The complete chloroplast genome of Sorbus folgneri (C.K.Schneid.) Rehder (Rosaceae)

Abstract

Sorbus folgneri (C.K.Schneid.) Rehder is widely distributed tree species across China which can be used as medicine, building materials and ornamental plants. In this study, the complete chloroplast (cp) genome sequence of S. folgneri was determined using next-generation sequencing. The entire cp genome was determined to be 163,464 bp in length. It contained large single-copy (LSC) and small single-copy (SSC) regions of 86,721 and 17,961 bp, respectively, which were separated by a pair of 29,391bp inverted repeat (IR) regions. The genome contained 133 genes, including 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of the genome is 36.4%. A phylogenetic tree reconstructed by 17 chloroplast genomes reveals that S. folgneri is most related with Sorbus alnifolia.

Keywords:

• Sorbus folgneri
• complete chloroplast genome
• phylogenetic analysis
• Rosaceae

The genus Sorbus L. comprises approximately 80 species and occurs widely throughout northern hemisphere (Lu and Spongberg 2003). There are about 50 species of Sorbus in China. Sorbus folgneri (C.K.Schneid.) Rehder is widely distributed across central and southern China which can be used as medicine, building materials, and ornamental plants. In addition, its phylogenetic position is unclear in previous studies because of the lack of genomic resources of genus Sorbus. Here, we characterized the complete chloroplast (cp) genome sequence of S. folgneri, the third complete plastome sequence from the genus Sorbus, based on the genome skimming sequencing data.

The total genomic DNA was extracted from the fresh leaves of S. folgneri (Lushan National Park, 29.32°N, 116.01°E) using the DNeasy Plant Mini Kit (Qiagen, Valencia, CA). The DNA was is stored at −80 °C in our lab. The whole genome sequencing was conducted by Nanjing Genepioneer Biotechnologies Inc. (Nanjing, China) on the Illumina Hiseq platform. The filtered sequences were assembled using the program SPAdes assembler 3.10.0 (Bankevich et al. 2012). Annotation was performed using the DOGMA (Wyman et al. 2004) and BLAST searches. The plastome of S. folgneri was determined to comprise double-stranded, circular DNA of 163,464 bp containing two inverted repeat (IR) regions of 29,391 bp each, separated by large single-copy (LSC) and small single-copy (SSC) regions of 86,721 and 17,961 bp, respectively (NCBI acc. no. MK161058). The genome contained 133 genes, including 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Eight full protein-coding genes, seven tRNA genes, and four rRNA genes were duplicated in IR region. Nineteen genes contained one intron and two genes (clpP and ycf3) contained two introns. The overall GC content of S. folgneri cp genome is 36.4% and the corresponding values in LSC, SSC, and IR regions are 34.2%, 30.3%, and 41.5%, respectively.

To investigate its taxonomic status, Alignment was performed on the 17 chloroplast genome (16 Rosaceae chloroplast genomes and the outgroup Ziziphus jujube) sequences using MAFFT v7.307 (Katoh and Standley 2013), and a maximum likelihood (ML) was constructed by FastTree version 2.1.10 (Price et al. 2010). The ML phylogenetic tree shows that S. folgneri is most related to Sorbus alnifolia in Maleae, with bootstrap support values of 100% (Figure 1).

Figure 1. Phylogenetic tree inferred by maximum-likelihood (ML) method based on the complete chloroplast genome of 17 representative species of Rosaceae. Ziziphus jujuba (Rhamnaceae) was used as an outgroup and the bootstrap support values are shown at the branches.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This research was supported by the National Natural Science Foundation of China [31300558], the Natural Science Foundation of Jiangsu Province [BK20130972], the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), and the Top-notch Academic Programs Project of Jiangsu Higher Education Institutions (TAPP).