Complete chloroplast genome of Prunus itosakura (Rosaceae), a wild flowering cherry from Japan

Abstract

Prunus itosakura is a flowering tree species with high ornamental and economic values. We determined the first complete chloroplast genome of P. itosakura using genome skimming approach. The cp genome was 157,813 bp long, with a large single-copy region (LSC) of 85,931 bp and a small single-copy region (SSC) of 19,120 bp separated by a pair of inverted repeats (IRs) of 26,381 bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. We also reconstructed the phylogeny of Prunus sensu lato using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The phylogenetic analysis indicated that P. itosakura is closely related with Prunus subhirtella var. subhirtella.

Keywords:

• Prunus itosakura
• Prunus sensu lato
• chloroplast genome
• phylogenomics

Prunus itosakura Siebold, also known as Cerasus spachiana Lavallée ex Ed. Otto (Katsuki and Iketani 2016), is a flowering tree species with high ornamental and economic values (Kuitert and Peterse 1999; Ohba 2001).The classification of the Prunus sensu lato (Rosaceae) has long been problematic; phylogenetic studies using a limited set of markers have often not been able to fully resolve relationships within this genus, indicating that a higher number of molecular characters are required for an improved understanding of relationships within this group (Shi et al. 2013; Chin et al. 2014). By taking advantages of next-generation sequencing technologies that efficiently provide the chloroplast (cp) genomic resources of our interested species, we can rapidly access the abundant genetic information for phylogenetic research and conservation genetics (Li et al. 2017; Liu et al. 2017). Therefore, we sequenced the whole chloroplast genome of P. itosakura to elucidate its phylogenetic relationship with other Prunus sensu lato.

Total genomic DNA was extracted from silica-dried leaves collected from the nursery in Tama Forest Science Garden (Hachioji, Japan) using a modified CTAB method (Doyle and Doyle 1987). The voucher specimen (Sun1704133) was collected and deposited in the Herbarium of Zhejiang Academy of Forestry. DNA libraries preparation and pair-end 125 bp read length sequencing were performed on the Illumina HiSeq 2500 platform. About 11.5 Gb of raw data were trimmed and assembled into contigs using CLC Genomics Workbench 8. All the contigs were then mapped to the reference cp genome of Prunus speciosa (Koidz.) Nakai (MH998233; Sun et al. 2019) using BLAST (NCBI BLAST v2.2.31) search and the draft cp genome of P. itosakura was constructed by connecting overlapping terminal sequences in Geneious R11 software (Biomatters Ltd., Auckland, New Zealand). Gene annotation was performed via the online program Dual Organellar Genome Annotator (DOGMA; Wyman et al. 2004).

The complete cp genome of P. itosakura (GenBank accession MN695296) was 157,813 bp long consisting of a pair of inverted repeat regions (IRs with 26,381 bp) divided by two single-copy regions (LSC with 85,931 bp; SSC with 19,120 bp). The overall GC contents of the total length, LSC, SSC, and IR regions were 36.7%, 34.6%, 30.2% and 42.6%, respectively. The genome contained a total of 129 genes, including 84 protein-coding genes, 37 tRNA genes and 8 rRNA genes.

We used a total of 22 additional complete cp genomes of the Prunus sensu lato species to clarify the phylogenetic position of P. itosakura. Prunus serotina Ehrh. (NC036133) and P. padus L. (NC026982) in Subg. Padus were used as the outgroup. We reconstructed a phylogeny employing the GTR + G model and 1000 bootstrap replicates under the maximum-likelihood (ML) inference in RAxML-HPC v.8.2.10 on the CIPRES cluster (Miller et al. 2010). The ML tree (Figure 1) was consistent with the most recent phylogenetic study on Prunus sensu lato (Shi et al. 2013; Chin et al. 2014). P. itosakura exhibited the closest relationship with Prunus subhirtella var. subhirtella Miq.. However, Prunus subhirtella var. subhirtella in Korea was considered to be a synonym of P. itosakura (Ohba 2001).

Figure 1. Phylogenetic tree reconstruction of 23 taxa of Prunus sensu lato using ML method. Relative branch lengths are indicated. Numbers near the nodes represent ML bootstrap value. The scientific names of some species are debated.

Disclosure statement

The authors are grateful to the opened raw genome data from public database. The authors report no conflicts of interest and are responsible for the content and writing of the paper.

Additional information

Funding

This research was supported by the Science and Technology Project of Zhejiang Province, China [2016F50024] and the Major scientific and technological projects for breeding new varieties of Agriculture of Zhejiang Province, China [2016C02056-12].