The complete chloroplast genome of Paeonia anomala subsp. veitchii.

The complete chloroplast genome of Paeonia anomala subsp. veitchii., an important traditional Chinese herbal medicine, was sequenced and characterized in this study. The genome size is 152 682 bp in length with 38.42% GC content. Two inverted repeats (25 653 bp) are separated by a large single copy (84 398 bp) and a short single copy (16 978 bp). The genome contains 130 individual genes, including 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Twenty-one genes contain one or two introns. Phylogenetic tree analysis of P. anomala subsp. veitchii and other 12 species belonging to Pentapetalae using MEGA6 with the neighbour-joining algorithm revealed that the chloroplast genome was clustered in subfamily Paeoniaceae.

Introduction

Paeonia anomala subsp. veitchii (Paeoniaceae) is widespread in Gansu, Ningxia, Qinghai, Shaanxi, Shanxi, Sichuan and Xizang provinces of China (Hong et al. 2001). The root of P. anomala subsp. veitchii called Paeoniae Radix Rubra, is a kind of important traditional Chinese medicine, which has the properties of eliminating pathogenic heat from both blood and liver, menstruating promotion and treating boils (Wang et al. 2012). Herein, we conducted a high-throughput sequencing analysis of the complete chloroplast (cp) genome of P. anomala subsp. veitchii. Furthermore, phylogenetic tree analysis was determined using MEGA 6 with the neighbour-joining algorithm (Tamura et al. 2013).

P. anomala subsp. veitchii plants in the wild were collected in Taibai mountain (Coordinate: 34°00′ N, 107°23′ E; Altitude: 2203.2 m). Fresh leaves were then harvested for total genomic DNA isolation followed by sequencing under an Illumina Hiseq 2500 sequencer (San Diego, CA). Sequence assembly was performed using MITObim v1.8 by comparing with the cp genomic sequence of P. obovata (Genebank accession KJ206533) as a reference (Hahn et al. 2013). Genes containing in the assembled cp genome were annotated using GENEIOUS R8 (Biomatters, Auckland, New Zealand) based on BLAST analyses and coupled with manual corrections for start and stop codons. The genome map was drawn by an internet tool – OGDRAW v1.2 (Lohse et al. 2013) (http://ogdraw.mpimp-golm.mpg.de/).

The P. anomala subsp. veitchi cp genome was a double-stranded circular DNA of 152 682 bp in length and deposited in Genebank under the accession of KT894821. Its structure was consistent with most cp genomes in various plant species (Qian et al. 2014; Sun et al. 2016), consisting of two inverted repeats (IRa and IRb) of 25 653 bp separated by a large single copy (LSC) of 84 398 bp and a short single copy (SSC) of 16 978 bp, respectively. The AT content of the genome was 61.58%, suggesting the typical AT rich of plant cp genomes (Yang et al. 2013). The genome encoded 130 individual genes, including 85 protein-coding genes (PCGs), 37 tRNA genes and 8 rRNA genes. Of these genes, 18 were duplicated in the IR regions, including 7 PCGs, 7 tRNAs genes and 4 rRNAs genes. In addition, 18 genes contain 1 intron and 3 genes have 2 introns.

A neighbour-joining phylogenetic tree constructed with the cp genome sequences from 13 plants showed that P. anomala subsp. veitchii was closely related to P. sp. Sd0052 and P. obovata, and clustered in the subfamily of Paeoniaceae (Figure 1). The P. anomala subsp. veitchii cp genome and its phylogenetic tree analysis clarified here should be useful for further studies on its population genetics, evolution, molecular authentication, as well as metabolic regulation by a plastomic engineering approach.

Figure 1.

Phylogenetic tree analysis of 13 Paeoniaceae species with MEGA6 using the CDS regions of the chloroplast genomes. Data sources: Vitis vinifera (DQ424856); Vitis rotundifolia (KF976463); Francoa sonchifolia (JQ809470); Liquidambar formosana (KC588388); Penthorum chinese (JX436155); Sedum sarmentosum (JX427551); Sedum takesimense (KF954541); Paeonia sp. Sd0052 (KF753636); Paeonia anomala subsp. veitchii (KT894821); Paenoia obovata (KJ206533); Silene latifolia (JF715055) and Agrostemma githago (KF527884).