Abstract
Cerasus jingningensis is a deciduous shrub endemic to Zhejiang province, China. In our study, we assembled and characterised the chloroplast (CP) genome of C. jingningensis based on high-throughput Illumina sequencing data. The CP genome is 157,913 bp in length with an overall GC content of 36.7%, and it consists of two inverted repeats of 26,427 bp each, a large single copy of 85,934 bp, and a small single copy of 19,125 bp. The genome harbours 131 genes, including 85 protein-coding genes, 37 tRNA genes, eight rRNA genes, and a pseudogene ycf1. Phylogenetic analysis revealed that C. jingningensis is a sister of C. serrulata var. spontanea.
Keywords: Cerasus jingningensis, chloroplast genome, phylogenetic analysis
Cerasus jingningensis is a deciduous shrub with purplish brown bark, greyish brown branchlets, pink flowers and purplish black drupes, and it can be cultivated as an ornamental plant. C. jingningensis is a new plant species endemic to Zhejiang province, China, and it is found only in mountains of Jingning She Autonomous County and Longyou County, Zhejiang province. C. jingningensis is morphologically similar to C. serrula (Sect. Serrula), another Cerasus species which is distributed in provinces of Guizhou, Qinghai, Sichuan, Xizang, and Yunnan in China (Wu et al. 2003). Cerasus species belongs to Prunoideae of family Rosaceae, and in recent years, the complete chloroplast genome sequences of several Prunoideae plants have been sequenced and characterised, and these included C. yedoensis, Amygdalus davidiana, and C. pseudocerasus (Cho et al. 2016; Feng et al. 2018; Zhang et al. 2018). However, the complete CP genome of C. jingningensis has not been characterised, and its phylogenetic position is still unresolved. In our study, we reported the CP chloroplast genome of C. jingningensis.
Fresh leaves were collected at an altitude of 1478 m in Dayanghu mountain (27°52′16′′N, 119°44′22′′E), Jingning She Autonomous County, and total genomic DNA was extracted following the CTAB protocol (Doyle and Doyle 1987). A voucher specimen (CHS2018069) is stored at the Molecular Biology Laboratory in Taizhou University. A DNA library was constructed, and it was then sequenced using the Illumina Hiseq X Ten system (Illumina, CA, USA). Approximately 6 Gb raw data of 150 bp paired-end reads were obtained, and the clean reads were assembled by NOVOPlasty (Dierckxsens et al. 2017). The CP genome was annotated by Dual Organellar GenoMe Annotator (DOGMA), and the gene borders were corrected manually (Wyman et al. 2004). The CP genome C. jingningensis (GenBank accession MN175194) is 157,913 bp in length, consisting two inverted repeats (IR), a large single copy (LSC), and a small single copy (SSC), and the sequence lengths are 26,427 bp, 85,934 bp, and 19,125 bp, respectively. The overall GC content of the CP genome is 36.7%, while the GC percentages in IR, LSC, and SSC are 42.5%, 34.6% and 30.2%, respectively. The genome possesses 131 genes, including 85 protein-coding genes, 37 tRNA genes, eight rRNA genes, and a pseudogene. Among these genes, seven tRNAs (trnV-GAC, trnR-ACG, trnN-GUU, trnL-CAA, trnI-GAU, trnI-CAU, trnA-UGC), four rRNAs (rrn4.5, rrn5, rrn16, rrn23), and seven protein-coding genes (ycf2, ycf1, rps12, rps7, rpl23, rpl2, ndhB, and atpF) contain two copies, while one copy of ycf1 is a pseudegene.
Complete genome sequences of A. kansuensis (KF990036), A. davidiana (NC_039735), C. pseudocerasus (KX255667), C. cerasoides (MF621234), Padus padus (KP760072), P. serotina (MF374324), Malus hupehensis (NC_040170), A. mongolica (KY073235), A. mira (NC_040125), C. maximowiczii (KP760071), C. takesimensis (NC_039379), A. persica (HQ336405), C. subhirtella var. subhirtella (KP760074), C. yedoensis (KU985054), and C. serrulata var. spontanea (KP760073) were downloaded from NCBI, and a phylogenetic tree was generated by PhyML 3.1 (Guindon et al. 2010). The results indicated that C. jingningensis grouped with Cerasus species, and it was closely related to C. serrulata var. spontanea (Sect. Serrula), a close relative of C. serrula, with a 100% bootstrap support (Figure 1).
Figure 1.
Maximum likelihood tree of 16 Prunoideae species based on chloroplast genome sequences, with Malus hupehensis as the outgroup. The numbers next to nodes are bootstrap support values.
Disclosure statement
The authors report no conflicts of interest.
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