Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Paeonia ostii

Abstract

Paeonia ostii, a common oil-tree peony, is important ornamentally and medicinally. However, there are few studies on the chloroplast genome of Paeonia ostii. We sequenced and analyzed the complete chloroplast genome of P. ostii. The size of the P. ostii chloroplast genome is 152,153 bp, including a large single-copy region (85,373 bp), a small single-copy region (17,054 bp), and a pair of inverted repeats regions (24,863 bp). The P. ostii chloroplast genome encodes 111 genes, including 77 protein-coding genes, four ribosomal RNA genes, and 30 transfer RNA genes. The genome contains forward repeats (22), palindromic repeats (28), and tandem repeats (24). The presence of rich simple-sequence repeat loci in the genome provides opportunities for future population genetics work for breeding new varieties. A phylogenetic analysis showed that P. ostii is more closely related to Paeonia delavayi and Paeonialudlowii than to Paeoniaobovata and Paeoniaveitchii. The results of this study provide an assembly of the whole chloroplast genome of P. ostii, which may be useful for future breeding and further biological discoveries. It will provide a theoretical basis for the improvement of peony yield and the determination of phylogenetic status.

Keywords: Paeonia ostii; chloroplast genome; phylogeny.

Figure 1

Gene map of the P. ostii chloroplast genome. Genes drawn inside the circle are transcribed clockwise, and those outsides are transcribed counterclockwise. Genes belonging to different functional groups are color-coded. The darker gray in the inner circle corresponds to DNA G+C content, while the lighter gray corresponds to A+T content. The gray arrowheads indicate the direction of the genes.

Figure 2

Analysis of repeated sequences in five Paeonia chloroplast genomes. (A) Totals of three repeat types; (B) frequency of forward repeats by length; (C) frequency of palindromic repeats by length; (D) frequency of tandem repeats by length.

Figure 3

Analysis of simple sequence repeats (SSRs) in the five Paeonia chloroplast genomes.

Figure 4

Comparison of five chloroplast genomes using mVISTA. Gray arrows and thick black lines above the alignment indicate gene orientation. Purple bars represent exons, blue bars represent untranslated regions (UTRs), pink bars represent noncoding sequences (CNS), gray bars represent mRNA, and white peaks represent differences of genomics. The y-axis represents the percentage identity (shown: 50–100%).

Figure 5

Comparison of border distance between adjacent genes and junctions of the LSC, SSC and two IR regions among the chloroplast genomes of five Paeonia species. Boxes above or below the main line indicate the adjacent border genes. The figure is not to scale with respect to sequence length, and only shows relative changes at or near the IR/SC borders.

Figure 6

ML phylogenetic tree reconstruction including 14 species based on all chloroplast genomes. The position of P. ostii is indicated in red font. Ceratophyllum demersum was used as the outgroup.