Skip to main content
NCBI home page
Mitochondrial DNA. Part B, Resources logoLink to Mitochondrial DNA. Part B, Resources
. 2021 Nov 23;6(12):3461–3462. doi: 10.1080/23802359.2021.2002202

The complete chloroplast genome sequence of Phyllagathi hainanensis (Melastomataceae) and phylogenetic analysis

Ai-Fang Weng a, Lang-Xing Yuan b, Qing-Hui Sun c, Hong-Xin Wang a,b,✉
PMCID: PMC8635600  PMID: 34869875

Abstract

Phyllagathi hainanensis (Merr. et Chun) C. Chen is a small shrubs of Melastomataceae. It is only distributed in Hainan provinces of China. The complete chloroplast genome of P. hainanensis is reported in this study. The complete chloroplast genome of P. hainanensis is 156,123 bp in length with a typical quadripartite structure, consisting of a large single-copy region (LSC, 85,497 bp), a single-copy region (SSC, 17,076 bp), and a pair of inverted repeats (IRs, 26,775 bp). There are 129 genes annotated, including 37 transfer RNA genes, 8 ribosomal RNA genes, and 84 proteincoding genes. The complete plastome sequence of P. hainanensis will provide a useful resource for phylogenetic studies in Melastomataceae.

Keywords: Phyllagathi hainanensis, chloroplast genome, phylogenetic tree, Melastomataceae

Phyllagathis hainanensis (Merr. et Chun) C. Chen belongs to Melastomataceae. The Phyllagathis is distributed mainly in the tropical and subtropical regions of Asia (Cellinese 2002; Chen and Renner 2007; Lin et al. 2017).There are 25–28 species of Phyllagathis in China (Chen 1984; Chen and Renner 2007). P. hainanensis is an endemic species to Hainan and occurs in sparse to the forests, mountain slopes, and hillsides with an altitude of 600–1400 m (Lin et al. 2015). The most recent analyses revealed that Phyllagathis is not monophyletic, showing close relationships with Allomorphia Blume, Blastus Lour., Fordiophyton Stapf, Oxyspora DC., Plagiopetalum Rehder, Sonerila Roxb., and Tigridiopalma C. Chen (Zeng et al. 2016; Zhou et al. 2019). At present, ca. 40 complete chloroplast genomes of Phyllagathis were all reported, the complete chloroplast genome of P. hainanensis is unknown. In this study, we annotated the chloroplast genome of P. hainanensis into GenBank public database with the accession MZ450795.

In this study, the fresh leaves of P. hainanensis were collected from Murui Mountain in Hainan province (110. 29°N, 19. 24°E, elevation 680 m). Voucher specimens were deposited in the herbarium of Sanya University (collector and collection number: Lang-xing Yuan, HNJXC1) .Genomic DNA of P. hainanensis leaves was extracted according to CTAB method (Doyle and Doyle 1987). Paired-end (PE) reads of 150 bp was conducted on an Illumina Hiseq-2500 platform at BGI-Shenzhen. Approximately, 4 GB raw data (32,192,787 Clean Reads) was generated and deposited in Sequence Read Archive (SRA) under accession number SRR14891646. China. The complete chloroplast genome was assembled by GetOrganelle. We used the pipeline PGA to performe gene annotation with P. sessilifolia (MK994926) as a reference. Analysis of boundaries between IRs and single copy regions was performed by online program GeSeq (Tillich et al. 2017).

The plastome of P. hainanensis was found to possess total length 156,123 bp with the typical quadripartite structure containing two inverted repeats (IRs) of 26,775 bp, a large single-copy (LSC) region of 85,497 bp and a small single-copy (SSC) region of 17,076 bp. There were 129 genes, including 37 transfer RNA genes, 8 ribosomal RNA genes, and 84 proteincoding genes. The total GC content of chloroplast genome in P. hainanensis was 36.98%.

We used RAxML (Stamatakis 2006) with 1000 bootstraps under the GTRGAMMAI substitution model to reconstruct a maximum-likelihood (ML) phylogeny of 13 published complete plastomes of Phyllagathis, using Astronia smilacifolia (MK994883.1) and Memecylon ligustrifolium (MK994913.1) as outgroups (Figure 1). Our analyses show that P. hainanensis is sister relationship with the remaining species of this genus. Our results provide valuable data and shed light on the phylogenomic study of Melastomataceae.

Figure 1.

Figure 1.

Open in a new tab

Phylogenetic tree based on 15 complete sequences of chloroplast genome in different species. The accession number in bold font was the newly sequenced Phyllagathi hainanensis in this study.

Funding Statement

This study was supported by Hainan Provincial Natural Science Foundation of China [No. 320RC672] and Innovation and Entrepreneurship Training Program for Provincial College Students in Hainan Province in 2020 [202013892031].

Disclosure statement

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

Data availability statement

The 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 MZ450795. Raw Illumina data were deposited in the NCBI Sequence Read Archive (SRA: SRR14891646, BioProject: PRJNA739828, and Bio-Sample: SAMN19837121).

References

  1. Cellinese N. 2002. Revision of the genus Phyllagathis Blume (Melastomataceae: Sonerileae) I. The species of Burma, Thailand, Peninsular Malaysia and Sumatra. Blumea. 47:463–492. [Google Scholar]
  2. Chen C. 1984. Melastomataceae. In: Flora Reipublicae Popularis Sinicae. Beijing: Science Press. 53: p. 135–293. [Google Scholar]
  3. Chen C, Renner SS.. 2007. Melastomataceae. In: Wu ZY, Raven PH, Hong DY eds. Flora of China. Beijing: Science Press; St. Louis: Missouri Botanical Garden Press. 13: p. 360–399. [Google Scholar]
  4. Doyle JJ, Doyle JD.. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 19:11–15. [Google Scholar]
  5. Lin CW, Chen CF, Yang TYA.. 2015. Two new taxa of Melastomataceae Trib. Sonerileae: Phyllagathis rajah and Sonerila metallica from Batang Ai, Sarawak, Borneo. Phytotaxa. 201(2):122–130. [Google Scholar]
  6. Lin CW, Chen CF, Yang TYA.. 2017. Ten new species of Phyllagathis (Trib. Sonerileae, Melastomataceae) from Sarawak, Borneo. Phytotaxa. 302(3):201–228. [Google Scholar]
  7. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22(21):2688–2690. [DOI] [PubMed] [Google Scholar]
  8. Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S.. 2017. GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 45(W1):W6–W11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Zeng SJ, Zou LH, Wang P, Hong WJ, Zhang GQ, Chen LJ, Zhuang XY.. 2016. Preliminary phylogeny of Fordiophyton (Melastomataceae), with the description of two new species. Phytotaxa. 247(1):45–61. [Google Scholar]
  10. Zhou QJ, Lin CW, Dai JH, Zhou RC, Liu Y.. 2019. Exploring the generic delimitation of Phyllagathis and Bredia (Melastomataceae): A combined nuclear and chloroplast DNA analysis. Jnl of Sytematics Evolution. 57(3):256–267. [Google Scholar]

Associated Data

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

Data Availability Statement

The 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 MZ450795. Raw Illumina data were deposited in the NCBI Sequence Read Archive (SRA: SRR14891646, BioProject: PRJNA739828, and Bio-Sample: SAMN19837121).

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

RESOURCES