The complete chloroplast genome of Persicaria pensylvanica (L.) M.Gómez (Polygonaceae): a comparative phylogenetic analysis of the genus Persicaria

Abstract

Persicaria pensylvanica (L.) M. Gómez (=Polygonum pensylvanicum L.), known as Pennsylvania smartweed or pinkweed, is an annual herb adaptable to various soil types in the family Polygonaceae. We present its chloroplast genome of 159,036 bp, with two inverted repeats (31,141 bp each), a large single-copy (83,604 bp), and a small single-copy (13,150 bp). Genome annotation revealed 131 functional genes, including 86 protein-coding, 37 transfer RNA, and eight ribosomal RNA genes. The phylogeny based on maximum-likelihood analysis suggested that P. pensylvanica is most closely related to P. maculosa and provided taxonomic insight into the sectional relationships within the genus Persicaria.

Introduction

Polygonaceae comprises annual or perennial herbs or vines, mainly distributed in the northern temperate and tropical regions. As one of the major groups within the Polygonaceae, the tribe Persicarieae exemplifies ecological adaptations to various habitats (Li et al. 2003; Fan et al. 2013; Sun et al. 2014; Cao et al. 2022). The genus Polygonum s. lat. is taxonomically difficult group due to phenotypic plasticity and polyploidy with various nomenclatural opinions, as species in the genus Persicaria are still described as species in the genus Polygonum. Within the genus Persicaria, previous studies recognized four sections: Cephalophilon, Echinocaulon, Eupersicaria, and Tovara (Kim and Donoghue 2008; Cao et al. 2022;  Zhang et al. 2022).

Persicaria pensylvanica (L.) M. Gómez (1896) is an annual herb widely distributed in North America and distinguished from other species by lenticular achenes, sheathing bracts with entire or ciliate margins, and somewhat glabrous to densely hispid peduncle trichomes (Figure 1; Mitchell and Dean 1978). This species is a common weed often infesting cotton and soybean plantations, resulting in reduced crop yields (Askew and Wilcut 2002). On the other hand, it is valued for its medicinal properties, as it produces two anticancer compounds, vanicosides A and B (Zimmermann and Sneden 1994; Abdi and Dego 2019). Despite its ecological and medicinal values, P. pensylvanica has insufficient genetic information.

Figure 1.

Plant image of Persicaria pensylvanica (L.) M. Gómez. (A) Gross morphology with leaves and flowers. Some core characteristic features of P. pensylvanica were presented; (B) sheathing bracts with ciliate margins and glandular trichomes on peduncles; and (C) a lenticular achene (seed). The original seeds were collected from Southborough, MA, U.S.A., and grown in a growth room at the Catholic University of Korea. Photo credit: Junhyun Hur.

We sequenced and characterized the complete chloroplast genome of P. pensylvanica to enhance genomic data for the genus Persicaria and to provide essential information for tracing evolutionary patterns by presenting a comparative chloroplast genome analysis of 36 species.

Materials and methods

We collected an individual plant with seeds from Southborough, MA, U.S.A. (42°16′29.3ʺN 71°30′23.5ʺW) in July 2023 and cultivated it in a growth room at the Catholic University of Korea (Figure 1). The voucher specimen was deposited in the Catholic University of Korea Herbarium, CUKH_20240010 (contact: Sang-Tae Kim, stkim@catholic.ac.kr). Total DNA was extracted from fresh leaves using the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany) and sequenced by a commercial service (Seeders Inc., Daejeon, South Korea) on an Illumina NovaSeq X platform (San Diego, CA). The de novo assembly was performed using NOVOPlasty v4.3.3 (Dierckxsens et al. 2017), and the genome sequence was confirmed by aligning the raw reads to the assembled genome using BWA-mem v0.7.17 (Li 2013) and SAMtools v1.13 (Li et al. 2009). The genome annotation and tRNA prediction were carried out using the programs Chloe v0.1.0 and tRNAscan-SE2.0, respectively, implemented in GeSeq (Tillich et al. 2017; Chan et al. 2021). All annotations were manually adjusted based on those from reference species, P. lapathifolia (GenBank No. ON229579), using Geneious Prime v2025.1.1. A circular genome map was generated using OGDRAW v1.3.1 (Greiner et al. 2019), and cis- and trans-splicing genes were identified using CPGView (Liu et al. 2023).

The complete chloroplast genomes from 35 species, representing 33 individual species belonging to the genus Persicaria and two outgroup species to the genus Bistorta, one of the most closely related groups, were obtained from GenBank (Table S1). Multiple sequence alignment with 36 genomes including P. pensylvanica was carried out using MAFFT v7.450 (Katoh and Standley 2013). After alignment, poorly aligned reads were removed using Trimal v1.5 (Capella-Gutiérrez et al. 2009). To examine structural variants at junction sites within the inverted repeat (IR) region, we employed IRscope (https://irscope.shinyapps.io/irapp; Amiryousefi et al. 2018), which compared and visualized junction sites across nine Eupersicaria species. To identify mutation hotspots, we calculated nucleotide diversity using DnaSP v6.12.03 (Rozas et al. 2017) with a sliding-window analysis (window length: 600 bp, step size: 200 bp) across 34 Persicaria species (Cao et al. 2022). The maximum-likelihood tree was constructed in IQ-TREE2 (Minh et al. 2020) using the TVM +F + I + G4 genetic model and 1000 ultrafast bootstrap replicates for branch support (Hoang et al. 2018).

Results

The complete chloroplast genome of P. pensylvanica is 159,036 bp, which includes a large single-copy (LSC) region (83,604 bp), a small single-copy (SSC) region (13,150 bp), and a pair of IRs regions (31,141 bp) (Figure 2). The total GC content in the P. pensylvanica chloroplast genome is 38.2%. The GC contents of LSC, SSC, and IR in the P. pensylvanica chloroplast genome are 36.6%, 33.2%, and 41.5%, respectively. The average sequencing depth across the assembled genome was 2345.141 with a range from 592 to 4249 (Fig. S1).

Figure 2.

The circular chloroplast genome map of Persicaria pensylvanica. The gray arrows showed the transcriptional direction of genes. Different colors represent genes with other functions. The inner circle’s gray portion indicates the chloroplast genome’s GC content.

The complete chloroplast genome of P. pensylvanica harbors a total of 131 genes, encompassing 86 protein-coding, 37 transfer RNA (tRNA), and eight ribosomal RNA (rRNA) genes (Table S2). Nineteen genes are duplicated in the IRs, while one gene (trnM-CAU) is duplicated in the LSC region. For the gene structure, 16 genes have a single intron, whereas three genes have two introns (Table S2). We identified 13 cis-splicing genes (Fig. S2) and a single trans-splicing gene (rps12) (Fig. S3). Exon 1 of the three exons coding for rps12 is in the LSC, while the remaining exons are in the IRB region (Figure 2).

The phylogenetic tree revealed that P. pensylvanica formed a clade with P. maculosa, P. lapathifolia, and P. lapathifolia var. salicifolia with 100% bootstrap support (Figure 3). The sectional relationship with 34 species in the genus Persicaria is consistent with previous reports (Kim and Donoghue 2008), as P. pensylvanica was placed in Eupersicaria.

Figure 3.

Phylogenetic relationships of 36 species from Polygonaceae (34 from the genus Persicaria and two from the genus Bistorta as outgroups) based on their complete chloroplast genome sequences. The genome of the species identified in bold is presented in this study. The phylogenetic tree was constructed using the maximum-likelihood (ML) method with 1000 bootstrap replicates. The bootstrap values were labeled at each branch node. The NCBI numbers for published sequences are summarized in Table S1.

The genome structures of nine species in the sect. Eupersicaria were highly conserved (Fig. S4). Scanning nucleotide diversity across the 34 aligned chloroplast genomes indicated that five regions (rps16–trnQ-UUG–psbK, ndhC–trnV-UAC, psaJ–rpl33, rps32–trnL-UAG–ccsA, and ndhl–ndhA–ndhH) were highly variable (Fig. S5).

Discussion and conclusions

Most species in the tribe Persicarieae are known as weedy plants and are universally distributed, but some are still restricted to local distributions. P. pensylvanica is generally found only in North America as an obnoxious weed and is known as an octaploid species from multiple hybridization events (Kim et al. 2008; Kim and Donoghue 2008). Our phylogenetic analysis showed that P. pensylvanica is strongly grouped with P. lapathifolia, one of the possible diploid parents, and P. maculosa, a tetraploid species originating from the hybridization between P. lapathifolia and P. foliosa (Kim et al. 2008). Our results are generally consistent with previous analyses but suggest the need for multiple sampling of the maternally inherited organelle genomes to clearly elucidate the reticulation history of this group (Figure 3).

We identified five highly variable regions in the genus Persicaria across 34 chloroplast whole genomes. The intergenic region between psaJ and rpl33, one of five regions that we found in this study, was consistent with the previous report (Cao et al. 2022) and these regions will be useful markers for further specific level of investigation in the tribe Persicarieae.

Funding Statement

This study was supported by the National Research Foundation of Korea (NRF) Grant funded by the Korean Government (MSIT) (No. 2022R1A2C1011598); National Institute of Biological Resources under Grant No. NIBR202405202.

Ethical approval

This study did not involve any ethical conflicts, the protection of species or endangered organisms, and the sampling adhered to local laws and regulations.

Disclosure statement

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

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI (https://www.ncbi.nlm.nih.gov/) under the accession number PX373531 (P. pensylvanica). The associated BioProject, SRA, and BioSample numbers are PRJNA1358763, SRP643204, and SAMN53126069, respectively.