The Chinese cherry Prunus pseudocerasus is a species of fruit tree within the family Rosaceae (Li and Bartholomew 2003). It originates in Southwest China, but now is widely dispersed in the temperate zone of Northern Hemisphere, mostly occurring on sunny mountain slopes or on the sides of ravines with an elevation of 300–1200 m (Chen et al. 2016; Li and Bartholomew 2003; Li et al. 2009). P. pseudocerasus possesses high economic and ornamental values. As a traditional fruit with peculiar flavor, its cultivation history can date back to approximately 3000 years ago in China (Liu and Liu 1993). Its fruit contains a variety of nutritional ingredients and trace elements, e.g. carotene, vitamin C, proteins, saccharides, iron and phosphorus (Yu and Li 1986). It has also long been used as the rootstock for sweet cherry ever since the latter’s introduction into China (Zhang and Gu 2016). Besides, the past decades has witnessed the significant role of Chinese cherry landscape in the booming rural tourism industry (Chen et al. 2016).

However, as indicated by recent field surveys (Chen et al. 2016; Li et al. 2009), many wild populations of P. pseudocerasus are under threat or even on the verge of extinction largely due to anthropogenic activities (e.g. road construction, deforestation, grazing and thoroughbred replacement). Urgent preservation and restoration practices have become necessary for this valuable germplasm. A good knowledge of its genetic diversity would be essential to the formulation of efficient strategies for its conservation, management and exploitation. To facilitate such purposes, its complete chloroplast (cp) genome was assembled from high-throughput Illumina sequencing data in this study. The annotated genomic sequence is available from GenBank with the accession number KX255667.

Total genomic DNA was extracted from silica-dried leaves of an individual with the DNeasy Plant Mini Kit (Qiagen, CA, USA), and used for the shotgun library preparation following the manufacturer’s protocol for the Illumina NextSeq 500 Sequencing System (Illumina, CA, USA). In all, 8.63 M of 150-bp paired raw reads were obtained, quality-trimmed with Trimmomatic v0.35 (Bolger et al. 2014), and used for the assembly of cp genome with MITObim v1.8 (Hahn et al. 2013). The cp genome of Prunus persica (HQ336405) (Jansen et al. 2011) was used as the initial reference as well as for the purpose of genome annotation. A physical map of the genome was drawn with the web-based tool OrganellarGenomeDraw (OGDRAW) (http://ogdraw.mpimp-golm.mpg.de/) (Lohse et al. 2013).

The cp genome of P. pseudocerasus was successfully assembled with an average coverage of 235-fold. It is 157,834 bp in length, and contains a pair of inverted repeat (IR) regions of 26,398 bp each, separated by a large single-copy (LSC) region of 85,954 bp and a small single-copy (SSC) region of 19,084 bp (Fig. 1). It harbors 131 genes, including 86 protein-coding genes (78 PCG species), 37 tRNA genes (29 tRNA species) and eight rRNA genes (four rRNA species). The majority of the gene species occur as a single copy, whereas 20 gene species occur in double copies, including eight PCG species (ndhB, rpl2, rpl23, rps7, rps12, rps19, ycf1 & ycf2), eight tRNA species (trnA-UGC, trnG-GCC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG & trnV-GAC) and all four rRNA species (rrn4.5, rrn5, rrn16 & rrn23). Except for trnG-GCC which resides within the LSC region, all the other 19 duplicated gene species are partially or completely located within the IR regions. Ten PCG species (atpF, ndhA, ndhB, petB, petD, rpl2, rpl16, rpoC1, rps12 & rps16) and six tRNA species (trnA-UGC, trnG-GCC, trnI-GAU, trnK-UUU, trnL-UAA & trnV-UAC) harbor a single intron, while two other PCG species (clpP & ycf3) have a couple of introns. This cp genome has an biased base composition (31.2% A, 18.7% C, 18.0% G & 32.1% T) with an overall A + T content of 63.3%. The A + T contents of the LSC, SSC and IR regions are 65.4, 69.7 and 57.5%, respectively.

Fig. 1
figure 1

Physical map of the chloroplast genome of Prunus pseudocerasus

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A good knowledge of its genetic relationship with related taxa would provide valuable background information for broadening the genetic basis of rootstock breeding programs (Zhang and Gu 2016). Thus, we further investigated its phylogenetic relationships with another 31 taxa with publicly available cp genomes within the order Rosales (Fig. 2). A neighbor-joining (NJ) phylogeny was reconstructed using the concatenated coding sequences of cp PCGs with MEGA6 (Tamura et al. 2013). The phylogenetic analysis corroborated the traditional taxonomy of the order Rosales with high bootstrap support. Specifically, the 22 species within the family Rosaceae were clustered into two groups, corresponding to the two distinct subfamilies: Maloideae and Rosoideae. P. pseudocerasus was found to be closely related to the four congeners P. maximowiczii, P. serrulata, P. subhirtella and P. yedoensis.

Fig. 2
figure 2

Phylogeny of 32 species within the order Rosales based on the neighbor-joining (NJ) analysis of the concatenated coding sequences of chloroplast PCGs. The bootstrap values were based on 500 resamplings, and are indicated next to the branches. The tree was rooted with Castanea mollissima and Theobroma cacao

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