The complete chloroplast genome sequence of Camellia mingii (Theaceae), a critically endangered yellow camellia species endemic to China

Abstract

Camellia mingii is a recently described and critically endangered new species from Southeast Yunnan Province, China. Genetic information of C. mingii would provide guidance for the conservation of this wild yellow camellia. Here, we reported and characterized its complete chloroplast (cp) genome using Illumina pair-end sequencing data. The total chloroplast genome size was 156,806 bp, including inverted repeats (IRs) of 26,020 bp, separated by a large single copy (LSC) and a small single copy (SSC) of 86,536 and 18,230 bp, respectively. A total of 132 genes, including 37 tRNA, eight rRNA, and 87 protein-coding genes were identified. Phylogenetic analysis showed that C. mingii was closely related to the clade containing C. huana and C. impressinervis.

Keywords:

• Camellia mingii
• chloroplast genome
• phylogenetic relationships
• endangered species

Camellia, with ca. 120 species (Ming 2000; Min and Bartholomew 2007), mainly distribute in East and Southeast Asia. The diversity center of the genus is Southern Yangtze River of China (Ming and Zhang 1996). Yellow camellias are a group of species of Camellia with yellow, shiny petals, they are valuable ornamental plants and are also used in traditional Chinese medicine and commercial teas (Chang and Ren 1998; Min and Bartholomew 2007). Camellia mingii S. X. Yang is a local endemic, currently known only in Funing Xian, Yunnan Province, China. It grows on limestone in evergreen broad-leaved forests at elevation of 800–1300 m. Only three populations of C. mingii in Funing County of Yunnan were found till now, the category of Critically Endangered (CR) was recommended. Both morphological comparison and molecular analyses support C. mingii as a new member of yellow camellias (Liu et al. 2019). A number of chloroplast genomes of Camellia have been published (Yang et al. 2013; Huang et al. 2014); however, only few of endangered camellias were reported (Wang et al. 2017; Liu et al. 2018; Xu et al. 2018). In this study, we present the complete chloroplast (cp) genome sequence of C. mingii using Illumina sequencing technology.

Fresh leaves were collected from an individual of C. mingii in Funing county of Yunnan province, the voucher specimen (S. X. Yang 5610) was deposited in the Herbarium of Kunming Institute of Botany, Chinese Academy of Sciences (KUN). Genomic DNA was isolated using a modified CTAB approach (Doyle and Doyle 1987). The 150 bp pair-end reads were generated using the Illumina Hi-Seq 2500 platform. Totally, 5,692,455 reads in size of 2.82 G were obtained for both ends. The chloroplast genome was de novo assembled using GetOrganelle script (Jin et al. 2018), with SPAdes 3.10.1 as assembler (Bankevich et al. 2012), then visualized by Bandage 0.8.1 (Wick et al. 2015) to determine paths of the cp genome. The resultant cp genome was annotated by aligning with those of its congeners (e.g. Camellia taliensis, NC022264; Camellia sinensis, KC143082) in Geneious 8.0.2 (Kearse et al. 2012). Phylogenetic analysis of 25 Camellia species and two outgroups followed our previous study (Yu et al. 2017).

The chloroplast genome of C. mingii was 156,806 bp, with a mean coverage of the cp genome of 80.0. The GenBank accession number of the chloroplast genome of C. mingii is MK473913. The GC content of the genome was 39.6%. The length of inverted repeats (IR), large single copy (LSC), and small single copy (SSC) was 26,020, 86,536, and 18,230 bp, respectively. The chloroplast genome of C. mingii contained 132 genes, with 8 rRNA genes, 37 tRNA genes, and 87 protein-coding genes. Annotation revealed that four rRNA genes, seven tRNA genes, and seven protein-coding genes were duplicated in the IR region.

The phylogenetic relationship between C. mingii and other congeneric species was reconstructed by comparison with other 24 chloroplast genomes of Camellia. The maximum likelihood phylogenetic tree revealed that C. mingii was closely related to C. huana and C. impressinervis, both belong to Camellia subgenus Thea sect. Archecamellia (Figure 1). However, the phylogenetic position of C. mingii need further investigation because of current limited sampling and the conflict between our results and the results from a previous study based on nuclear GBSSI sequences (Liu et al. 2019). The complete cp genome of C. mingii would be useful for the genetic diversity studies of this endangered yellow camellia species and facilitate the understanding of the conservation and restoration of C. mingii.

Figure 1. Maximum likelihood tree of the genus Camellia based on 27 complete chloroplast genome sequences, including C. mingii (GenBank ID: MK473913) sequenced in this study. The bootstrap support values are shown above the branches. Two representative taxa of Theaceae (Polyspora axillaris, NC035645; Pyrenaria oblongicarpa, NC035694) were used as outgroups.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by National Science Foundation of China [Grant No. 31700182, 31770219], a grant from State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan of Yunnan University [Grant No. 2018KF007] and CAS “Light of West China” Program.