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.

Archiclematis and Naravelia were considered to be two small genera closely related to the large cosmopolitan genus Clematis. They have been included into Clematis s.l. in recent years according to molecular phylogenetic evidence. There is still little genomic information available for Archiclematis and Naravelia species. In this study, six complete chloroplast genomes from Archiclematis, Naravelia and Clematis were reported based on Illumina sequencing. The gene order and organization of the chloroplast genomes of Archiclematis and Naravelia are the same with that of Clematis. Analysis of eight complete chloroplast genomes showed that the plastomes of Clematis s.l. are typically circular, with a total length ranging from 159,513 bp to 159,783 bp. The total number of genes is identical within the broadly defined genus Clematis. We also identified variation hotspots, plastid repeats and SSRs for Clematis s.l. species. Our plastid phylogenomic analyses recovered the inclusion of Archiclematis and Naravelia into Clematis. The present study provides important phylogenomic data of Ranunculaceae and illuminates the phylogenetic relationships among Clematis species.

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