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

Xiaori Zhan; Zhenhao Zhang; Yong Zhang; Yadi Gao; Yanyun Jin; Chenjia Shen; Huizhong Wang; Shangguo Feng

doi:10.3390/genes13122291

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

Genes (Basel). 2022 Dec 5;13(12):2291. doi: 10.3390/genes13122291.

Authors

Xiaori Zhan^{1

2}, Zhenhao Zhang^{1

2}, Yong Zhang³, Yadi Gao¹, Yanyun Jin^{1

2}, Chenjia Shen^{1

2}, Huizhong Wang^{1

2}, Shangguo Feng^{1

2}

Affiliations

¹ College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China.
² Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China.
³ Quzhou Academy of Agriculture and Forestry Sciences, Quzhou Municipal Bureau of Agriculture and Rural Affairs, Quzhou 324000, China.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genomics
Microsatellite Repeats
Phylogeny
Physalis* / genetics
Solanaceae* / genetics

Grants and funding

Our work was funded by the National Natural Science Foundation of China (31970346, 32000255); the Zhejiang Provincial Natural Science Foundation of China (LY20H280012); the key project at the central government level for the ability establishment of sustainable use for valuable Chinese medicine resources (2060302), the Zhejiang Provincial Key Research & Development Project Grants (2018C02030).