The complete chloroplast genome sequence of Pyrus phaeocarpa Rehd.

Abstract

Pyrus phaeocarpa Rehd. belongs to the Pyrus genus (Rosaceae) with high commercial value in China. Many trees in the wild have been destroyed affected by human activities and needed to be protection urgently. In this study, we reported the complete chloroplast genome sequence of P. phaeocarpa using Illumina sequencing technology. The complete chloroplast genome of P. phaeocarpa was 160,203 bp in length, containing a large single copy (LSC, 88,200 bp), a small single copy (SSC, 19,231 bp), and a pair of inverted repeats (IRs, 26,385 bp). The chloroplast genome GC content was 36.54%, contained 113 unique genes, including 30 tRNA, four rRNA, and 79 protein-coding genes. Phylogenetic analysis revealed that P. phaeocarpa was close to P. pashia, P. pyrifolia, and P. ussuriensis, provided strong support for the relationship of Pyrus.

Keywords:

• Pyrus phaeocarpa Rehd
• chloroplast genome
• phylogenetic analysis

Pyrus is the second most important rosaceous fruit species, origin from tertiary or possibly even more ancient periods based on paleontological data (Rubtsov 1944; Hummer and Janick 2009). Pyrus phaeocarpa is of the genus Pyrus of Rosaceae, Rosales, which is distributed among northern China (Bell et al. 1996). The rootstock often used as stock to graft pear cultivars as important germplasm resources for genetic breeding of pears (Gu and Stephen 1994). This species is hermaphrodite and has important research value in system evolution of the genus Pyrus. In recent years, some wild resources have been destroyed due to frequent human activities, understanding its genomics will contribute to the formulation of protection strategies and interspecific relationships of Pyrus.

The young leaves sample of wild P. phaeocarpa was collected from Xiangyang, Shanxi, China (112°1'6.3″E, 35°27'43.4″N), the voucher specimen (PPR001) was deposited at the herbarium of Museum of Beijing Forestry University. Total genomic DNA was extracted using CTAB method (Doyle and Doyle 1987) and sequenced on the Illumina Hiseq X–Ten Sequencing platform at Yuanyi, Beijing, China (http://www.ori–gene.cn/). Raw reads were quality control used the FastQC software (Andrews 2010), then clean reads were assembled into a single draft sequence with the reference chloroplast genome of P. hopeiensis (MF521826) (Li et al. 2018) using SOAPdenovo and BLAT (Kent 2002; Luo et al. 2012). The draft sequence was filled the gaps with high–quality short sequences using SOAPdenovo GapCloser software (Luo et al. 2012). The sequence was annotated using CpGAVAS (Liu et al. 2012), then manually auxiliary annotation by using DOGMA (Wyman et al. 2004). The P. phaeocarpa chloroplast genome sequence has been submitted to GenBank using Bankit (https://www.ncbi.nlm.nih.gov/books/NBK63590/) (accession number: MK488091).

The complete chloroplast genome of P. phaeocarpa was 160,203 bp in length with 36.54% overall GC content, consist of a small single copy (SSC) region of 19,231 bp, a large single copy (LSC) region of 88,200 bp, and a pair repeat regions of inverted repeat (IRa and IRb) of 26,385 bp by each. The chloroplast genome encodes 113 unique genes, including 79 protein–coding genes, 30 tRNA genes, and four rRNA genes.

The phylogenetic relationship of P. phaeocarpa was determined based on six representative species of Pyrus and three outgroups (Sorbus ulleungensis, Eriobotrya japonica, and Sorbus torminalis) using PAUP* 4.10 (Swofford 2003) by Maximum Parsimony (MP). Bayesian inference (BI) was performed with Mrbayes v3.2.3 (Ronquist et al. 2012). The phylogenetic tree showed that P. phaeocarpa was close to P. pashia, P. pyrifolia, and P. ussuriensis (Figure 1), which is coherent with a previous report that considered P. phaeocarpa might have developed from the hybridization of P. betulaefolia, P. pyrifolia and P. ussuriensis (Jiang et al. 2016) may have a closer evolutionary relationship.

Figure 1. Phylogenetic relationships of the 10 species inferred from Maximum Parsimony (MP) and Bayesian inference (BI) based on complete genome sequences. MP bootstrap values/pp values for Bayesian analysis are shown at each node.

Disclosure statement

The authors have declared that no competing interests exist.

Additional information

Funding

This work was supported by the Key Study Projects (Agriculture) of Shanxi Province (grant no. 201803D221016–3 to Dong-Xu Zhang).