The complete chloroplast genome sequence of Populus pamirica Kom. (Salicaceae)

Abstract

Populus pamirica Kom. was merely found in Pamir and formed a rare type of riparian forest. Here we assembled the complete chloroplast genome of P. pamirica, which is 157,418 bp in length, with 129 functional genes including eight rRNA, 36 tRNA, and 85 protein-coding genes. The GC content of P. pamirica is 36.6%. Our phylogenetic inference suggested that P. pamirica had close relationship with P. szechuanica. Further studies such as combining nrDNA data are needed to confirm the systematic position of P. pamirica.

Keywords:

• Populus pamirica Kom
• complete chloroplast genome
• phylogeny

Populus L. is a woody genus, which was classified as six sections. Populus pamirica Kom. belonging Sect. Tacamahaca is similar to P. pilosa and P. laurifolia in morphology. P. pamirica is found in Pamir Plateau, including southern Xinjiang, Pakistan and Tajikistan. This species grows along the river and on the forest edge of spruce. Within Sect. Tacamahaca, ten complete chloroplast genomes have been reported and nine of which are from America and East Asia, only one in Central Asia (Tuskan et al. 2006; Zhang et al. 2018). Thus, the phylogenetic relationship of Central Asian species still remains poorly resolved. In this study, we report the complete chloroplast genome sequence of P. pamirica.

Fresh leaves were collected from natural individual of P. pamirica in Khunjerab National Park of Pakistan (N 36°47′31″, E 74°53′74″), and the voucher specimens were deposited at Herbarium, Institute of Botany, CAS (PE) (collection number is FPH-0368). CTAB method (Doyle and Doyle 1987) was used to extract the total genome DNA which was then send to Novogene Company (http://www.novogene.com, China) for 2 × 150 bp pair end sequencing using Illumina HiSeq 4000 platform. Referring to the genome of P. trichocarpa, the Map tool of Geneious R11 (Kearse et al. 2012) was used to filter available reads, which were used for de novo assembly using Geneious R11, then we used Fine Tuning function to bridge gaps. Plann (Huang and Cronk 2015) was employed to annotate the chloroplast genome sequence, and the verification was also performed using Genious R11.

The complete chloroplast genome of P. pamirica is 157,418 bp in length and contains a large single-copy (LSC) region of 85,401 bp, a small single-copy (SSC) region of 16,717 bp, and a pair of inverted repeat (IR) regions of 27,650 bp. This plastome contains 129 genes, including 85 protein-coding genes, eight ribosomal RNA genes and 36 transfer RNA genes. The GC content of the total sequence is 36.6%. The IR regions (41.9%) possess higher GC content than the LSC (34.3%) and SSC (30.5%) regions.

To infer the phylogenetic position of P. pamirica, we constructed Bayesian inference using Mrbayes 3.2.6 (Ronquist and Huelsenbeck 2003) based on 16 published complete chloroplast genome sequences of Populus and Salix. The sequences were aligned by MAFFT v6.833 (Katoh et al. 2005). Our result firstly showed the phylogenetic position of P. pamirica, which fell into a clade formed by P. szechuanica, P. laurifolia and P. koarna along with this species

Figure 1. Bayesian phylogram of Populus pamirica as well as other related species inferred from the complete plastome sequences.

(Figure 1). Within this clade, P. pamirica was closely related to P. szechuanica. However, hybridization frequently occurred in Populus (Eckenwalder 1984; Feng et al. 2013; Wang et al. 2014). Further studies such as combining nrDNA data are needed to confirm the systematic position of P. pamirica.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This study is supported by the National Natural Science Foundation of China [grant no. 31110103911, 31620103902 & J1310002], and Science & Technology Basic Resources Investigation Program of China [grant no. 2017FY100100].