Skip to main content
NCBI home page
Mitochondrial DNA. Part B, Resources logoLink to Mitochondrial DNA. Part B, Resources
. 2021 Mar 18;6(3):1014–1015. doi: 10.1080/23802359.2021.1894999

Characterization of the complete chloroplast genome of Syzygium nervosum

Pan Li 1, Weiyue Guo 1, Kang Lei 1, Lusha Ji 1,✉
PMCID: PMC7995873  PMID: 33796721

Abstract

Syzygium nervosum A.Cunn. ex DC (also named as Cleistocalyx operculatus) is a member of genus Syzygium mainly distributed in China, Vietnam and some other tropical countries and belongs the family of Myrtaceae. Syzygium nervosum is a popular medicinal plant, some species of genus Syzygium have been used in folk medicine. In this study, we sequenced the sample of Syzygium nervosum and determined its complete chloroplast genome. The complete chloroplast genome of Syzygium nervosum is 158,979 bp in length, and contained a large single copy (LSC) with 88,099 bp in length, a small single copy (SSC) with 18,756 bp in length and two inverted repeat (IR) regions of 26,062 bp each. It includes 85 protein coding genes, 8 rRNA and 37 tRNA, and 37% overall GC content. Each of trnK-UUU, rps16, trnG-UCC, atpF, rpoC1, trnL-UAA, trnV-UAC, petB, petD, rpl16, rpl2, ndhB, trnI-GAU, trnA-UGC and ndhA genes contain an intron, the gene clpP and ycf3 contain 2 introns. The phylogenetic position shows that Syzygium nervosum has the closest relationship with Syzygium aromaticum.

Keywords: Syzygium nervosum, Myrtaceae, complete chloroplast genome

Syzygium nervosum A.Cunn. ex DC (also named as Cleistocalyx operculatus) is a member of genus Syzygium mainly distributed in China, Vietnam and some other tropical countries and belongs the family of Myrtaceae (Tran et al. 2019). S. nervosum is a kind of popular medicinal plant, the buds of S. nervosum have been used in various beverages in Southern China since ancient times (Woo et al. 2002; Mai and Chuyen 2007; Dung et al. 2009). S. nervosum also is the important raw martial of essential oil that had excellent anti-inflammatory activities both in vitro and in vivo (Dung et al. 2009). People have learnt S. nervosum for hundreds of years and constantly discovered new function of S. nervosum for human ’s life. However, the study about complete chloroplast genome of Syzygium was very deficient especially S. nervosum, and there was no information about complete chloroplast genome of S. nervosum in database of NCBI. So in this study we sequenced the sample of S. nervosum and determined its complete chloroplast genome.

The sample of Syzygium nervosum was collected from South China Botanical Garden, Tianhe District, Guangzhou, Guangdong Province (N113°22′34″, E23°11′32″), and the fresh leaves had been used to extract total genomic DNA based CTAB method (Doyle and Doyle 1987) and construct the libraries with an average length of 350 bp using the NexteraXT DNA Library Preparation Kit (Illumina, San Diego, CA). Then the libraries were sequenced on Illumina Novaseq 6000 platform, 3.05 Gb Illumina raw sequence reads were edited using the NGS QC Tool Kit v2.3.3. High-quality reads were assembled into contigs using the de novo assembler SPAdes 3.11.0 software (Bankevich et al. 2012) and annotated by Plann software (Huang and Cronk 2015). The complete sequence and annotation results were submitted to GenBank, under the accession number (MW054699) and the sample was stored at Laboratory of Molecular Biology, Liaocheng University, Liaocheng. (Voucher specimen: CO20200701LP) (Lusha Ji, email: jilusha2020@163.com).

The complete chloroplast genome of Syzygium nervosum is 158,979 bp in length, and contains a large single copy (LSC) with 88,099 bp in length, a small single copy (SSC) with 18,756 bp in length and two inverted repeat (IR) regions of 26,062 bp each. There are 130 genes, which includes 85 protein coding genes, 8 rRNA and 37 tRNA, and 37% overall GC content. Each of trnK-UUU, rps16, trnG-UCC, atpF, rpoC1, trnL-UAA, trnV-UAC, petB, petD, rpl16, rpl2, ndhB, trnI-GAU, trnA-UGC and ndhA genes contain an intron, the gene clpP and ycf3 contain 2 introns.

To confirm the phylogenetic position and understand the relationship of Syzygium nervosum within Myrtaceae. The complete chloroplast genome of 13 species in family Myrtaceae were collected and aligned with Syzygium nervosum by MAFFT7.037 (Katoh and Standley 2013). Subsequently, the phylogenetic tree was constructed by IQTREE v1.6 (Nguyen et al. 2015; Hoang et al. 2018) with 1000 bootstraps replicates using Best-fit model. By using Canavalia rosea (LC554221) as out group we got the final ML tree, then the Figure 1 shows that Syzygium nervosum has the closest relationship with Syzygium aromaticum (MN746306.1).

Figure 1.

Figure 1.

Open in a new tab

Maximum-likelihood phylogenetic tree for Syzygium nervosum based on 14 species complete chloroplast genomes in family Myrtaceae.

Funding Statement

This work was supported by Shandong Provincial Natural Science Foundation of China [NO. ZR2019PC041] and the National Natural Science Foundation of China [Grant No. 32001982].

Disclosure statement

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

Data availability statement

The chloroplast genome sequence data that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/) under the accession no. MW054699. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA693034, SRR13479128, and SRS8071277, respectively.

References

  1. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 19(5):455–477. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Doyle JJ, Doyle JL.. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 19:11–15. [Google Scholar]
  3. Dung NT, Bajpai VK, Yoon JI, Kang SC.. 2009. Anti-inflammatory effects of essential oil isolated from the buds of Cleistocalyx operculatus (roxb.) merr and perry. Food Chem Toxicol. 47(2):449–453. [DOI] [PubMed] [Google Scholar]
  4. Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS.. 2018. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol. 35(2):518–522. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Huang DI, Cronk QCB.. 2015. Plann: a command-line application for annotating plastome sequences. Appl Plant Sci. 3(8):1500026. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. 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] [PMC free article] [PubMed] [Google Scholar]
  7. Mai TT, Chuyen NV.. 2007. Anti-hyperglycemic activity of an aqueous extract from flower buds of cleistocalyx operculatus (roxb.) merr and perry. Biosci Biotechnol Biochem. 71(1):69–76. [DOI] [PubMed] [Google Scholar]
  8. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ.. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 32(1):268–274. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Tran PT, Ngo TQ-M, Lee S, Kim O, Tran HNK, Hwangbo C, Min BS, Lee J-H.. 2019. Identification of anti-osteoclastogenic compounds from Cleistocalyx operculatus flower buds and their effects on RANKL-induced osteoclastogenesis. J Funct Foods. 60:103388. [Google Scholar]
  10. Woo AYH, Waye MMY, Kwan HS, Chan MCY, Chau CF, Cheng CHK.. 2002. Inhibition of atpases by Cleistocalyx operculatus. a possible mechanism for the cardiotonic actions of the herb. Vascul Pharmacol. 38(3):163–168. [DOI] [PubMed] [Google Scholar]

Associated Data

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

Data Availability Statement

The chloroplast genome sequence data that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/) under the accession no. MW054699. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA693034, SRR13479128, and SRS8071277, respectively.

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

RESOURCES