Structural rearrangements of Anemone species' chloroplast genome has been reported based on genetic mapping of restriction sites but has never been confirmed by genomic studies. We used a next-generation sequencing method to characterize the complete chloroplast genomes of five species in the tribe Anemoneae. Plastid genomes were assembled using de novo assembling methods combined with conventional Sanger sequencing to fill the gaps. The gene order of the chloroplast genomes of tribe Anemoneae was compared with that of other Ranunculaceae species. Multiple inversions and transpositions were detected in tribe Anemoneae. Anemoclema, Anemone, Hepatica, and Pulsatilla shared the same gene order, which contained three inversions in the large single copy region (LSC) compared to other Ranunculaceae genera. Archiclematis, Clematis, and Naravelia shared the same gene order containing two inversions and one transposition in LSC. A roughly 4.4 kb expansion region in inverted repeat (IR) regions was detected in tribe Anemoneae, suggesting that this expansion event may be a synapomorphy for this group. Plastome phylogenomic analyses using parsimony and a Bayesian method with implementation of partitioned models generated a well resolved phylogeny of Ranunculaceae. These results suggest that evaluation of chloroplast genomes may result in improved resolution of family phylogenies. Samples of Anemone, Hepatica, and Pulsatilla were tested to form paraphyletic grades within tribe Anemoneae. Anemoclema was a sister clade to Clematis. Structual variation of the plastid genome within tribe Anemoneae provided strong phylogenetic information for Ranunculaceae.

Two complete chloroplast genome sequences of Asteropyrum, as well as those of 25 other species from Ranunculaceae, were assembled using both Illumina and Sanger sequencing methods to address the structural variation of the cp genome and the controversial systematic position of the genus. Synteny and plastome structure were compared across the family. The cp genomes of the only two subspecies of Asteropyrum were found to be differentiated with marked sequence variation and different inverted repeat-single copy (IR-SC) borders. The plastomes of both subspecies contains 112 genes. However, the IR region of subspecies peltatum carries 27 genes, whereas that of subspecies cavaleriei has only 25 genes. Gene inversions, transpositions, and IR expansion-contraction were very commonly detected in Ranunculaceae. The plastome of Asteropyrum has the longest IR regions in the family, but has no gene inversions or transpositions. Non-coding regions of the cp genome were not ideal markers for inferring the generic relationships of the family, but they may be applied to interpret species relationship within the genus. Plastid phylogenomic analysis using complete cp genome with Bayesian method and partitioned modeling obtained a fully resolved phylogenetic framework for Ranunculaceae. Asteropyrum was detected to be sister to Caltha, and diverged early from subfamily Ranunculoideae.

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The morphologically based taxonomic status of Clematis acerifolia var. elobata has been controversial. This study used two nuclear (ITS and ETS) and six plastid (rps16, rpl16, accD, trnS-trnG, atpB-rbcL, and trnV-atpE) molecular markers, and a DNA barcoding analysis to address the taxonomic status of C. acerifolia var. elobata and the relationship among other Clematis species. Our results showed that the discrimination power of ITS, ETS, and atpB-rbcL was better than that of the other tested DNA regions. When all tested sequences combined, most of the sampled taxa were resolved. Though the two taxa are closely related, they have differentiated clearly and formed two clades respectively. The mean divergence of the two taxa was 0.78%, which was higher than closely related Clematis species such as C. heracleifolia and C. pinnata (0.50 %). Considering molecular divergence, morphological differences, and distribution area, we raised C. acerifolia var. elobata to species level.