Comparative chloroplast genomes and phylogenetic analyses of Pinellia

Abstract

Background: Pinellia Tenore (Araceae) is a genus of perennial herbaceous plants, all of which have medicinal value. The chloroplast (cp) genome data of Pinellia are scarce, and the phylogenetic relationship and gene evolution remain unclear.

Methods and results: We sequenced and annotated the Pinellia pedatisecta cp genome and combined it with previously published genomes for other Pinellia species. We used bioinformatics methods to analyse the genomic structure, repetitive sequences, interspecific variation, divergence hotspots, phylogenetic relationships, divergence time estimation and selective pressure of four Pinellia plastomes. Results showed that the cp genomes of Pinellia varied in length between 168,178 (P. pedatisecta MN046890) and 164,013 bp (P. ternata KR270823). A total of 68-111 SSR loci were identified as candidate molecular markers for further genetic diversity study. Eight mutational hotspot regions were determined, including psbI-trnG-UCC, psbM-rpoB, ndhJ-trnT-UGU, trnP-UGG-trnW-CCA, ndhF-trnN-GUU, ndhG-ndhE, ycf1-rps15 and trnR-ycf1. Gene selection pressure suggested that four genes were subjected to positive selection. Phylogenetic inferences based on the complete cp genomes revealed a sister relationship between Pinellia and Arisaema plants whose divergence was estimated to occur around 22.48 million years ago. All Pinellia species formed a monophyletic evolutionary clade in which P. peltata, rather than P. pedatisecta, earlier diverged, indicating that P. pedatisecta is not the basal taxon of Pinellia but P. peltata may be.

Conclusions: The cp genomes of Pinellia will provide valuable information for species classification, identification, molecular breeding and evolutionary exploration of the genus Pinellia.

Keywords: Chloroplast genome; Divergence time estimation; Evolution; Phylogeny; Pinellia.

Fig. 1

Chloroplast genome map of P. pedatisecta assembled in this study. The centre of the figure provides length information of the cp genome. In the first inner circle, the proportion of the shaded parts represents the GC content of each part. The gene names are labelled on the outermost layer. The transcription directions for the inner and outer genes are listed clockwise and anticlockwise, respectively

Fig. 2

The SSRs (A), interspersed repeated sequences (B), and interspecific nucleotide diversity (C) among the chloroplast genomes of Pinellia. X-axis in Fig. 3C: position of a window. Y-axis in Fig. 3C: sequence divergence (K values) between species of each window. K(a): K values between P. pedatisecta and P. peltata; K(b): K values between P. pedatisecta and P. ternata; K(c): K values between P. ternata and P. peltata

Fig. 3

Phylogenetic trees constructed with the whole cp genomes (A) and their protein-coding sequences (B) by using ML method. Numbers near each branch are bootstrap values

Fig. 4

Positive selection sites logo of four Pinellia plastomes