Abstract
The peel of Citrus reticulata can be useful as a kind of traditional Chinese medicine in China. The circular complete chloroplast genome of Citrus reticulata was 160,101 bp in length with the typical quadripartite structure of angiosperms, including 87,721 bp large single-copy region (LSC), 18,394 bp small single-copy region (SSC) of and a pair of 26,993 bp inverted repeat (IR) regions. The overall nucleotide composition of chloroplast genome sequence is 30.5% A, 31.0% T, C (19.6%), G (18.9%), and the total G + C content of 38.5%. A total of 138 genes were annotated in chloroplast genome of C. reticulata. The phylogenetic tree result showed that C. reticulata was evolutionarily close to Citrus sinensis in the family Rutaceae the genus Citrus by the maximum-likelihood (ML) method.
C. reticulata belongs to the family Rutaceae the genus Citrus and the peel of C. reticulata can be useful as a kind of traditional Chinese medicine that also can be used to treat orthopedic diseases in China. Citrus reticulata is one of the most important citrus crops worldwide, which has been one of the centers of mandarin cultivation for four millennia in China (Lun et al. Citation2018). Citrus reticulata as a kind of fruits are attracting increasing attention because of their ease of peeling, nutritional importance, and appetizing flavor. It can be used for medicinal purposes and as healthful food ingredients (Damián-Reyna et al. Citation2017). In China, the peel of C. reticulata can be used as a kind of herb medicine, which can treat orthopedic diseases and enhancing the anti-inflammatory activity and many more diseases (Ho and Lin Citation2008). Here, the complete chloroplast genome of C. reticulata was assembled and characterized, which can use to study the phylogenetic relationship of the genus Citrus plants species, also can provide more traditional Chinese medicine for the future research and utilization.
The fresh samples of C. reticulata were obtained from the market near Zhejiang Chinese Medical University located at Hangzhou, Zhejiang and China (119.89E, 30.09 N) and preserved in liquid nitrogen for further research. The total genomic DNA of C. reticulata was stored in Zhejiang Chinese Medical University (No. ZJCMU-006). Genomic DNA was extracted from the fresh leaves and sequenced. The quality controlled and removed to the collected raw sequences using FastQC (Andrews Citation2015). The chloroplast genome of L. sinense was assembled using MitoZ (Meng et al. Citation2019) and annotated using Geneious (Kearse et al. Citation2012). All the coding and other genes in the chloroplast genome were predicted using CPGAVAS (Liu et al. Citation2012) and corrected using DOGMA (Wyman et al. Citation2004).
The circular complete chloroplast genome of C reticulata (GenBank Accession number: NK9277641) was 160,101 bp in length with the typical quadripartite structure of angiosperms, including 87,721 bp large single-copy region (LSC), 18,394 bp small single-copy region (SSC) of and a pair of 26,993 bp inverted repeat (IR) regions. The overall nucleotide composition of chloroplast genome sequence is 30.5% A, 31.0% T, C (19.6%), G (18.9%), and the total G + C content of 38.5%. The chloroplast genome of C. reticulata contained 138 genes, including 93 protein-coding genes, 37 transfer RNA genes, and eight ribosomal RNA genes. Twenty-two genes were found to contain one IR, including 11 protein-coding genes, seven tRNA genes, and four rRNA genes.
Phylogenetic relationship analysis was carried out using 47 conserved protein-coding genes with those of 14 plant species complete chloroplast genomes that sequences were aligned using MAFFT (Katoh and Standley Citation2013) and conducted by maximum-likelihood (ML) method using MEGA X (Kumar et al. Citation2018). 2000 bootstraps values were used in maximum-likelihood (ML) method and at all the nodes under the substitution model. At last, the phylogenetic tree was drawn and edited using MEGA X (). The phylogenetic tree result showed that C. reticulata was evolutionarily close to Citrus sinensis (NC_008334) in the family Rutaceae the genus Citrus. This study will provide more useful information for phylogenetic relationship of the genus Citrus species and also can improve more traditional Chinese medicine for future research and utilization.
Figure 1. The phylogenetic maximum-likelihood (ML) tree of 14 species based on 47 conserved protein-coding genes. Numbers in the nodes are bootstrap values from 2000 replicates. Accession numbers for tree reconstruction are listed in the figure.
Disclosure statement
No potential conflict of interest was reported by all the authors. This study does not contain any studies with human participants or animals performed by any of the authors.
Data availabity statement
The data that support the findings of this study are openly available in Citrus reticulata at http://doi.org/[doi].
The data that support the findings of this study are available from the corresponding author, upon reasonable request.
References
- Andrews S. 2015. FastQC: a quality control tool for high throughput sequence data. Available online at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
- Damián-Reyna AA, González-Hernández JC, Maya-Yescas R, de Jesus Cortes-Penagos C, Del Carmen Chavez-Parga M. 2017. Polyphenolic content and bactericidal effect of Mexican Citrus limetta and Citrus reticulata. J Food Sci Technol. 54(2):531–537.
- Ho SC, Lin CC. 2008. Investigation of heat treating conditions for enhancing the anti-inflammatory activity of citrus fruit (Citrus reticulata) peels. J Agric Food Chem. 56(17):7976–7982.
- Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780.
- Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28(12):1647–1649.
- Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 35(6):1547–1549.
- Liu C, Shi L, Zhu Y, Chen H, Zhang J, Lin X, Guan X. 2012. CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. BMC Genomics. 13:715–2164.
- Lun W, Fa H, Huang Y, He JX, Yang SZ, Zeng JW, Deng CL, Jiang XL, Fang YW, Wen SH, et al. 2018. Genome of wild mandarin and domestication history of mandarin. Mol Plant. 11(8):1024–1037.
- Meng GL, Li YY, Yang CT, Liu SL. 2019. MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Res. 47(11):e63.
- Wyman SK, Jansen RK, Boore JL. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics. 20(17):3252–3255.