Complete Plastome of Physalis angulata var. villosa, Gene Organization, Comparative Genomics and Phylogenetic Relationships among Solanaceae

Abstract

Physalis angulata var. villosa, rich in withanolides, has been used as a traditional Chinese medicine for many years. To date, few extensive molecular studies of this plant have been conducted. In the present study, the plastome of P. angulata var. villosa was sequenced, characterized and compared with that of other Physalis species, and a phylogenetic analysis was conducted in the family Solanaceae. The plastome of P. angulata var. villosa was 156,898 bp in length with a GC content of 37.52%, and exhibited a quadripartite structure typical of land plants, consisting of a large single-copy (LSC, 87,108 bp) region, a small single-copy (SSC, 18,462 bp) region and a pair of inverted repeats (IR: IRA and IRB, 25,664 bp each). The plastome contained 131 genes, of which 114 were unique and 17 were duplicated in IR regions. The genome consisted of 85 protein-coding genes, eight rRNA genes and 38 tRNA genes. A total of 38 long, repeat sequences of three types were identified in the plastome, of which forward repeats had the highest frequency. Simple sequence repeats (SSRs) analysis revealed a total of 57 SSRs, of which the T mononucleotide constituted the majority, with most of SSRs being located in the intergenic spacer regions. Comparative genomic analysis among nine Physalis species revealed that the single-copy regions were less conserved than the pair of inverted repeats, with most of the variation being found in the intergenic spacer regions rather than in the coding regions. Phylogenetic analysis indicated a close relationship between Physalis and Withania. In addition, Iochroma, Dunalia, Saracha and Eriolarynx were paraphyletic, and clustered together in the phylogenetic tree. Our study published the first sequence and assembly of the plastome of P. angulata var. villosa, reported its basic resources for evolutionary studies and provided an important tool for evaluating the phylogenetic relationship within the family Solanaceae.

Keywords: Physalis angulata var. villosa; SSRs; comparative genomics; phylogenetic relationship; plastome; repeat analysis.

Figure 1

Plant morphology of P. angulata var. villosa in natural habitats.

Figure 2

Gene map of the plastome of P. angulata var. villosa. Genes outside the circles are transcribed in a counterclockwise direction, and genes inside the circles in a clockwise direction. Known functional genes are color coded. AT and GC contents are denoted by the light and dark grays in the inner circle, respectively. LSC indicates large single-copy region and SSC indicates small single-copy region, whereas IRA and IRB indicate inverted repeats.

Figure 3

Amino acid frequencies in the P. angulata var. villosa plastome protein-coding sequences.

Figure 4

Repeated sequences in the plastomes of nine Physalis species. (A), Three repeat types (forward, reverse and palindromic repeats) in the nine Physalis plastomes; (B), Numbers of repeat (forward, reverse and palindromic) sequences by length.

Figure 5

Simple sequence repeats (SSRs) types, distribution and presence in P. angulata var. villosa and other representative species from Physalis. (A), Numbers of different SSR motifs in different repeat types detected in the P. angulata var. villosa plastome. (B), Numbers of SSRs in different regions (IRA, IRB, LSC, and SSC) of the P. angulata var. villosa plastome. (C), Numbers of different SSR types detected in the genomes of the nine Physalis species.

Figure 6

Sequence alignment of nine plastomes in the genus Physalis performed with mVISTA, using annotation of P. angulata var. villosa as reference. The y-axis presents the percentage identity, within 50–100%. Protein-encoding regions are indicated in blue and non-coding regions in red. A reduction in sequence identity is indicated by a reduction in the blue/red shadowing (white spaces).

Figure 7

Comparison of the borders of the IR, SSC and LSC regions among nine Physalis plastomes. Numbers above indicate the distances in bp between the ends of the genes and the border sites.

Figure 8

Maximum likelihood (ML) phylogenetic tree of the complete plastomes of 80 species of seven tribes (Physaleae, Capsiceae, Solaneae, Datureae, Lycieae, Hyoscyameae and Nicotianeae) from three subfamily (Solanoideae, Nicotianoideae and Petunioideae) of Solanaceae. Numbers above branches indicate bootstrap support levels.