Comparative analysis of complete chloroplast genomes of 11 species in Ranunculeae (Ranunculaceae) and their phylogenetic inferences.

This is all the alignments which used to constructed a phylogenetic tree in our study about Ranunculeae. The tribe Ranunculeae, in the family Ranunculaceae, consists of about 650 species from 19 genera with worldwide distribution. In the present study, we report and characterize the complete chloroplast genome sequences of 9 species in Ranunculus, Ceratocephala and Halerpestes using a next-generation sequencing method. We also retrieved plastome sequences from one other Ranunculeae genera to characterize the chloroplast genome of the family. The complete plastomes of Ranunculeae showed a typical quadripartite structure and encoded an identical set of 112 genes (with exclusion of duplication), including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. The results show that the length and GC content of chloroplast genome vary slightly among different genera, and are basically conserved in the gene arrangement across this tribe. We also compared chloroplast genomes across the Ranunculeae samples and revealed similarities in some features, including nucleotide content, codon usage, RNA editing sites, and simple sequence repeats (SSRs). And we used the maximum-likelihood (ML) and Bayesian inference (BI) methods for phylogenetic inference of the chloroplast genome data. The generic relationship of Ranunculeae was well resolved by the complete plastome sequences, showing potential value in inferring phylogeny within the family.