundThe 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.ResultsIn 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.ConclusionsThe 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.

Dataset Information

Sanicula lamelligera

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets