The complete chloroplast genome of Populus tomentosa narrow crown, native to Northern China

Abstract

Populus tomentosa narrow crown [P. tomentosa (NC)], natural distributes in northern China, is an economically important ecotype of P. tomentosa. In this study, we assembled its complete chloroplast (cp) genome. The total genome size of P. tomentosa (NC) is 156,368 bp in length, containing a large single copy region of 84,623 bp, a small single copy region of 16,533 bp, and a pair of inverted repeat regions of 27,606 bp. We annotated 130 genes in the genome, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, 12 genes of which have 1 intron and 3 genes contain 2 introns. The overall GC content of the whole genome is 36.8%. Phylogenetic analysis using 24 complete cp genome of Salicaceae suggested that P. tomentosa (NC) is most closely related to P. alba. var. pyramidalis.

Keywords:

• Populus tomentosa narrow crown
• northern China
• chloroplast genome

The Chinese white poplar (Populus tomentosa Carr.), as one of the main commercial hybrid species, is an indigenous species in northern China, which plays a vital role in ecological and environmental protection (Eckenwalder 1996; Zhu and Zhang 1997; Zhang et al. 2004; Zhang et al. 2006). Many wild P. tomentosa ecotypes have arisen during the evolution of the species (Zhang et al. 2007). Among them, P. tomentosa narrow crown [P. tomentosa (NC)] is one of the economically important ecotype of P. tomentosa. In addition, its morphological characteristics such as bark color, bark smoothness, and branches erect are remarkably similar to that of P. alba. var. pyramidalis. Knowledge of its genetic information would contribute to the study of genome diversity and species relationship. In this study, we assembled and characterized the complete chloroplast (cp) genome of P. tomentosa (NC) based on the Illumina pair-end sequencing data.

The samples of P. tomentosa (NC) were collected from Baoding city (Hebei, China; Coordinates: 115°47′E, 38°87′N; Altitude: 26 m). Total genomic DNA was isolated from fresh leaves of the P. tomentosa (NC) using the Ezup plant genomic DNA preps Kit (Sangon Biotech, Shanghai, China). The voucher specimens of P. tomentosa (NC) were deposited at the herbarium of Southwest Forestry University, and DNA samples were correctly stored at Key Laboratory of State Forestry Administration on Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, China. Based on the known sequence of the Populus chloroplast genome, 33 primer pairs were designed and the whole cp genome of P. tomentosa (NC) were amplified using the LA-PCR with Takara PrimeSTAR GXL DNA polymerase followed the method described by Yang et al. (2014) (Table S1). PCR products were sequenced by next generation sequenceing in Nextomics Biosciences. The annotation of the genome was performed using the program Geneious R8 (Biomatters Ltd, Auckland, New Zealand), and then manually confirmed by comparing with the cp genome of P. trichocarpa.

The plastome of P. tomentosa (NC) is a single circular molecule with the length of 156,368 bp. The complete cp genomes displayed the typical quadripartite structure, including a large single copy (LSC) region of 84,623 bp, a small single copy (SSC) region of 16,533 bp, and a pair of inverted repeats (IR) region of 27,606 bp. The overall GC content of the whole genome is 36.8%, while the corresponding values of the LSC (34.6%) and SSC (30.6%) are low than that of the IR regions (42.0%). This cp genome contains 130 functional genes, including 85 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. Among them, 12 genes (atpF, ndhA, ndhB, petB, rpoC1, rpl2, trnK-UUU, trnG-UCC, trnL-UAA, trnV-UAC, trnI-GAU, and trnA-UGC) contain a single intron, and 3 genes (ycf3, rps12, and clpP) have 2 introns. There are 18 genes duplicated in the IR regions, of which 7 are protein-coding genes, 7 are tRNA, and 4 are rRNA genes.

The phylogenetic relationship of P. tomentosa (NC) to other species in Salicaceae was evaluated by comparing the 24 species of Salicaceae chloroplast. Two species, Poliothyrsis sinensis and Flacourtia indica in the family of Flacourtiaceae, were used as out-group. The 26 complete cp sequences were aligned by the MAFFT version 7 software (Katoh and Standley 2013) Phylogenetic analysis was conducted base on maximum likelihood (ML) analyses were implemented in IQ-TREE 1.5.5 (Nguyen et al. 2015) under the GTR + F+R2 nucleotide substitution model, which was selected by ModelFinder (Kalyaanamoorthy et al. 2017). Support for the inferred ML tree was inferred by bootstrapping with 1000 replicates (Gao et al. 2018). The phylogenetic analysis showed that P. tomentosa (NC) appeared to be closely related to P. alba. var. pyramidalis (Figure 1).

Figure 1. Phylogenetic relationships among 24 complete chloroplast genomes of Salicaceae. Bootstrap support values are given at the nodes. Chloroplast genome accession number used in this phylogeny analysis: P. adenopoda: KX425622; P.alba: AP008956; P. alba. var. pyramidalis: MG262344; P. balsamifera: KJ664927; P. cathayana: KP729175; P. davidiana: KX306825; P. euphratica:KJ624919; P. fremontii: KJ664926; P. ilicifolia: KX421095; P. lasiocarpa: KX641589; P. nigra: KX377117; P. qiongdaoensis: KX534066; P. rotundifolia: KX425853; P. simonii: MG262356; P. tomentosa narrow crown: MK252102; P. tremula: KP861984; P. tremula × alba: KT780870; P. szechuanica: MG262357; P. trichocarpa: EF489041; P. yunnanensis: KP729176; S. hypoleuca: MG262363; S. rehderiana: MG262367; S. suchowensis: KM983390; S. taoensis: MG262369; Flacourtia indica: MG262341; Poliothyrsis sinensis: MG262343.

Data Archiving Statement

The chloroplast genome data of the Populus tomentosa narrow crown will be submitted to Genebank of NCBI through the revision process. The accession numbers from Genebank must be supplied before the final acceptance of the manuscript.

Disclosure statement

The authors report no conflict of interest.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China under Grant [Number 31460205, 31860219, 31360184].