Skip to main content
NCBI home page
Mitochondrial DNA. Part B, Resources logoLink to Mitochondrial DNA. Part B, Resources
. 2025 Feb 2;10(3):162–166. doi: 10.1080/23802359.2025.2449686

The complete chloroplast genome and phylogenetic analysis of Emilia prenanthoidea (Asteraceae)

Yacheng Huang a, Ni Zhao b, Min Liang a, Xuying Wang a, Shudong Zhang a, Chao Zhao b,✉, Linya Liu a,✉
PMCID: PMC11792124  PMID: 39912104

Abstract

Emilia prenanthoidea (Emilia prenanthoidea DC. Prodr. (DC.), 1838) belongs to the Asteraceae family and is a popular Miao medicinal plant in Guizhou, China. It has anti-inflammatory and antitumor properties. It is often used as a medication for healing injury, clearing heat and detoxifying, boosting blood circulation and eliminating blood stasis, and lowering inflammation and diuresis. This is the first reported study on the complete chloroplast genome of E. prenanthoidea. The E. prenanthoidea chloroplast genome is 151, 406 bp long, contains a pair of inverted repeats (IRs 24,705 bp), and is separated into a large single-copy (84,010 bp) and a short single-copy (17,986 bp) region. One hundred thirty genes were predicted, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Nine protein-coding genes (rps16, rpoC1, atpF, petB, petD, rpl16, rpl2, ndhB, ndhA) had a single intron, two protein-coding genes (ycf3, clpP) had two, and the remainder had none. The phylogenetic analysis found Emilia prenanthoidea and Emilia sonchifolia clustered on a single branch, with Pericallis hybrida as its sister group. This study enhances our understanding of the evolutionary relationships within the Asteraceae family and provides valuable insights for developing germplasm-specific molecular markers.

Keywords: Asteraceae, Emilia prenanthoidea, chloroplast genome, phylogenetic analysis

Introduction

Emilia prenanthoidea (Emilia prenanthoidea DC. Prodr. (DC.), 1838), often called fine red dorsal leaf or earpick herb, is a member of the Asteraceae family (Chen 1999). Originating in Guizhou, China, this plant has a long history of medicinal usage and can be used therapeutically (Zhang et al. 2012). It grows on hillsides, slopes, sparse or dense woodlands, and moist areas, thriving at 550 to 1420 meters. It is primarily found in Guizhou (Duyun, Du’an, Liuping, Leishan, Kaili, Tianzhu, Liping, Xingren, Zhenfeng), Zhejiang, Yunnan, Guangdong, Guangxi, Sichuan, and Fujian. According to Huang et al. (2009), E. prenanthoidea is employed in traditional Chinese medicine for its bitter and cooling properties. It aids detoxification, promotes blood circulation, resolves blood stasis, reduces inflammation, and supports diuresis. Modern research has highlighted its anti-inflammatory and antitumor properties (Jiang 2017; Zhao 2020; Zhao et al. 2020; Li 2022). Current research primarily focuses on its chemical composition, quality control, and pharmacological effects (Zhao et al. 2010; Jiang 2017; Jiang et al. 2017; Zhao et al. 2017; Li 2022). However, little research has been conducted on its genome, particularly the chloroplast. Thus, we used high-throughput Illumina sequencing to analyze the chloroplast genome comprehensively. This study aimed to improve knowledge of E. prenanthoidea by offering comprehensive genomic data that can support systematic studies, genetic breeding, and further development of this species.

Materials and methods

Plant material, DNA extraction, and sequencing

The Emilia prenanthoidea used in this study were collected from Longli Township, Jinping County, Qiandongnan Miao and Dong Autonomous Prefecture, Guizhou Province (Figure 1) (N26°25″ 31. 68″ E109°06′ 03. 00″). A specimen was deposited at the School of Biological Sciences and Technology, Liupanshui Normal University (collected by Yacheng Huang and yachenghuang1314@126.com) under the voucher number SKY2209. The genomic DNA was extracted and sequenced using the Illumina Novaseq 4000 platform, as previously described (Zhang et al. 2019). The raw data from high-throughput sequencing was processed, yielding 2.2GB of clean reads through base recognition analysis, which was saved in FASTQ format.

Figure 1.

Figure 1.

Open in a new tab

A Representative image of Emilia prenanthoidea. Ni Zhao captured the photograph in Longli Township, Jinping County, Qiandongnan Miao and Dong Autonomous Prefecture, Guizhou Province (N26°25′31. 68", E109°06′03. 00"). key characteristics: the stems are erect or slightly inclined, up to 90 cm tall, and either glabrous or sparsely hairy. The basal leaves are obovate or obovate-oblong, the Middle stem leaves are oblong or linear-oblong, and the upper leaves are small and linear-lanceolate. The inflorescences are loosely corymbose at the stem tips, with thin peduncles. The involucres are cylindrical or narrowly bell-shaped, while the florets feature crimson or purplish-red corollas with toothed margins and lanceolate lobes. The achenes are cylindrical and glabrous, with five ribs and numerous fine white pappus hairs. The fruiting period extends from May to October.

Chloroplast genome assembly and annotation

Emilia prenanthoidea’s chloroplast genome was de novo assembled using the GetOrganelle pipeline (https://github.com/Kinggerm/GetOrganelle) and the 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/) confirmed the tRNA genes. In addition, we applied CPGView (Liu et al. 2023) to structures to visualize the intron-containing genes. The BWA aligner generated the SAM file, which was then converted to a BAM file by SAMtools to evaluate the depth coverage map (Li and Durbin 2009).

Phylogenetic analysis

The phylogenetic tree in the present study was constructed using 27 chloroplast genomes, 23 chloroplast genome sequence representatives of the Asteraceae family, and four Calyceraceae species as outgroups. To determine E. prenanthoidea’s phylogenetic position, a phylogenomic analysis was performed using the maximum likelihood (ML) and Bayesian inference (BI) methods (Ronquist et al. 2012; Stamatakis 2014). OrthoFinder version 2.2.7 was used for phylogenetic analysis (Amaral et al. 2022), whereas ggtree version 1.14.6 was utilized for mapping using ML and 1000 bootstrap replicates (Yu 2020). BI was performed using MRBAYES 3.2.0 (Zhao et al. 2017) under the GTR model, and the resultant tree was visualized in Figtree (Rambaut 2007). The 27 complete chloroplast genome sequences were aligned using MAFFT version 7.0 (Katoh and Standley 2013).

Results

General features of the chloroplast genome

The complete chloroplast genome sequence of E. prenanthoidea was submitted to the GenBank database (accession number: PP646496.1). The raw reads were deposited in the GenBank Sequence Read Archive (accession number: SRR29279324). The sequencing depth and coverage are good, with an average sequencing depth of 281X. There are no uncovered regions, making the assembly results highly reliable (Figure S3). The E. prenanthoidea chloroplast genome was a circular genome with a full-length sequence of 151,406 bp (Figure 2) and a GC content of 37%. It consisted of an 84,010 bp large single-copy region (GC content 35%) and a small single-copy region of 17,986 bp (GC content 30%), separated by a pair of identical 24,705 bp inverted repeats (GC content 43%). The chloroplast genome had 130 genes, 85 protein-coding genes, 37 tRNA, and eight rRNA. Most of the genes were found in single copies, whereas four rRNA genes (4.5S, 5S, 16S, 23S rRNA), seven tRNA genes (trnI-CAU, trnL-CAA, trnV-GAC, trnI-GAU, trnA-UGC, trnR-ACG, trnN-GUU), and six protein-coding genes (i.e. rps12, rpl2, rpl23, ycf2, ndhB, rps7) occurred in double copies. Nine protein-coding genes (rps16, rpoC1, atpF, petB, petD, rpl16, rpl2, ndhB, ndhA) contained a single intron, whereas two (ycf3, clpP) had two introns (Figures S1 and S2). The ML and BI analyses generated the same tree topology. The chloroplast genome phylogenetic tree (Figure 3) showed that E. prenanthoidea is closely related to Emilia sonchifolia, Pericallis hybrida, and Dendrosenecio killimanjari.

Figure 2.

Figure 2.

Open in a new tab

CPGview-generated circular map of Emilia prenanthoidea’s chloroplast genome, featuring six default tracks. The first track shows dispersed repeats from the center outward, consisting of direct (D) and palindromic (P) repeats, represented by red and green arcs, respectively. The second track depicts long tandem repeats as short blue bars, while the third shows short tandem repeats or microsatellites as colored bars of varying lengths. The fourth track outlines the genome’s structural sections, including the small single-copy (SSC), inverted repeats (IRa, IRb), and large single-copy (LSC) regions. The fifth track illustrates the genome’s GC content, while the sixth track displays the genes color-coded according to their functional classification. The codon usage bias, if any, is shown in parentheses after the gene names. Genes transcribed clockwise are on the inner side, whereas those transcribed anticlockwise are on the outer side. The lower left corner displays a legend for the functional classification of the genes.

Figure 3.

Figure 3.

Open in a new tab

The maximum-likelihood (ML) tree of Asteraceae inferred from the complete chloroplast genome sequences. The phylogenetic tree was constructed by maximum-likelihood (ML) analysis based on complete chloroplast genome sequences, including Emilia prenanthoidea (PP646496.1). Numbers at nodes represent ML bootstrap percentages (1000 replicates). The sequences utilized to construct the phylogenetic tree include: Emilia prenanthoidea (PP646496; from this study), Emilia sonchifolia (MZ677242 (Siu et al. 2023)), Pericallis hybrida (KT285537 (Wang et al. 2019)), Dendrosenecio kilimanjari (MG560045), Jacobaea vulgaris (HQ234669), Ligularia mongolica (MF539932), Ligularia jaluensis (MF539931), Ligularia fischeri (KT988070 (Lee et al. 2016)), Erigeron annuus (OL350834 (Zhou et al. 2022)), Conyza bonariensis (MF276802 (Hereward et al. 2017)), Solidago decurrens (MT991010), Oritrophium peruvianum (KX063861), Ambrosia trifida (MG029118), Ambrosia artemisiifolia (MF362689), Helianthus debilis (KU312928), Eclipta prostrata (KU361242 (Park et al. 2016)), Eclipta alba (MF993496), Mikania micrantha (KX154571), pluchea indica (MG452144), Taraxacum officinale (KU361241 (Kim et al. 2016)), Taraxacum mongolicum (KU736961 (Kim et al. 2016)), Saussurea japonica (MK953481), Cirsium arvense (KY562583), Gamocarpha alpina (OM892822), Gamocarpha macrocephala (PP502768), Acicarpha tribuloides (OR711909), and Boopis anthemoides (OM892821).

Discussion

This study assembled and annotated the complete chloroplast genome of Emilia prenanthoidea for the first time. The genomic structure of E. prenanthoidea is comparable to that of most other angiosperms, with a pair of inverted repeats (IRs), a small single-copy (SSC), and a large single-copy (LSC) region. Phylogenetic analysis resulted in the creation of the chloroplast genome phylogenetic tree (Figure 3). It demonstrated that E. prenanthoidea is closely related to Emilia sonchifolia, Pericallis hybrida, and Dendrosenecio kilimanjari. This is consistent with previous studies (Kim et al. 2016; Wang et al. 2019; Siu et al. 2023), which supplied critical data for Asteraceae classification. It significantly increased our understanding of the evolutionary relationships within the Asteraceae and Calyceraceae families and the development of species-specific molecular markers, both crucial for the Asteraceae and Calyceraceae families.

Conclusion

This is the first report on the complete chloroplast genome sequence of Emilia prenanthoidea. E. prenanthoidea and E. sonchifolia formed a single branch in the phylogenetic tree, with Pericallis hybrida as its sister group. The E. prenanthoidea chloroplast genome presented in the present study is vital for future in-depth research into the ornamental and ecological significance of E. prenanthoidea development and phylogeny. Furthermore, the results will contribute toward developing species-specific markers to validate E. prenanthoidea herbal medicine at the variety level.

Supplementary Material

Supplementary figure.docx
TMDN_A_2449686_SM5748.docx (1.7MB, docx)
GraphicalAbstractS2.png
TMDN_A_2449686_SM5747.png (184.4KB, png)
GraphicalAbstractS3.png
TMDN_A_2449686_SM5746.png (127.2KB, png)
GraphicalAbstractS1.png
TMDN_A_2449686_SM5745.png (245.4KB, png)

Funding Statement

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 The College Student Innovation Training Programs [S202310977030]

Ethical approval

No permission was required to collect Emilia prenanthoidea because it is widely distributed in wild areas, roadsides, open forests or wet parts of forests.The plant species was collected from the Longli township, Jinping county, Qiandongnan Miao and Dong Autonomous Prefecture, Guizhou Province (N26°25′31. 68″, E109°06′03. 00″).

Authors’ contributions

L.Y. L and C. Z designed the experiment and obtained the funding. N. Z and M. L performed laboratory work. Y.C. H, S.D. Z and X.Y. W performed bioinformatics analyses. Y.C. H, N. Z and C. Z performed wrote and revised the manuscript, all authors agree to be accountable for all aspects of the work All authors have read and agreed to the published version of the manuscript.

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 Emilia prenanthoidea was deposited in GenBank under the accession PP646496.1 (https://www.ncbi.nlm.nih.gov/nuccore/PP646496.1). The associated high throughput sequencing data files are available from the BioProject, Bio-Sample, and SRA submission under the accession numbers PRJNA1119234, SAMN41643422, and SRR29279324, respectively.

References

  1. Amaral DT, Romeiro-Brito M, Bonatelli IAS.. 2022. Exploring phylogenetic relationships and divergence times of bioluminescent species using genomic and transcriptomic data. Methods Mol Biol. 2525:409–423. doi: 10.1007/978-1-0716-2473-9_32. [DOI] [PubMed] [Google Scholar]
  2. Chen YL. 1999. Flora of China. Science Press. 77th volume, Part 1, Angiospermophyta Dicotyledonae, Asteraceae (V) Seneciangeae Calendulinae. [Google Scholar]
  3. Hereward JP, Werth JA, Thornby DF, Keenan M, Chauhan BS, Walter GH.. 2017. Complete chloroplast genome of glyphosate resistant Conyza bonariensis (L.) Cronquist from Australia. Mitochondrial DNA Part B Resour. 2(2):444–445. doi: 10.1080/23802359.2017.1357441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Huang XC, Huang XZ, Huang ZC, Liu XQ.. 2009. Primary color Atlas of Chinese herbal medicine in Orthopedics and Traumatology. Guangxi Science and Technology Press. [Google Scholar]
  5. Jiang ZM. 2017. Study on the relationship between quality control and anti-inflammatory spectrum effect of Emilia prenanthoidea. Guizhou Normal University. [Google Scholar]
  6. Jiang ZM, Gong XJ, Zhou X.. 2017. Ational medicine determination the content of quercetin in Emilia prenanthoidea. Chin J Expriment For Chin Med. 23(4):5. [Google Scholar]
  7. Katoh K, Standley DM.. 2013. MAFFT multiple sequence alignment Software Version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780. doi: 10.1093/molbev/mst010. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Kim JK, Park JY, Lee YS, Lee HO, Park HS, Lee SC, Kang JH, Lee TJ, Sung SH, Yang TJ.. 2016. The complete chloroplast genome sequence of the Taraxacum officinale F.H.Wigg (Asteraceae). Mitochondrial DNA Part B Resour. 1(1):228–229. doi: 10.1080/23802359.2016.1155425. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Kim JK, Park JY, Lee YS, Woo SM, Park HS, Lee SC, Kang JH, Lee TJ, Sung SH, Yang TJ.. 2016. The complete chloroplast genomes of two Taraxacum species, T. platycarpum Dahlst. and T. mongolicum Hand.-Mazz. (Asteraceae). Mitochondrial DNA Part B Resour. 1(1):412–413. doi: 10.1080/23802359.2016.1176881. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Lee J, Lee H, Lee SC, Sung SH, Kang JH, Lee TJ, Yang TJ.. 2016. The complete chloroplast genome sequence of Ligularia fischeri (Ledeb.) Turcz. (Asteraceae). Mitochondrial DNA Part B Resour. 1(1):4–5. doi: 10.1080/23802359.2015.1137793. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Li H, Durbin R.. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 25(14):1754–1760. doi: 10.1093/bioinformatics/btp324. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Li L. 2022. Study on the mechanism of inhibition of human gastric cancer MKN-45 cells by alcohol extract of Emilia prenanthoides DC. Guizhou Normal University. [Google Scholar]
  13. Liu C, Shi LC, Zhu YJ, Chen HM, Zhang JH, Lin XH, Guan XJ.. 2012. CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. BMC Genomics. 13(1):715–715. doi: 10.1186/1471-2164-13-715. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Liu SY, Ni Y, Li JL, Zhang XY, Yang HY, Chen HM, Liu C.. 2023. CPGView: a package for visualizing detailed chloroplast genome structures. Mol Ecol Resour. 23(3):694–704. doi: 10.1111/1755-0998.13729. [DOI] [PubMed] [Google Scholar]
  15. Lowe TM, Chan PP.. 2016. tRNAscan-SE on-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res. 44(W1):W54–57. doi: 10.1093/nar/gkw413. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Park JY, Lee YS, Kim JK, Lee HO, Park HS, Lee SC, Kang JH, Lee TJ, Sung SH, Yang TJ.. 2016. The complete chloroplast genome of Eclipta prostrata L. (Asteraceae). Mitochondrial DNA Part B Resour. 1(1):414–415. doi: 10.1080/23802359.2016.1176882. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP.. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 61(3):539–542. doi: 10.1093/sysbio/sys029. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Siu TY, Kong BL, Wong KH, Wu HY, But GWC, Shaw PC, Lau DTW.. 2023. Characterization and phylogenetic analysis of the complete chloroplast genome of Emilia sonchifolia (L.) DC. Mitochondrial DNA B Resour. 8(1):20–22. doi: 10.1080/23802359.2022.2055980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30(9):1312–1313. doi: 10.1093/bioinformatics/btu033. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Wang B, Li M, Yuan YJ.. 2019. The complete chloroplast genome of Pericallis hybrida (Asteridae). Mitochondrial DNA Part B Resour. 4(1):233–234. doi: 10.1080/23802359.2018.1542999. [DOI] [Google Scholar]
  21. Yu G. 2020. Using ggtree to visualize data on tree-like structures. Curr Protoc Bioinformatics. 69(1):e96. doi: 10.1002/cpbi.96. [DOI] [PubMed] [Google Scholar]
  22. Zhang SD, Zhang C, Ling LZ.. 2019. The complete chloroplast genome of Rosa berberifolia. Mitochondrial DNA Part B Resour. 4(1):1741–1742. doi: 10.1080/23802359.2019.1610093. [DOI] [Google Scholar]
  23. Zhang SZ, Zhang ZY, Xing FW, Liao WB, Chen XM.. 2012. Flora of Shenzhen. China Forestry Publishing House. Fairylake Botanical Garden, Shenzhen. Chin Acad Sci. 3:612–613. [Google Scholar]
  24. Zhao C, Jiang ZM, Gong XJ, Zhou X.. 2017. Identification of national medicinal materials with Emilia prenanthoidea by TLC. J Guizhou Normal Univ. Natural Sci Edi. 35(4):100–104. doi: 10.16614/j.cnki.issn1004-5570.2017.04.014. [DOI] [Google Scholar]
  25. Zhao C, Zhou X, Gong XJ, Zn Y, Chen HG.. 2010. Analysis of volatile Oil in Emilia Prenanthoidea by SPME/GC/MS. Chin J Spectr Lab. 27(4):1601–1603. doi: 10.3969/j.issn.1004-8138.2010.04.090. [DOI] [Google Scholar]
  26. Zhao DN. 2020. Study on pharmacokinetics and anti-chronic pelvic inflammatory disease pharmacodynamics of ethanol extract of Emilia prenanthoidea in rats. Guizhou Normal University. [Google Scholar]
  27. Zhao DN, He GX, Zhou X.. 2020. Pharmacodynamics of Emilia prenanthoides DC. alcohol extract in rats with chronic pelvic inflammatory disease. Natural Prod Res Develop. 32:1761–1766. doi: 10.16333/j.1-6880.2020.10.018 [DOI] [Google Scholar]
  28. Zhou JY, Li JJ, Peng SB, An XM.. 2022. Characterization of the complete chloroplast genome of the invasive plant Erigeron annuus (L.) Pers. (Asterales: Asteraceae). Mitochondrial DNA Part B Resour. 7(1):188–190. doi: 10.1080/23802359.2021.2018946. [DOI] [PMC free article] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Supplementary figure.docx
TMDN_A_2449686_SM5748.docx (1.7MB, docx)
GraphicalAbstractS2.png
TMDN_A_2449686_SM5747.png (184.4KB, png)
GraphicalAbstractS3.png
TMDN_A_2449686_SM5746.png (127.2KB, png)
GraphicalAbstractS1.png
TMDN_A_2449686_SM5745.png (245.4KB, png)

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 Emilia prenanthoidea was deposited in GenBank under the accession PP646496.1 (https://www.ncbi.nlm.nih.gov/nuccore/PP646496.1). The associated high throughput sequencing data files are available from the BioProject, Bio-Sample, and SRA submission under the accession numbers PRJNA1119234, SAMN41643422, and SRR29279324, respectively.

Articles from Mitochondrial DNA. Part B, Resources are provided here courtesy of Taylor & Francis

RESOURCES