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Mitochondrial DNA B Resour
Mitochondrial DNA B Resour
Mitochondrial DNA. Part B, Resources
2380-2359
Taylor & Francis

10.1080/23802359.2024.2392762
2392762
Version of Record
Data Note
Plastome Report
The complete chloroplast genome of Pilea notata C. H. Wright, 1899 (Urticaceae)
N. Zhao et al.
Zhao Ni ab
Liu Linya b
Zhang Shudong b
Zhao Chao a
Gong Xiaojian a
Huang Yacheng b
a Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang, China
b School of Biological Sciences and Technology, Liupanshui Normal University, Liupanshui, China
Supplemental data for this article can be accessed online at https://doi.org/10.1080/23802359.2024.2392762.

CONTACT Xiaojian Gong gongxiaojian1@163.com Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang, China
Yacheng Huang yachenghuang1314@126.com School of Biological Sciences and Technology, Liupanshui Normal University, Liupanshui, China
16 9 2024
2024
16 9 2024
9 9 12371242
26 3 2024
9 8 2024
KnowledgeWorks Global Ltd.16 9 2024
published online in a building issue16 9 2024
© 2024 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
2024
The Author(s)
https://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent.

Abstract

Pilea notata (Pilea notata C. H. Wright_C. H. Wright, 1899) is Pilea Lindl. of Urticaceae, which is a commonly used Miao medicine in Guizhou province. The P. notata chloroplast genome is 150,979 bp, contains a pair of inverted repeats (IRs 25,743bp), and is separated by a large single-copy region (81,446bp) and a small single-copy region (18,047bp). A total of 131 genes, including 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis showed that P. notata, P. verrucosa and P. monilifera united as a single branch, while Pilea cadierei was defined as a sister group of this branch.

Graphical Abstract

Keywords

Chloroplast genome
phylogenetic analysis
Pilea notata
Urticaceae
the Scientific Research and Cultivation Project of Liupanshui Normal University LPSSY2023KJZDPY07 Science and Technology Program of Liupanshui 52020-2022-PT-03 52020-2023-0-2-15 Scientific Research Program of Liupanshui Normal University LPSSYLPY202316 This work was supported by the Scientific Research and Cultivation Project of Liupanshui Normal University [LPSSY2023KJZDPY07], Science and Technology Program of Liupanshui [52020-2022-PT-03, 52020-2023-0-2-15], and Scientific Research Program of Liupanshui Normal University [LPSSYLPY202316].
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pmcIntroduction

Pilea notata (Pilea notata C. H. Wright_ C. H. Wright, 1899) is a perennial juice-rich herb in the Pilea Lindl of Urticaceae (Wang and Li 2005; Ye et al. 2021), it is a dioecious plant, alias water hemp leaf, goat grass, soil licorice, white goat, sweet grass, etc. It is a well-known herbal medicine for the Hmong in Guizhou, and is called ‘SHUI WU DA’ in Guizhou Miao language (Wang and Li 2005), and functions on treating many diseases, such as hot and humid jaundice, red and white belt, shower turbidity, urine blood, children summer heat, malaria mother, indigestion, fall, injury, trauma infection and so on (Ye et al. 2021). Moreover, the extract obtained from P. notata also has antibacterial (Gan, Liang, and Jiang 2014; Gan, Liang, Zhao, et al. 2014; Gan et al. 2015), antioxidant (Gan et al. 2015), anti-inflammatory and analgesic (Sun et al. 2009; Guo 2018) effects. P. notata grows in the forest or ditch side Shady wetlands and its shade resistance ability is relatively strong and due to the deep green color of its leaves, it was rated as excellent color leaf plant resources, and could be used as indoor ornamental plants and urban greening plants (Huang 2007; Xiao 2021). In addition, it also shows good comprehensive purification ability and resistance to formaldehyde with strong carbon monoxide, carbon dioxide, and adsorption of benzene and phenol. Recent studies also suggest that P. notata may be a heavy metal cobalt-rich plant with some evolutionary effects on heavy metal pollution (Zhang 2011; Zhu 2011; Chen et al. 2018; Zhang et al. 2023). The complete chloroplast genome identification was supposed to reveal the systematic relationship between species more comprehensively, and the sequencing, assembly annotation, and phylogenetic analysis would facilitate the study of genetic breeding and cultivation of P. notata. To provide a better understanding and utilization of P. notata, the complete chloroplast genome of this species was firstly analyzed from high-throughput Illumina sequencing reads.

Materials and methods

Plant material, DNA extraction, and sequencing

The P. notata used in this study were collected from the Qianling Mountain, Yunyan District, Guiyang City, Guizhou Province (Figure 1; N26°36′5.01″, E106°41′19.90″, 1100 m) and a specimen was deposited at School of Biological Sciences and Technology, Liupanshui Normal University (collected by Yacheng Huang and yachenghuang1314@126.com.) under the voucher number (SKY2208). The genomic DNA was extracted and sequenced on the Illumina Novoseq 4000 platform as previously described (Zhang et al. 2019). The clean image data files obtained from high throughput sequencing were converted into 1.9 GB of clean reads by base recognition analysis, and the results were stored in FASTQ file format.

Figure 1. Pilea notata used in this study. The image was taken by Ni Zhao at Qianling Mountain, Yunyan District, Guiyang City, Guizhou Province (N26°36′5.01″, E106°41′19.90″). core features: have a creeping stem. Stem fleshy, slender, slightly swollen middle, 25–70 cm high, 2–4 mm thick, glabrous, thin upper part pubescent, densely striped stalactite. Leaves papery, nearly equal in size to the same pair, narrowly ovate, ovate-lanceolate or ovate, 4–11 cm long, 1.5–4.5 cm wide, apex caudate or acuminate, base rounded, thinly broadly cuneate, margin shallowly serrate from lower to apex, rare double serrate, dark green, glossy above, light green below, stalactite striate, 0.5–0.6 mm long, densely covered on both sides, obviously, there are three basal veins, and the two side arcs extend to the upper part and the side veins ring junction, the side veins 8–13 pairs, slightly oblique spread as network veins; petiole slender, 17 cm long, often glabrous, rarely pubescent; stipule large, greenish, oblong, 8–12 mm long, shedding. Flowers dioecious; male flower sequence corymbose raceme, 2–5 cm long, with few branches, corymbose clusters sparsely on the flower branches; the female cyme is short and dense.

Chloroplast genome assembly and annotation

The complete chloroplast genome of P. notata was de novo assembled using the GetOrganelle pipeline (https://github.com/Kinggerm/GetOrganelle) and all genes were annotated using CPGAVAS (Liu et al. 2012). The online tRNAscan-SE Search Service (Lowe and Chan 2016) (http://lowelab.ucsc.edu/tRNAscan-SE/) was used to further confirm tRNA genes. The circular genome map and detailed structure of the chloroplast genome were drawn using the CPGview package (Liu et al. 2023). In addition, the CPGView (Liu et al. 2023) was applied to visualize the intron-containing genes. The SAM file is generated using BWA aligner and converted into a BAM file via SAMtools for evaluating the depth coverage map (Li and Durbin 2009).

Phylogenetic analysis

In this study, the 19 chloroplast genome sequence representatives of the Urticaceae were downloaded, three species of the genus Urticaceae were used as outgroup. The sequence alignment of these 19 chloroplast complete genome sequences was performed using the MAFFT online site (https://mafft.cbrc.jp/alignment/server/) (Katoh and Standley 2013) and analyzed using MEGA 7 (Kumar et al. 2016) to generate a phylogenetic tree.

Results

General features of the chloroplast genome

The complete chloroplast genome sequence of P. notata had been submitted to the GenBank database (accession number: OQ198624.1). The raw reads were deposited in the GenBank Sequence Read Archive (accession no. SRR28371196). The P. notata chloroplast genome was a circular genome with a full-length sequence of 150,979 bp (Figure 2) and a GC content of 37%, consisting of an 81,446 bp large single-copy region (GC content 34%) and a small single-copy region of 18,047 bp (GC content 30%), separated by a pair of identical 25,743 bp inverted repeats (GC content 43%). The complete chloroplast genome included 131 genes, 86 protein-coding genes, 37 tRNA, and eight rRNA. Most of the genes occurred in a single copy, while four rRNA genes (i.e. 4.5S, 5S, 16S, and 23S rRNA), seven tRNA genes (i.e. trnI-CAU, trnL-CAA, trnV-GAC, trnI-GAU, trnA-UGC, trnR-ACG, and trnN-GUU), and six protein-coding genes (i.e. ndhB, rpl2, rpl23, rps7, rps12, and ycf2) occurred in double. Nine protein-coding genes (rps16, atpF, rpoC1, petB, petD, rpl16, rpl2, ndhB, ndhA) were single-intron genes, and two protein-coding genes (ycf3, clpP) had two introns (Supplementary Figure S1 and Figure S2). And the average depth of coverage of individual bases was 227 folds (Supplementary Figure S3).

Figure 2. Circular map of the complete chloroplast genome of Pilea notata generated by CPGview. The map contains six tracks in default. From the center outward, the first track shows the dispersed repeats. The dispersed repeats consist of direct (D) and palindromic (P) repeats, connected with red and green arcs. The second track shows the long tandem repeats as short blue bars. The third track shows the short tandem repeats or microsatellite sequences as short bars with different colors. The small single-copy (SSC), inverted repeat (IRa and IRb), and large single-copy (LSC) regions are shown on the fourth track. The GC content along the genome is plotted on the fifth track. The genes are shown on the sixth track. The optional codon usage bias is displayed in the parenthesis after the gene name. Genes are color-coded by their functional classification. The transcription directions for the inner and outer genes are clockwise and anticlockwise, respectively. The functional classification of the genes is shown in the bottom left corner.

Phylogenetic analysis

Pilea notata is a perennial herb of the Pilea Lindl of Urticaceae. The sequence alignment of these 19 chloroplast complete genome sequences was performed using the MAFFT online site (https://mafft.cbrc.jp/alignment/server/) (Katoh and Standley 2013) and analyzed using MEGA 7 (Kumar et al. 2016) to generate a phylogenetic tree. The phylogenetic analysis showed high bootstrap values for most of the nodes in the phylogenetic tree (Figure 3). Of their phylogenetic position, as shown in the phylogenetic tree, P. notata, Pilea verrucosa, and Pilea monilifera united as a single branch, and P. notata was mostly related to P. verrucosa, with a bootstrap support value of 99%, while Pilea cadierei was defined as a sister group of this branch. This study adds to our understanding of the origin and evolution of P. notata, as well as its genetic links with other species.

Figure 3. The maximum-likelihood (ML) tree of Urticaceae is inferred from the complete chloroplast genome sequences. Phylogenetic tree constructed by maximum-likelihood (ML) analysis based on complete chloroplast genome sequences, including Pilea notata C. H. Wright (OQ198624.1) sequenced in this study. Numbers at nodes correspond to ML bootstrap percentages (1000 replicates). The sequences used for tree construction are as follows: Pilea notata C. H. Wright, 1899 (OQ198624.1; this study), Pilea mollis (MT726018.1; Li et al. 2021), Pilea glauca (MT726015.1; Li et al. 2021), Pilea microphylla (MT876480.1), Pilea thymifolia (MT726017.1), Pilea pumila (MT876481.1), Pilea peploides (MW302174.1), Pilea cavaleriei (MW302172.1), Pilea sinocrassifolia (ON496933.1), Pilea peperomioides (MT726016.1; Li et al. 2021), Pilea plataniflora (MW302175.1), Pilea cavernicola (OP921230.1), Pilea cadierei (MT876479.1), Pilea monilifera (MW302173.1), Pilea verrucosa (MT876482.1), Pilea dolichocarpa (MT465762.1), Urtica angustifolia (MZ145046.1; Liu et al. 2023), Urtica fissa (MZ313540.1; Li et al. 2022), and Urtica lobatifolia (MW246155.1).

Discussion

Compared with nuclear and mitochondrial genomes, chloroplast genomes are highly conserved and widely used in phylogenetic and evolutionary studies. There are over 447 species in this genus, distributed in tropical and subtropical regions of the world, and about 90 species in China (Chen et al. 2018). Phylogenetic analysis was performed to understand the phylogenetic relationship of P. notata with other species. With the development of high-throughput sequencing technology, the chloroplast genome sequence plays an important role in species identification as a super barcode (Li et al. 2021). In this study, phylogenetic relationship based on the complete chloroplast sequences showed high bootstrap support. The phylogenetic tree was in agreement with the previous studies, the results of Li and Yang et al. showed that P. monilifera, P. verrucosa united as a single branch, while P. cadierei was defined as a sister group of this branch, which was consistent with the results of this study (Li et al. 2022; Yang et al. 2022). So this study contributed vital data for Pilea Lindl genus taxonomy. Significantly, it enhanced the understanding of the phylogenetic relationships within the Urticaceae, and facilitated to develop species-specific molecular markers, which was crucial for Urticaceae.

Conclusion

This study is the first report of the complete chloroplast genome sequence of P. notata. In the phylogenetic tree, P. notata, P. verrucosa, and P. monilifera united as a single branch, while P. cadierei was defined as a sister group of this branch. The P. notata cp genome reported in this study provided a useful resource for future in-depth research on the ornamental and ecological value of the development and phylogeny of P. notata. In addition, the results would facilitate the development of species-specific markers to authenticate P. notata herbal drug at the variety level.

Ethical approval

No permission was required to collect P. notata because it is widely distributed in the forest or ditch side Shady wetlands. The plant species was collected from the Qianling Mountain, Yunyan District, Guiyang City, Guizhou Province (GPS coordinates: N26°36′5.01″, E106°41′19.90″).

Supplementary Material

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Author contributions

Ni Zhao, Linya Liu, Shudong Zhang, and Chao Zhao collected the specimen material, conducted the experiment, analyzed the sequence data, and drafted the paper. Xiaojian Gong and Yacheng Huang contributed to the conception and design of this work. All the authors carefully read, revised, and approved the final manuscript to be published.

Disclosure statement

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

Data availability statement

The data that support the findings of this study are openly available in NCBI (https://www.ncbi.nlm.nih.gov/). The complete chloroplast genome of P. notata was deposited in GenBank under the accession OQ198624.1 (https://www.ncbi.nlm.nih.gov/nuccore/OQ198624.1). The associated high throughput sequencing data files are available from the BioProject, Bio-Sample, and SRA submission under the accession numbers PRJNA1087281, SAMN40436524, and SRR28371196, respectively.
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