Abstract
Quercus phillyraeoides A. Gray is an evergreen oak species native to East Asia, and it plays a vital role in mountain ecosystems. In this study, we assembled the complete chloroplast genome of Q. phillyraeoides based on sequencing data. The genome was circular and 161,384 bp in length, consisting of a large single-copy region (90,617 bp), small single-copy region (19,035 bp), and two short inverted repeat regions (25,866 bp). We found that the cp genome encodes for 131 genes, including 85 protein-coding genes (PCGs), 8 rRNA genes, and 37 tRNA genes. The results of the phylogenetic analysis of the complete cp genome sequence illustrated that Q. phillyraeoides is a member of the section Quercus and it is most closely related to Q. tarokoensis.
Keywords: Chloroplast genome, Quercus phillyraeoides, phylogenetic analysis
The evergreen oak species Quercus phillyraeoides A. Gray is native to China and Japan. In China, it is widely distributed in the subtropical area, and it grows at an altitude range from 200 to 1700 m a.s.l. (Xie et al. 2011). As one of the dominant trees of subtropical mixed mesophytic forests, it is of high ecological significance for preserving mountain ecosystems, including erosion control in montane forests and providing habitats and food for different species. It is also an economically important tree species for producing excellent charcoal without smoke, which is particularly popular in Japan and Korea. However, few studies were focused on genomic resources of this species (Liu et al. 2013), which is why the plastid genome sequence of the species is still unknown. The aim of this research was to report the complete cp genome sequence of Q. phillyraeoides in order to provide the basis for future genetic studies on this and other relevant species.
Fresh leaves of Q. phillyraeoides were collected from a mature tree from the Nanjing Botanical Garden Memorial Sun Yat-Sen (NBG; Nanjing, China). The voucher specimen (accession no. 2019110101) was preserved at the Herbarium of Nanjing Forest Police College. Total genomic DNA was extracted and purified using the method described in Doyle and Doyle (1987). The whole genome sequencing on the BGISEQ-500 platform was performed by Biodata Biotechnology Co. Ltd (Hefei, China). In total, 35.09 M clean reads were obtained and assembled de novo using NOVOplasty 2.7.2 (Dierckxsens et al. 2016). Annotation was performed using DOGMA (Wyman et al., 2004). All tRNA sequences were confirmed using the web-based online tool tRNAScan-SE (Schattner et al. 2005) with default settings. The complete chloroplast genome sequence of Q. phillyraeoides was deposited in the GenBank with the accession number MN882701.
The plastome of Q. phillyraeoides was determined to comprise double-stranded, circular DNA of 161,384 bp containing two inverted repeat (IR) regions of 25,866 bp, each separated by large single-copy (LSC) and small single-copy (SSC) regions of 90,617 and 19,035 bp, respectively (NCBI acc. no. MN882701). The genome contained 131 genes, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The six protein-coding genes, five tRNA genes, and four rRNA genes were duplicated in the IR region. Nineteen genes contained two exons and four genes (clpP, ycf3, and two rps12) contained three exons. The overall GC content of Q. phillyraeoides cp genome was 36.8%, and in LSC, SSC, and IR regions, this content is 34.6, 30.9, and 42.7%, respectively.
In order to investigate the taxonomic status of Q. phillyraeoides, whole chloroplast genomes of 32 Fagales species and two outgroup species (Theobroma cacao and Populus trichocarpa) were aligned using MAFFT version 7 (Katoh and Standley 2013). The maximum likelihood (ML) tree was reconstructed by FastTree version 2.1.10 (Price et al. 2010). The ML phylogenetic tree showed that among the species from the section Quercus, Q. phillyraeoides is most closely related to Q. tarokoensis, with bootstrap support values of 100% (Figure 1).
Figure 1.
Maximum likelihood tree of 32 species of Fagales (Fagaceae and Betulaceae) and two outgroup taxa (Theobroma cacao and Populus trichocarpa) constructed in FastTree based on plastid genome sequences. Bootstrap support values are shown near the branching points.
Funding Statement
This work was supported by the project of field rescue and breeding of rare and endangered species, the State Forestry and Grassland Administration (2019).
Disclosure statement
No potential conflict of interest was reported by the authors.
References
- Dierckxsens N, Mardulyn P, Smits G. 2016. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Research. 45:e18. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Doyle J J, Doyle J D. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 19:11–15. [Google Scholar]
- Katoh K, Standley D M. 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]
- Liu H Z, Takeichi Y, Kamiya K, Harada K. 2013. Phylogeography of Quercus phillyraeoides (Fagaceae) in Japan as revealed by chloroplast DNA variation. J Forest Res. 18(4):361–370. [Google Scholar]
- Price M N, Dehal P S, Arkin A P. 2010. FastTree 2-approximately maximum-likelihood trees for large alignments. PLOS One. 5(3):e9490. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schattner P, Brooks AN, Lowe TM. 2005. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 33(Web Server issue):W686–W689. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wyman S K, Jansen R K, Boore J L. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics. 20(17):3252–3255. [DOI] [PubMed] [Google Scholar]
- Xie C P, Fang Y, Fang Y M. 2011. Geographical distribution of Quercus phillyraeoides A. Gray. Trop Geogr. 31:8–13. [Google Scholar]