The complete chloroplast genome sequence of Populus wilsonii and its phylogenetic analysis

Abstract The complete chloroplast genome of Populus wilsonii was reconstructed by reference-based assembly using whole-genome sequencing data. The total chloroplast genome size of P. wilsonii was 158,080 bp in length, including a pair of inverted repeat regions (IRs) of 27,749 bp each, a large single-copy region (LSC) of 85,949 bp and a small single-copy region (SSC) of 16,633 bp. A total of 133 genes were predicted from the chloroplast genome, including 86 protein-coding genes, 39 tRNA genes and eight rRNA genes. Among these genes, 20 genes occurred in IRs, containing nine protein-coding genes, seven tRNA genes and four rRNA genes. The GC content of P. wilsonii chloroplast genome was 36.6%. The phylogenetic analysis with 15 other species showed that P. wilsonii was closely clustered with Populus cathayana. The complete chloroplast genome of P. wilsonii provides new insights into Populus evolutionary and genomic studies.

Populus is a genus of deciduous flowering plants, which was traditionally divided into six sections based on leaf and flower characters. Populus wilsonii is grouped into Populus section Leucoides, and its leaves are 8-20 cm long, 7-15 cm wide. Being native to China, P. wilsonii is found in Gansu, Hubei, Shaanxi, Sichuan, Xizang and Yunnan provinces. This poplar is related to Populus lasiocarpa, whose chloroplast genome was reported recently (Zhang et al. 2017). Given to both natural and artificial inter-specific hybrids, the classification of polar is very difficult. The genetic relationships and evolutionary history of poplar are still poorly investigated (Liu et al. 2016). The chloroplast genome was widely used in genetic and evolutionary studies (Rogalski et al. 2015). In this study, we reported the complete chloroplast genome sequence of P. wilsonii.
The sample of P. wilsonii was collected from Shennongjia Protected Area (Hubei, China; 31 41 0 40.38 00 N, 110 26 0 1.26 00 E). The total DNA was extracted from fresh leaves using the DNeasy Plant Mini Kit (Qiagen Inc., Valencia, CA) and then used for whole-genome sequencing on Hiseq 2500 platform (Illumina Inc., San Diego, CA). A total of 97.35 GB 100 bp paired-end raw reads were retrieved and then 67.81 GB quality-trimmed clean reads were used for the chloroplast genome reconstruction by the program MITObim v1.9 with default parameters (Hahn et al. 2013). The chloroplast sequence of Populus trichocarpa (NC_009143.1) was used as a reference (Tuskan et al. 2006). The chloroplast genome of P. wilsonii was annotated through the program DOGMA to predict protein-coding genes, transfer RNA (tRNA) genes and ribosome RNA (rRNA) genes (Wyman et al. 2004).
To dip into the phylogenetic position of P. wilsonii, 16 complete chloroplast genomes were downloaded from NCBI, including 13 poplar and three other species. A maximum parsimony (MP) tree was constructed using MEGA 5.05 (Tamura et al. 2011). The phylogenetic tree showed that P. wilsonii and Populus cathayana were grouped together with a 100% bootstrap support (Figure 1). The complete chloroplast genome of P. wilsonii filled an important gap in providing chloroplast genome information for section Leucoides, providing further insights into Populus evolutionary and genomic studies.

Disclosure statement
None of the co-authors has any conflict of interest to declare. The authors alone are responsible for the content and writing of the paper.

Funding
This work was supported by the National Natural Science Foundation of China (31500547).