The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax (Araliaceae)

Abstract

Panax stipuleanatus (Araliaceae) is an endangered and medicinally important plant endemic to China. However, phylogenetic relationships within the genus Panax have remained unclear. In this study, we sequenced the complete plastome of P. stipuleanatus and included previously reported Panax plastomes to better understand the relationships between species and plastome evolution within the genus Panax. The plastome of P. stipuleanatus is 156,069 base pairs (bp) in length, consisting of a pair of inverted repeats (IRs, each 25,887 bp) that divide the plastome into a large single copy region (LSC, 86,126 bp) and a small single copy region (SSC, 8169 bp). The plastome contains 114 unigenes (80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes). Comparative analyses indicated that the plastome gene content and order, as well as the expansion/contraction of the IR regions, are all highly conserved within Panax. No significant positive selection in the plastid protein-coding genes was observed across the eight Panax species, suggesting the Panax plastomes may have undergone a strong purifying selection. Our phylogenomic analyses resulted in a phylogeny with high resolution and supports for Panax. Nine protein-coding genes and 10 non-coding regions presented high sequence divergence, which could be useful for identifying different Panax species.

Keywords: Araliaceae; Comparative genomics; Panax stipuleanatus; Phylogenomics; Plastome.

Fig. 1

The geographic distribution and morphological features of Panax stipuleanatus H. T. Tsai & K. M. Feng. A, geographic distribution; B, aerial part; C, inflorescence; D, fruit; E, rootstock.

Fig. 2

Plastome map of the Panax stipuleanatus. Genes shown outside of the outer layer circle are transcribed counterclockwise, whereas those genes inside of this circle are transcribed clockwise. The colored bars indicate the known protein-coding genes, tRNA, and rRNA. The dashed, darker gray area of the inner circle denotes the GC content, while the lighter gray area indicates the AT content of the genome. LSC, large single-copy; SSC, small single-copy; IR, inverted repeat.

Fig. 3

Comparison of the borders of the LSC, SSC, and IR regions among the eight Panax plastomes. LSC, large single-copy; SSC, small single-copy; IR, inverted repeat.

Fig. 4

Visualized alignment of the eight Panax plastomes. The mVISTA-based identity plots show the sequence identity among the eight Panax plastome, for which P. ginseng serves as the reference. Gray arrows indicate the position and direction of each gene. Genome regions are color-coded as protein coding, rRNA, tRNA, or conserved non-coding regions. Black lines define the regions of sequence identity shared with P. ginseng (using a 50%-identity cutoff criterion).

Fig. 5

Non-synonymous substitution (Ka), synonymous substitution (Ks), and the Ka/Ks values for the Panax plastid protein-coding genes.

Fig. 6

Phylogenetic tree reconstruction of the genus Panax via maximum likelihood (ML), based on (A) the whole plastome; (B) the protein-coding exons; (C) the large single-copy (LSC) regions; (D) the small single-copy (SSC) regions; (E) the inverted repeated (IR) regions; and (F) the introns and intergenic spacers. The numbers above the line represent the ML-bootstrap values (1000 replicates).