Chloroplast genomes elucidate diversity, phylogeny, and taxonomy of Pulsatilla (Ranunculaceae)

Qiu-jie Li,Zhao-yang Chang,Liang Zhao,Na Su,Ling Zhang,Xiao-hui Zhang,Daniel Potter,Jun-ru Wang,Ru-chang Tong

doi:10.1038/s41598-020-76699-7

Abstract

Pulsatilla (Ranunculaceae) consists of about 40 species, and many of them have horticultural and/or medicinal value. However, it is difficult to recognize and identify wild Pulsatilla species. Universal molecular markers have been used to identify these species, but insufficient phylogenetic signal was available. Here, we compared the complete chloroplast genomes of seven Pulsatilla species. The chloroplast genomes of Pulsatilla were very similar and their length ranges from 161,501 to 162,669 bp. Eight highly variable regions and potential sources of molecular markers such as simple sequence repeats, large repeat sequences, and single nucleotide polymorphisms were identified, which are valuable for studies of infra- and inter-specific genetic diversity. The SNP number differentiating any two Pulsatilla chloroplast genomes ranged from 112 to 1214, and provided sufficient data for species delimitation. Phylogenetic trees based on different data sets were consistent with one another, with the IR, SSC regions and the barcode combination rbcL + matK + trnH-psbA produced slightly different results. Phylogenetic relationships within Pulsatilla were certainly resolved using the complete cp genome sequences. Overall, this study provides plentiful chloroplast genomic resources, which will be helpful to identify members of this taxonomically challenging group in further investigation.

Highlights

DNA barcoding is an effective tool to identify many plant species rapidly and accurately[1,2,3,4]
Their quadripartite structure is similar to the majority of cp genomes of land plants, which are composed of a pair of inverted repeats (IR) (31,184–31,416 bp), separated by the large single copy region (LSC) (81,615–82,149 bp) and small single copy region (SSC) r egions[26,27] (Fig. 1; Table 2)
These genomes which we reported are highly conserved in gene order, gene content and intron number, which is in Scientific Reports | (2020) 10:19781 |

Summary

Introduction

DNA barcoding is an effective tool to identify many plant species rapidly and accurately[1,2,3,4]. We identify microsatellites (SSRs), larger repeat sequences, and highly variable regions, with the aim of developing DNA barcodes and testing the feasibility of phylogenetic analyses of Pulsatilla using the chloroplast genome. In order to facilitate identification of closely related species of Pulsatilla, we sought to identify highly variable regions of the chloroplast genome, as previously d escribed[9,27,41,42,43,44].

Results

Conclusion