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. 2021 Aug 1;6(8):2425–2426. doi: 10.1080/23802359.2021.1955027

The complete chloroplast genome sequence of Camellia zhaiana (Theaceae), a critically endangered species from China

Fang-Yuan Wu a, Shi-Cheng Ma b, Pin-Ming Ye c, Hang Ye a, Jin-Lin Ma a,✉
PMCID: PMC8330765  PMID: 34377796

Abstract

Camellia zhaiana S.X. Yang (Theaceae) is a recently described species reported from Guangxi, China. It was proposed as a critically endangered species according to the IUCN Red List Categories and Criteria. In this study, we report and characterize the complete chloroplast (cp) genome of C. zhaiana using Illumina pair-end sequencing data. This is the first report of a cp genome of a species classified in Camellia section. Longipedicellata. The cp genome of C. zhaiana is 156,627 bp in length and includes a large single-copy region (LSC, 86,196 bp), a small single-copy region (SSC, 18,281 bp), and a pair of inverted repeat regions (IRs, 26,075 bp). The genome contains 135 genes, including 40 tRNA, eight rRNA, and 87 protein-coding genes. Phylogenetic analysis showed a strongly supported sister relationship between C. zhaiana and C. longipedicellata, which is a species classified in sect. Longipedicellata. These data support the previous systematic findings of C. zhaiana and advance the bioinformatics of the genus Camellia.

Keywords: Camellia zhaiana, chloroplast genome, Illumina sequencing, phylogenetic analysis

Camellia contains about 120 species distributed in East and Southeast Asia (Ming 2000; Ming and Bartholomew 2007). The Southern Yangtze River of China is the center of species diversity for the genus (Ming and Zhang 1996). Camellia zhaiana is one of these species and was recently reported as new to science (Liu et al. 2020). It was said to be classified in sect. Longipedicellata, and to resemble C. longipedicellata (Liu et al. 2020). It grows in the evergreen broad-leaved forests of limestone mountains at the elevation range 30-100 m (Liu et al. 2020). It is distinct in being the only species from China with red flowers and a long pedicle (Liu et al. 2020). Although the morpho-anatomy of C. zhaiana was well described, no DNA sequences of this species are published. In this study, we present the complete chloroplast (cp) genome sequence of C. zhaiana to determine its systematic position in Camellia and to contribute to the future phylogenetic and taxonomic studies of the genus.

Fresh leaves of C. zhaiana were collected from Long’an county of Guangxi, China (23°05′7.00″N, 107°44′2.91″E). The voucher specimen (S.X. Yang, P. M. Ye & F. Y. Wu 6023) was deposited at the Herbarium at Kunming Institute of Botany (KUN, http://www.kun.ac.cn, Jing-Hua Wang, wangjh@mail.kib.ac.cn), Chinese Academy of Sciences. Total genomic DNA was extracted using a modified hexadecyltrimethylammonium bromide (CTAB) method (Doyle and Doyle 1987). The 150 bp pair-end reads were generated using the Illumina Hi-Seq 2500 platform. The clean data was de novo assembled by GetOrganelle (Jin et al. 2020), followed by using Bandage 0.8.1 (Wick et al. 2015) to assess the completeness of the assembly. PGA (Qu et al. 2019) was used to annotate the chloroplast genome using the default settings. Phylogenetic analysis of C. zhaiana was performed with 26 Camellia species and two outgroups (Polyspora axillaris and Pyrenaria oblongicarpa) using RAxML version 8.2.12 (Stamatakis 2014) with the GTR + GAMMA nucleotide substitution model and 1,000 bootstrap replicates following a previous study (Yu et al. 2017).

The circular complete chloroplast genome of C. zhaiana (GenBank accession number is MW755302) is 156,627 bp in length, with a mean sequencing depth of 70.6×. The GC content of the genome is 37.3%. This genome includes a large single-copy region (LSC, 86,196 bp), a small single-copy region (SSC, 18,281 bp), and two inverted repeat regions (IR, 26,075 bp). In total, it contains 135 genes, with 40 tRNA, eight rRNA, and 87 protein-coding genes.

The maximum likelihood phylogenetic tree revealed that C. zhaiana and C. longipedicellata formed a monophyletic clade with full bootstrap support (BS = 100%) (Figure 1). This result supported the taxonomic treatment that C. zhaiana belongs in sect. Longipedicellata and resembles C. longipedicellata (Liu et al. 2020). According to the classification of Ming (2000), five species were recognized. The cp genome provides a reference for further study on the phylogeny of Camellia, as well as the protection and utilization of C. zhaiana.

Figure 1.

Figure 1.

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Maximum likelihood tree of Theaceae based on 29 complete chloroplast genome sequences, including Camellia zhaiana (GenBank ID: MW755302) sequenced in this study. The bootstrap support values are shown beside the nodes. Two representative taxa of Theaceae (Polyspora axillaris, NC035645; Pyrenaria oblongicarpa, NC035694) were used as outgroups.

Funding Statement

This work was supported by the Open Research Fund of Guangxi Key Laboratory of Special Non-wood Forest Cultivation & Utilization [Grant No. 19-B-01-03, JB-20-01-04].

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 GenBank of NCBI at https://www.ncbi.nlm.nih.gov/nuccore/MW755302, reference number MW755302. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA725163, SRR14326647, and SRS8774896 respectively.

References

  1. Doyle JJ, Doyle JL.. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 19(1):11–15. [Google Scholar]
  2. Jin JJ, Yu WB, Yang JB, Song Y, dePamphilis CW, Yi TS, Li DZ.. 2020. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 21(1):241. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Liu ZW, Ye PM, Li ZH, Wei XJ, Liu ED, Zhang ZR, Ma JL, Yang SX.. 2020. Camellia zhaiana (sect. Longipedicellata), a new species of Theaceae from Guangxi. China. Phytotaxa. 460(3):225–229. [Google Scholar]
  4. Ming TL. 2000. Monograph of the genus Camellia. Kunming (Yunnan): Yunnan Science and Technology Press. [Google Scholar]
  5. Ming TL, Bartholomew B.. 2007. Theaceae. In: Wu CY, Raven PH, editors. Flora of China. Beijing, China and Saint Louis (MO): Science Press and Missouri Botanical Garden Press; p. 366–478. [Google Scholar]
  6. Ming TL, Zhang WJ.. 1996. The evolution and distribution of genus Camellia. Acta Botanica Yunnanica. 18(1):1–13. [Google Scholar]
  7. 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):50. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30(9):1312–1313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Wick RR, Schultz MB, Zobel J, Holt KE.. 2015. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 31(20):3350–3352. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Yu XQ, Gao LM, Soltis DE, Soltis PS, Yang JB, Fang L, Yang SX, Li DZ.. 2017. Insights into the historical assembly of East Asian subtropical evergreen broadleaved forests revealed by the temporal history of the tea family. New Phytol. 215(3):1235–1248. [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 data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/nuccore/MW755302, reference number MW755302. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA725163, SRR14326647, and SRS8774896 respectively.

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