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. 2021 May 24;6(6):1729–1731. doi: 10.1080/23802359.2021.1930600

The complete chloroplast genome of Pluchea pteropoda Hemsl, a mangrove associate plant

Zhenbiao Liang a, Xuena Xie b, Yongshan Liang b, Haiyong Zhang a, Weiguo Zhao a, Lei Tang a,✉, Zhi Chao b,✉
PMCID: PMC8158197  PMID: 34104753

Abstract

Pluchea pteropoda Hemsl is a mangrove associate plant of Asteraceae with medicinal properties such as anti-inflammation and fever-relieving. Here, our study presented the complete chloroplast (cp) genome of Pluchea pteropoda Hemsl. The cp genome of P. pteropoda was 152,300 bp in length, including a large single copy (LSC) region of 84,127 bp, a small single copy (SSC) region of 18,093 bp and a pair of inverted repeats (IR) regions of 25,040 bp. A total of 111 unique genes were found, comprising 79 protein-coding genes, 28 tRNA genes, and 4 rRNA genes. The GC content of the cp genome was 37.5%. Phylogenetic analysis suggested that P. pteropoda nested in Pluchea clade, which was closely related to Ageratina adenophora and Senecio scandens. The work provides beneficial data for following researches on the genetic variation, species delimitation, phylogeny and classification of Pluchea genus.

Keywords: Chloroplast genome, phylogenomic analysis, Pluchea pteropoda

Pluchea pteropoda Hemsl is a mangrove associates’ plant in the Asteraceae family. The species inhabits land-based sandy beaches, rock crevices or places where high tide can reach, along the coasts of South China and the Indochina peninsula (Linh et al. 2013). Many plants of the genus Pluchea have antioxidant, anti-inflammatory and neuropharmacological effects (Thongpraditchote et al. 1996; Sen et al. 2002; Barros et al. 2006). It has been found that methanol extracts from barks and leaves of P. pteropoda showed certain antibacterial activity (Yuliani et al. 2015). In Vietnam, P. pteropoda has long been used as a folk medicinal herb, often used to treat fevers (Luger et al. 2000). So far, only the cp genome of P. indica has been reported in the genus Pluchea. Herein, we reported the cp genome of P. pteropoda, in order to provide significant information for its further studies.

The materials of P. pteropoda were collected from Xinzhou Town, Danzhou City, Hainan Province, China (109°17′33.43″E, 19°42′11.48″N). The voucher specimen (Chao Zhi 20200405016) was identified by Professor Zhi Chao and deposited in the herbarium of the School of Traditional Chinese Medicine, Southern Medical University (contact Zhi Chao, chaozhi@smu.edu.cn). Total genomic DNA was extracted from 100 mg fresh leaves using cetyltrimethylammonium bromide (CTAB) method (Yang et al. 2014). The Pair-end (PE) sequencing was performed on BGISEQ500 system at the Beijing Genomics Institution (BGI), Shenzhen, China. The cp genome of P. pteropoda was assembled by SPAdes (Bankevich et al. 2012) with Pluchea indica reference (Accession No. NC038194). The Geneious (v20.0.4) (Drummond et al. 2012) and Plastid Genome Annotator (PGA) (Qu et al. 2019) were used for genome annotation. The annotated sequence had been deposited in GenBank (Accession No. MW554520).

The complete cp of P. pteropoda displayed a typical quadripartite structure with 152,300 bp in length, including a large single copy (LSC) region of 84,127 bp, a small single copy (SSC) region of 18,093 bp and a pair of inverted repeats (IR) regions of 25,040 bp. A total of 111 unique genes were annotated, consisting of 79 protein-coding genes, 28 tRNA genes, and 4 rRNA genes. Eighteen genes containing intron were found. Among them, fifteen genes contained one intron and three genes (clpP, rps12, ycf3) contained two introns. The overall GC content of the chloroplast genome was 37.5%.

A phylogenetic analysis was performed based on 14 cp genomes to reveal the phylogenetic position of Pluchea pteropoda. The cp genomes were aligned with MAFFT (Katoh and Standley 2013) and then adjusted manually by Mega7 (Kumar et al. 2016). The GTR + F+G4 was selected as best-fit model of DNA evolution by ModelFinder (Kalyaanamoorthy et al. 2017). Phylogenetic tree was constructed using RAxML version 8.2.10 (Stamatakis 2014) with 1000 bootstrap replicates. Ultimately, the phylogenetic analysis result showed that P. pteropoda nested in Pluchea clade and was closely related to Ageratina adenophora and Senecio scandens (Figure 1).

Figure 1.

Figure 1.

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Maximum-likelihood (ML) tree based on the chloroplast genome of 14 taxa. The numbers at the nodes are bootstrap values from 1000 replicates.

Funding Statement

This work was supported by the Science & Technology Project of Guangdong Provincial Administration of Traditional Chinese Medicine [Grant No. 20201377].

Disclosure statement

The authors declared that they had no conflict of interest.

Data availability statement

The data that support the findings of this study are openly available in GenBank at https://www.ncbi.nlm.nih.gov/genbank/. See supplementary material for reference numbers.

References

  1. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 19:455–477. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Barros IM, Lopes LD, Borges MO, et al. 2006. Anti-inflammatory and anti-nociceptive activities of Pluchea quitoc (DC.) ethanolic extract. J Ethnopharmacol. 106:317–320. [DOI] [PubMed] [Google Scholar]
  3. Drummond A. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28:1647–1649. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS.. 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 14:587–589. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Katoh K, Standley DM.. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30:772–780. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Kumar S, Stecher G, Tamura K.. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 33:1870–1874. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Linh TM, Giang VH, Lien LQ, Van NT, Ban NK, Minh CV.. 2013. Antibacterial activity of some mangrove species in Xuan Thuy national park, Nam Dinh, Vietnam. V J Bio. 35(3):342–343. [Google Scholar]
  8. Luger P, Weber M, Dung NX, Ngoc PH, Tuong DT, Rang DD.. 2000. The crystal structure of Hop-17(21)-en-3β-yl acetate of Pluchea pteropoda Hemsl. from Vietnam. Cryst Res Technol. 35(3):355–362. [Google Scholar]
  9. Qu XJ, Moore MJ, Li DZ, Yi TS.. 2019. PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes. Plant Methods. 15(1):1–12. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Sen T, Dhara AK, Bhattacharjee S, et al. 2002. Antioxidant activity of the methanol fraction of Pluchea indica root extract. Phytother Res. 16:331–335. [DOI] [PubMed] [Google Scholar]
  11. Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30:1312–1313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Thongpraditchote S, Matsumoto K, Temsiririrkkul R, et al. 1996. Neuropharmacological actions of Pluchea indica less root extract in socially isolated mice. Biol Pharm Bull. 19:379. [DOI] [PubMed] [Google Scholar]
  13. Yang JB, Li DZ, Li HT.. 2014. Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs. Mol Ecol Resour. 14:1024–1031. [DOI] [PubMed] [Google Scholar]
  14. Yuliani S, Yanuwiadi B, et al. 2015. Total phenolic and flavonoid contents of pluchea indica less leaves extracts from some altitude habitats. Int J Chemtech Res. 8:1618–1619. [Google Scholar]

Associated Data

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

Data Availability Statement

The data that support the findings of this study are openly available in GenBank at https://www.ncbi.nlm.nih.gov/genbank/. See supplementary material for reference numbers.

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