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Genome Note

The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae)

[version 1; peer review: 1 approved with reservations]
Hoang Danh Nguyen1, Thi Diem Quynh Nguyen2, Minh Thiet Vu1, Hoang Dang Khoa Do
https://orcid.org/0000-0002-7970-9359
1
Hoang Danh Nguyen1, Thi Diem Quynh Nguyen2, Minh Thiet Vu1, Hoang Dang Khoa Do
https://orcid.org/0000-0002-7970-9359
1
PUBLISHED 31 Aug 2023
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This article is included in the Genomics and Genetics gateway.

Abstract

Phyllanthus acidus (L.) Skeels (Phyllanthaceae) is a potential medicinal plant recognized for its sour and tart tasted fruits. In this study, the chloroplast genome of P. acidus was sequenced, assembled, and characterized. The chloroplast genome size was 156,331 bp and the overall GC content was 36.9%. Additionally, the chloroplast genome had a quadripartite structure consisting of a large single copy (LSC; 85,807 bp in length; GC content: 34.6%), a small single copy (SSC; 19,262 bp in length; GC content: 30.6%), and two inverted repeat regions (IR; 25,631 bp in length; GC content: 43.1%). A total of 113 unique genes were annotated in the chloroplast genome, comprising 79 protein-coding genes, 30 tRNAs, and four rRNAs. The phylogenetic analysis based on 79 protein-coding genes revealed the paraphyly of the Phyllanthus genus. These findings provided additional genetic information for further research on P. acidus and the cp genome in the Phyllanthaceae family.

Keywords

Malpighiales, Phyllanthaceae, phylogenetic relationships, plastome, star gooseberry

Corresponding author: Hoang Dang Khoa Do
Competing interests: No competing interests were disclosed.
Grant information: This research is funded by Nguyen Tat Thanh University, Ho Chi Minh city, Vietnam to Nguyen Hoang Danh.
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Copyright:  © 2023 Nguyen HD et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
How to cite: Nguyen HD, Nguyen TDQ, Vu MT and Do HDK. The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 1; peer review: 1 approved with reservations]. F1000Research 2023, 12:1059 (https://doi.org/10.12688/f1000research.140134.1) First published: 31 Aug 2023, 12:1059 (https://doi.org/10.12688/f1000research.140134.1) Latest published: 31 Aug 2023, 12:1059 (https://doi.org/10.12688/f1000research.140134.1)

Introduction

Phyllanthus acidus (L.) Skeels, also known as star gooseberry, belongs to the Phyllanthaceae family and commonly distributes in the wet tropical regions, including South/ Southeast Asia, Central Africa, the Caribbean region, and Central/South America (POWO 2022). P. acidus has been traditionally used to treat various diseases, including inflammation, gastrointestinal problems, rheumatism, bronchitis, Alzheimer, and hepatic diseases (Jain et al. 2011; Chakraborty et al. 2012; Srirama et al. 2012; Uddin et al. 2016). The leaves and roots of P. acidus also possess antidotal properties against viper venom (Jayvir 1998). Moreover, P. acidus exhibited the potential for alleviating hypertension (Leeya et al. 2010).

The chloroplast (cp) genome is extremely effective at inferring phylogeny since it is predominantly maternally inherited, has a conversed structure and gene content, and has a slow mutation frequency (Palmer et al. 1988). Additionally, the cp genomes provide essential data for conducting studies on population genetics, molecular identification, and genetic engineering (Powell et al. 1995; Daniell et al. 2016; Cao et al. 2022). In the current study, the characteristics of the P. acidus cp genome and its phylogenetic implication were explored to gain more information about the evolution and phylogenetic relationships within the Phyllanthaceae family and closely related taxa.

Methods

Sample collection

The P. acidus sample (young branches with leaves) was collected from Can Tho, Viet Nam (9°56′55.7″N, 105°30′16.0″E) and labeled with voucher number: NTT-2022.12.CR (contact person: Dr. Do Hoang Dang Khoa, dhdkhoa@ntt.edu.vn). It was deposited at the NTT Hi-tech Institute, Nguyen Tat Thanh University. No specific permit was required to collect and study the species in Vietnam. The leaf sample was dried with silica gel and stored in a -80°C freezer until conducting DNA extraction.

Data collection and analysis

The total genomic DNA extraction from the dried leaves was carried out using the Cetyltrimethylammonium bromide (CTAB) protocol (Doyle & Doyle 1987). The quality of genomic DNA samples was checked using gel electrophoresis and NanoDrop OneC Spectrophotometer. The DNA samples that showed a clear band on agarose gel and had a 260/280 ratio between 1,8-2 and a 260/230 ratio between 2.0-2.2 were selected for conducting the next-generation sequencing step. Subsequently, the library was prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, USA). The library was sequenced using Illumina Miseq platform to generate paired-end reads of 150 bp (Ktest Science Co. Ltd., Vietnam). The raw reads were qualified and filtered low-quality reads (Q score < 20 and length < 100 bp) and reads containing primers or adapters using FastQC v0.12.1 and Trimmomatic v0.39 programs (Andrews 2010; Bolger et al. 2014). For the assembly of cp genome, the NOVOPlasty v4.3.1 program was used (Dierckxsens et al. 2017). Preliminary annotation was conducted by Geseq with default parameters (Tillich et al. 2017). The complete annotation genome was illustrated using OrganellarGenomeDRAW v1.3.1 (Greiner et al. 2019). All 79 protein-coding regions in the cp genomes of P. acidus and 16 related taxa from the Phyllanthaceae were extracted and aligned for phylogenetic analysis using MUSCLE v5 program (Edgar 2004). The chloroplast genome of Acalypha hispida (Euphorbiaceae; Genbank accession no. NC_070339) was selected as an outgroup. A maximum likelihood phylogenetic tree was reconstructed using IQTREE with 1000 bootstrap replicates and GTRGAMMA substitution model (Nguyen et al. 2015).

Results

Approximately 349.8 MB of clean reads were obtained and used for completing the cp genome of P. acidus. The assembly process utilized 1,166,034 paired-end reads, resulting in an average coverage depth of 2,234.3X (Nguyen, Nguyen, Do, and Vu, 2023; Nguyen, Do, and Vu, 2023) The quadripartite cp genome of P. acidus (GenBank accession number OR050568) had a length of 156,331 bp and consisted of an LSC region of 85,807 bp, a SSC region of 19,262 bp, and a pair of IR regions of 25,631 bp (Figure 1). The overall GC content of the genome was 36.9%, and the GC content of the LSC, SSC, and IR regions were 34.6%, 30.6%, and 43.1%, respectively. The cp genome of P. acidus contained a total of 130 genes, including 85 protein-coding regions, 37 tRNA genes, and eight rRNA genes (Table 1). Among 85 protein-coding genes, 17 genes contained intron, of which ycf3 and clpP contained two introns. In IR regions, a total of 19 genes were duplicated, including eight protein-coding regions (i.e., rps19, rpl2, rpl23, ycf1, ycf2, ndhB, rps12, and rps7), seven tRNAs (trnI_CAU, trnL_CAA, trnV_GAC, trnI_GAU, trnA_UGC, trnR_ACG, and trnN_GUU), and four rRNAs (rrn16S, rrn23S, rrn4.5S, and rrn5S). Notably, rps19 and ycf1 duplications were incomplete. The phylogenetic analysis revealed a paraphyly of Phyllanthus species, in which Breynia futicosa and Glochidion chodoense formed a clade with Phyllanthus amarus (Figure 2). Therefore, more genomic data and samples of Phyllanthaceae species are required for further phylogenetic studies.

6528a77b-4b69-422a-8acd-875b1e0bcbd7_figure1.gif

Figure 1. Map of the cp genome of Phyllanthus acidus.

Genes located inside the circle are transcribed in a clockwise direction, while genes outside the circle are transcribed counterclockwise. The inner circle depicted in dark gray that represents the GC content, while the light-gray circle represents the AT content of the genome. LSC: large single copy; SSC: small single copy; IRA/IRB: inverted repeat regions.

Table 1. List of genes in the chloroplast genome of Phyllanthus acidus.

Groups of genesName of genes
Ribosomal RNAsrrn4.5(2x), rrn5(2x), rrn16(2x), rrn23(2x)
Transfer RNAstrnA_UGC*(2x), trnC_GCA, trnD_GUC, trnE_UUC, trnF_GAA, trnG_UCC*, trnG_GCC, trnH_GUG, trnI_GAU*(2x), trnK_UUU*, trnL_CAA(2x), trnL_UAA*, trnL_UAG, trnfM_CAU, trnM_CAU(2x), trnM_CAU, trnN_GUU(2x), trnP_UGG, trnQ_UUG, trnR_ACG(2x), trnR_UCU, trnS_GCU, trnS_GGA, trnS_UGA, trnT_GGU, trnT_UGU, trnV_GAC(2x), trnV_UAC*, trnW_CCA, trnY_GUA
Photosystem IpsaA, psaB, psaC, psaI, psaJ
Photosystem IIpsbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ
CytochromepetA, petB*, petD*, petG, petL, petN
ATP synthasesatpA, atpB, atpE, atpF*, atpH, atpI
Large unit of RubiscorbcL
NADH dehydrogenasendhA*, ndhB*(2x), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK
ATP-dependent protease subunit PclpP*
Envelop membrane proteincemA
Large units of ribosomerpl2*(2x), rpl14, rpl16*, rpl20, rpl22, rpl23(2x), rpl32, rpl33, rpl36
Small units of ribosomerps2, rps3, rps4, rps7(2x), rps8, rps11, rps12*(2x), rps14, rps15, rps16*, rps18, rps19(2xa)
RNA polymeraserpoA, rpoB, rpoC1*, rpoC2
Initiation factorinfA
Other genesaccD, ccsA, matK
Hypothetical proteins and conserved reading framesycf1(2xa), ycf2(2x), ycf3*, ycf4

* Gene with introns; 2x – duplicated gene in IR region; 2xa – incomplete duplicated gene in IR region.

6528a77b-4b69-422a-8acd-875b1e0bcbd7_figure2.gif

Figure 2. The ML phylogenetic tree of Phyllanthus acidus and related species based on the 79 protein-coding sequences of cp genome .

The asterisk indicates P. acidus sequenced in this study. The numbers next to each node are bootstrap values.

Data availability

NCBI Short Read Archive (SRA): DNA-seq of Phyllanthus acidus. Accession number SRR24772537; https://www.ncbi.nlm.nih.gov/sra/SRR24772537 (Nguyen, Nguyen, Do, and Vu, 2023).

NCBI Assembly database: Phyllanthus acidus chloroplast, complete genome. Accession number OR050568; https://www.ncbi.nlm.nih.gov/nuccore/OR050568 (Nguyen, Do, and Vu, 2023).

Acknowledgements

The authors thank to anonymous reviewers for their helpful comments to improve the quality of this manuscript.

References

  •  Andrews S: FastQC: A Quality Control Tool for High Throughput Sequence Data.2010.
  •  Bolger AM, Lohse M, Usadel B: Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15): 2114–2120. PubMed Abstract | Publisher Full Text | Free Full Text
  •  Cao D-L, et al.: Application of chloroplast genome in the identification of Traditional Chinese Medicine Viola philippica. BMC Genomics. 2022; 23(1): 540. Publisher Full Text
  •  Chakraborty R, et al.: Antiinflammatory, antinociceptive and antioxidant activities of Phyllanthus acidus L. extracts. Asian Pac. J. Trop. Biomed. 2012; 2(2): S953–S961. Publisher Full Text
  •  Daniell H, et al.: Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol. 2016; 17(1): 134. PubMed Abstract | Publisher Full Text | Free Full Text
  •  Dierckxsens N, Mardulyn P, Smits G: NOVOPlasty: De novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 2017; 45(4): gkw955. Publisher Full Text
  •  Doyle JJ, Doyle JL: A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 1987; 19: 11–15.
  •  Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32(5): 1792–1797. PubMed Abstract | Publisher Full Text | Free Full Text
  •  Greiner S, Lehwark P, Bock R: OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res. 2019; 47(W1): W59–W64. PubMed Abstract | Publisher Full Text | Free Full Text
  •  Jain NK, et al.: Effects of Phyllanthus acidus (L.) Skeels fruit on carbon tetrachloride-induced acute oxidative damage in livers of rats and mice. Zhong Xi Yi Jie He Xue Bao = Journal of Chinese Integrative Medicine. 2011; 9(1): 49–56. PubMed Abstract | Publisher Full Text
  •  Jayvir A: Nature heals, a glossary of selected indigenous medicinal plants of India. Indian J. Pharm. 1998; 30(2): 126.
  •  Leeya Y, et al.: Hypotensive activity of an n-butanol extract and their purified compounds from leaves of Phyllanthus acidus (L.) Skeels in rats. Eur. J. Pharmacol. 2010; 649(1–3): 301–313. PubMed Abstract | Publisher Full Text
  •  Nguyen L-T, et al.: IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 2015; 32(1): 268–274. PubMed Abstract | Publisher Full Text | Free Full Text
  •  Nguyen DH, Nguyen TDQ, Do KHD, et al.: DNA-seq of Phyllanthus acidus. NCBI Short Read Archive. [Dataset]. 2023. Reference Source
  •  Nguyen DH, Do KHD, Vu TM: Phyllanthus acidus chloroplast, complete genome. [Dataset]. GenBank. 2023. Reference Source
  •  Palmer JD, et al.: Chloroplast DNA variation and plant phylogeny. Ann. Mo. Bot. Gard. 1988; 75: 1180–1206. Publisher Full Text
  •  Powell W, et al.: Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines. Proc. Natl. Acad. Sci. 1995; 92(17): 7759–7763. PubMed Abstract | Publisher Full Text | Free Full Text
  •  POWO: Plants of the World Online. Facilitated by the Royal Botanic Gardens, Kew.2022.
  •  Srirama R, et al.: Hepatoprotective activity of Indian phyllanthus. Pharm. Biol. 2012; 50(8): 948–953. Publisher Full Text
  •  Tillich M, et al.: GeSeq – versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017; 45(W1): W6–W11. PubMed Abstract | Publisher Full Text | Free Full Text
  •  Uddin MS, et al.: Neuroprotective Effect of Phyllanthus acidus L. on Learning and Memory Impairment in Scopolamine-Induced Animal Model of Dementia and Oxidative Stress: Natural Wonder for Regulating the Development and Progression of Alz. Adv. Alzheimer's Dis. 2016; 05(02): 53–72. Publisher Full Text

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Nguyen HD, Nguyen TDQ, Vu MT and Do HDK. The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 1; peer review: 1 approved with reservations]. F1000Research 2023, 12:1059 (https://doi.org/10.12688/f1000research.140134.1)
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Reviewer Report 22 Jan 2024
Jessica D. Rey, Plant Molecular Phylogenetics Laboratory, Institute of Biology, College of Science, University of the Philippines Manila, Manila, Metro Manila, Philippines 
Approved with Reservations
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https://doi.org/10.5256/f1000research.153464.r202362
This is a good genome note on the sequencing and assembly of the plastome of Phyllanthus acidus. However, the paper lacks enough details on the reasons behind investigating the species (i.e., limited genetic and genomic resources? problems with identification?).
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Rey JD. Reviewer Report For: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 1; peer review: 1 approved with reservations]. F1000Research 2023, 12:1059 (https://doi.org/10.5256/f1000research.153464.r202362)
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