The complete chloroplast genome of Fuchsia standishii J. Harrison, 1840 (Onagraceae) from Yunnan, China

Abstract

Fuchsia standishii J. Harrison, 1840, a perennial shrub, is renowned for its vividly colored and uniquely shaped blooms, which have an extended flowering season. Commonly cultivated as an ornamental potted plant, it is utilized in traditional Chinese medicine. In this study, we successfully sequenced and assembled the complete chloroplast genome of F. standishii using high-throughput Illumina sequencing technology. The assembled chloroplast genome displays a typical quadripartite structure, with a total length of 156,391 bp. It consists of a pair of inverted repeat regions (IRs), each measuring 25,069 bp, separated by a large single-copy region (LSC) of 87,754 bp and a small single-copy region (SSC) of 18,499 bp. The overall GC content of the genome is 37.60%. The genome includes a total of 129 genes, comprising 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis of 17 complete chloroplast genomes revealed that F. standishii forms a monophyletic group with the entire Circaea. This study provides a molecular foundation for future phylogenetic research on Fuchsia.

Introduction

Fuchsia standishii J. Harrison, 1840 is a flowering plant species native to South America and New Zealand, belonging to the Onagraceae family (Garibaldi et al. 2012). Fuchsia standishii is the basionym of Fuchsia hybrida. Notably, it is the exclusive representative of the Fuchsia genus in China (Figure 1). Widely cultivated and esteemed as an ornamental potted plant, its flowers can enhance the nutritional, sensory, and functional qualities of food formulations (Castillo-Carrión et al. 2024). In studies conducted by Rios et al. (2017), F. standishii emerges as a crucial component in the formulation of horchata, a beverage widely integrated into the traditional practices of Southern Ecuador due to its recognized anti-inflammatory, analgesic, and diuretic properties (Rios et al. 2017). Renowned for its diverse therapeutic properties encompassing anti-inflammatory, antioxidant, antifungal, cardiotonic, sedative, and stomachache-alleviating effects, it is a valuable botanical resource (Csepregi et al. 2016).

Figure 1.

F. standishii is a shrub with opposite leaves that are either ovate or narrow. Its flowers have a red, bell-shaped tube, with petals available in various colors, including purple, red, pink, and white. The petals are wide and obovate. The immature fruit is green and obovate oblong. A. Plant; B. Flower; C. Immature fruit. Photos of F. standishii were taken by Siying Li.

Despite its medicinal importance, the chloroplast genome of F. standishii has not been previously documented, hindering a comprehensive understanding of its genetic characteristics and evolutionary history. This study focuses on sequencing the complete chloroplast genome of F. standishii to lay the groundwork for further exploration and research in this field.

Materials and methods

Fresh leaves were gathered at Dali County (geospatial coordinates: 100°11′6″E, 25°84′95″N). And that is stored in the Herbarium of Dali University (http://yxy.dali.edu.cn/yhxy/, wangshuang0541@126.com, Wang Shuang) with a voucher number WS2022111804. For whole-genome DNA sequencing, we extracted total genomic DNA using a modified CTAB method (Doyle and Doyle 1987), which was then fragmented into 150 bp for library construction and sequenced by the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) (Zhang et al. 2023). This process yielded 4.64 GB of sequence data. The trimmed reads were assembled using NOVOPlasty v.4.3.1 (Dierckxsens et al. 2017). Genome annotation was performed by Geneious Prime v.2023.2.1 (Kearse et al. 2012). Manual corrections were made by comparing the sequence with the reference chloroplast genome of Circaea cordata (GenBank accession number: NC_060876.1). The annotated genome sequence has been submitted to GenBank (accession number: OR896387.1). We retrieved the complete chloroplast genomes of 17 Onagraceae species from GenBank. All sequences were initially aligned using MAFFT v.7.149 (Katoh and Standley, 2013). A maximum likelihood (ML) tree was constructed using IQ-TREE-1.6.8 (Nguyen et al. 2015; Wascher and Kubatko, 2021) and the TVM+F + I + R4 model, which was selected using ModelFinder (Kalyaanamoorthy et al. 2017). Using Bowtie2, the raw data is mapped back onto the assembled chloroplast genome sequence (Langdon, 2015). Sorting and depth statistics are performed using samtools (Li et al. 2009). Finally, statistical plotting is conducted with a step length of one bp. CPGview was employed to generate cis-spliced and trans-spliced genes. (Liu et al. 2023).

Results

The chloroplast genome of the subject organism measures 156,391 bp and exhibits the typical quadripartite circular structure, consisting of two inverted repeat regions (IRa and IRb, each 25,069 bp), a large single-copy region (LSC, 87,754 bp), and a small single-copy region (SSC, 18,499 bp) (Figure 2). The coverage depth map of the assembly of the chloroplast genome is shown in Figure S1 and the sequencing depth at the lowest loci is 270x. This genome includes a total of 129 genes, inclusive of 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Each of 13 protein-coding genes (rps16, atpF, rpoC1, petB, petD, rpl16, rpl2(×2), ndhB(×2), ndhA) have one intron, while two protein-coding genes (ycf3 and clpP) have two introns (Figure S2), and the rps12 gene was trans-spliced gene (Figure S3). The total GC content of the chloroplast genome is 37.60%. To unravel the phylogenetic affiliation between F. standishii and its relatives, we conducted a maximum likelihood (ML) analysis and constructed a phylogenetic tree (Figure 3). The resulting analysis demonstrated that F. standishii forms a monophyletic group with the entire Circaea genus. These findings contribute significantly to the phylogenetic and evolutionary understanding of the Fuchsia.

Figure 2.

The chloroplast genome map of F. standishii illustrates genes transcribed in a clockwise direction on the inner circumference and counterclockwise on the outer circumference. The dark gray inner circle represents GC content, while the light gray denotes another content. Various colors distinguish different functional genes. A prominent line on the large circle marks the boundaries of the IRa and IRb, dividing the genome into SSC and LSC regions. This informative and detailed chloroplast genome map was skillfully created using the CPGview tool.

Figure 3.

The phylogenetic tree was reconstructed using the maximum-likelihood (ML) optimality criterion based on 17 chloroplast genome sequences with 1,000 bootstrap replicates. The following sequences were used: Circaea cordata NC 060876.1 (Luo et al. 2021), Circaea repens NC 061018.1 (Luo et al. 2021), Circaea glabrescens NC 061017.1 (Luo et al. 2021), Circaea alpina subsp. caulescens NC 061022.1 (Luo et al. 2021), Circaea alpina subsp. micrantha NC 061010.1 (Luo et al. 2021), F. standishii OR896387.1 (This study), Ludwigia adscendens NC_081012.1 (No reference), Ludwigia hexapetala OR166255.1 (No reference), Epilobium cylindricum NC 061016.1 (Luo et al. 2021), Epilobium tibetanum NC 061026.1 (Luo et al. 2021), Epilobium williamsii NC 061012.1 (Luo et al. 2021), Epilobium amurense subsp. cephalostigma NC 061015.1 (Luo et al. 2021), Epilobium hirsutum NC 058317.1 (No reference), Chamaenerion conspersum NC_061020.1 (No reference), Chamaenerion angustifolium PQ030842.1 (No reference), Oenothera glazioviana EU262890.2 (Massouh et al. 2016), Oenothera biennis EU262889.2 (Massouh et al. 2016).

Discussion and conclusions

F. standishii is highly regarded for its ornamental and medicinal properties, making it a favorite among enthusiasts. In our research, we present the complete chloroplast genome sequence of F. standishii for the first time, revealing a distinctive circular structure that spans 156,391 bp and contains a total of 129 genes. Phylogenetic analysis of 17 species within the Onagraceae family strongly indicates that F. standishii forms a monophyletic group with the entire genus Circaea, a finding consistent with previous molecular studies (Levin et al. 2003). Chloroplast genomes from the genus Circaea and Fuchsia are known to be maternally inherited (Corriveau and Coleman, 1988; Zhang et al. 2003). F. standishii forms a monophyletic group with the entire genus Circaea may be linked to the structural and sequence variations observed in chloroplast genomes within the Onagraceae, which differ between biparentally and maternally inherited genomes. In conclusion, our study not only enhances the genomic information available for F. standishii but also establishes a foundation for understanding genetic diversity, evolution, and phylogeny within the genus Fuchsia.

Funding Statement

This work was supported by the ''Three Districts’' Science and Technology Talent Support Plan of Yunnan Province [KY2313135640, KY2313135540].

Author contributions

Siying Li analyzed the data, created figures, drafted the paper, and approved the final version. Shuang Wang and Min Fan planned the experiments, provided materials and analysis tools, revised the content, and endorsed the final draft. All authors take responsibility for all aspects of the research.

Ethical approval

This research was executed in compliance with the Yunnan Provincial Biodiversity Conservation Regulations, thereby dispensing with the need for ethical or institutional consent.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The data that support the finding of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov, reference number OR896387.1 for F. standishii. The associated BioProject, BioSample, and SRA numbers are PRJNA1055330, SAMN38990677, and SRR27372010, respectively.