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. 2019 Dec 11;5(1):90–91. doi: 10.1080/23802359.2019.1698337

The complete chloroplast genome sequence of Actinidia styracifolia C. F. Liang

Aihong Yang 1, Shujuan Liu 1, Tengyun Liu 1, Miao Hu 1, Yongda Zhong 1, Lipan Liu 1, Faxin Yu 1,✉
PMCID: PMC7721030  PMID: 33366436

Abstract

The complete chloroplast (cp) genome sequence of Actinidia styracifolia C. F. Liang was assembled using Illumina pair-end sequencing data in this study. The assembled plastome was 156,845 bp in length, including a large single copy (LSC) region of 88,624 bp and a small single copy (SSC) region of 20,535bp, which were separated by two inverted repeat (IR) regions of 23,843 bp. The plastome contains 113 different genes, consisting of 79 unique protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis based on chloroplast genomes revealed that A. styracifolia has a close genetic relationship with A. eriantha.

Keywords: Actinidia styracifolia, complete chloroplast genome, phylogenetic analysis

Actinidia, with 54 species and 21 varieties, is mainly distributed in East and South Asia (Huang et al. 2013). As an important fruit tree, A. chinensis, A. chinensis var. deliciosa and A. arguta have received considerable attention (Yao et al. 2015; Lin et al. 2018); however, little is known about narrowly distributed Actinidia species. A. styracifolia C. F. Liang is characterized by rich vitamin C in the fruits and now scattered distributed in Hunan, Guizhou, Jiangxi and Fujian province, China (Huang et al. 2013). It was recommended as Vulnerable species (VU) by the International Union for Conservation of Nature (IUCN). Knowledge of complete chloroplast (cp) genome would contribute greatly to reveal the phylogeny status and develop optimum conservation strategies for A. styracifolia. In this study, we assembled and characterized the complete chloroplast (cp) genome of A. styracifolia from Illumina pair-end sequencing data.

Fresh leaves were collected from a single individual of A. styracifolia sampled in Xunwu county (24°58′9″N, 115°47′44″E) of Jiangxi province, China. We preserved this sample into our Kiwifruit Germplasm Genebank (28°22′27″N, 116°0′59″E) by grafting. The voucher specimen (LBG00148294) was deposited in the Herbarium of Lushan Botanical Garden, Chinese Academy of Sciences (LBG). Genomic DNA was isolated using a modified CTAB method (Doyle and Doyle 1987). The whole-genome sequencing was obtained 150 bp paired-end reads using the Illumina Hiseq Platform. In total, 5.5 G raw reads were obtained, quality-trimmed and assembled against the plastome of Actinidia chinensis (GenBank: NC_026690.1) (Yao et al. 2015) using the program NOVOPlasty (Dierckxsens et al. 2017).

The complete chloroplast genome of A. styracifolia (GenBank accession number MN627226) exhibits the typical quadripartite structure of angiosperms, with a size of 156,845 bp in length. It comprises two inverted repeat (IR) regions of 23,843 bp separated by the large single-copy (LSC) region of 88,624 bp and small single-copy (SSC) region of 20,535 bp. The GC content of the LSC, SSC, and IRa/b regions is 35.45, 31.08 and 43.09%, respectively, and the overall GC content of the genome is 37.2%. The cp genome of A. styracifolia contains 113 unique genes, with 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The majority of the genes are single copy; however, 17 gene species in the IR regions are totally duplicated, including 5 protein-coding genes (ycf2, ycf15, ndhB, rps7, and rps12), 8 tRNA genes (trnH-GUG, trnI-CAU, trnL-CAA, trnV-GAC, trnI-GAU, trnA-UGC, trnR-ACG, and trnN-GUU) and all four rRNA genes. Compared with most other angiosperms, A. styracifolia lost its clpP gene, a conspicuous synapomorphic characteristic during the cp genome evolution of Actinidiaceae (Wang et al. 2016).

To confirm the phylogenetic position of A. styracifolia, eleven complete chloroplast genome sequences of Actinidiaceae were aligned using MAFFT v.7 (Katoh and Standley 2013), and maximum likelihood (ML) analysis was performed in RAxML8.0 (Stamatakis 2014) with 1000 bootstrap replicates. The phylogenetic analysis of 11 Actinidia chloroplast genomes showed that A. styracifolia was closely related to A. eriantha (Figure 1).

Figure 1.

Figure 1.

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Phylogenetic relationships of 11 Actinidiaceae species based on complete chloroplast genomes. Bootstrap support values >50% are given at the nodes. GenBank accession numbers: A. chinensis (NC_026690.1), A. deliciosa (NC_026691.1), A. rufa (NC_039973.1), A. callosa var. henryi (NC_043861.1), A. styracifolia (MN627226), A. eriantha (NC_034914.1), A. arguta (NC_034913.1), A. polygama (NC_031186.1), A. tetramera (NC_031187.1), A. kolomikta (NC_034915.1), Clematoclethra scandens subsp. Hemsleyi (KX345299.1).

Funding Statement

This work was supported by the Key research and development projects of Jiangxi Province [20161BBH80064; 20181BBF60010], the Key research and development projects of Jiangxi Academy of Sciences [2018-YZD2-06], and the Special project for the construction of modern agricultural industrial technology system in Jiangxi Province [JXARS-05].

Disclosure statement

No potential conflict of interest was reported by the authors.

References

  1. Dierckxsens N, Mardulyn P, Smits G. 2017. NOVOPlasty: De novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45(4):e18. [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. Huang HW, Zhong CH, Jiang ZW, Li XW, Yao XH, Li DW, Wang SM, Li ZZ, Gong JJ, Liu YF, et al. 2013. Actinidia: taxonomy, resources, domestication, cultivation. Beijing: Science Press. [Google Scholar]
  4. 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]
  5. Lin M, Qi X, Chen J, Sun L, Zhong Y, Fang J, Hu C. 2018. The complete chloroplast genome sequence of Actinidia arguta using the PacBio RS II platform. PLoS One. 13(5):e0197393. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. 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]
  7. Wang WC, Chen SY, Zhang XZ. 2016. Chloroplast genome evolution in Actinidiaceae: clpP loss, heterogenous divergence and phylogenomic practice. PLoS One. 11(9):e0162324. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Yao X, Tang P, Li Z, Li D, Liu Y, Huang H. 2015. The first complete chloroplast genome sequences in Actinidiaceae: genome structure and comparative analysis. PLoS One. 10(6):e0129347. [DOI] [PMC free article] [PubMed] [Google Scholar]

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