The complete chloroplast genome sequence of Populus tremula (Salicaceae)

Abstract

The complete chloroplast genome sequence of Populus tremula was characterized from Illumina pair-end sequencing. The chloroplast genome of P. tremula was 156,862 bp in length, containing a large single-copy region (LSC) of 84,971 bp, a small single-copy region (SSC) of 16,605 bp, and two inverted repeat (IR) regions of 27,640 bp. The overall GC content is 30.69%, while the correponding values of the LSC, SSC, and IR regions are 64.5%, 69.3%, and 60.1%, respectively. The genome contains 131 complete genes, including 86 protein-coding genes (62 protein-coding gene species), 37 tRNA genes (29 tRNA species) and 8 rRNA genes (4 rRNA species). The Neighbour-joining phylogenetic analysis showed that P. tremula and Populus davidiana clustered together as sisters to other Populus species.

Keywords:

• P. tremula
• chloroplast genome
• phylogenetic analysis
• genetic information

Introduction

Populus tremula (Salicaceae) is among the most geographically widespread (across latitudes) and ecologically important tree species in Northern Hemisphere, which has persisted largely in an undomesticated state that is highly resistant to different environmental stresses (Hou et al. 2018). P. tremula has high ecological and economic value with high levels of intraspecific genetic diversity. P. tremula has wide geographic distribution, high intraspecific polymorphism, adaptability to different environments, combined with a relatively small genome size. Consequently, P. tremula represents an excellent model for understanding how different evolutionary forces have sculpted the variation patterns in the genome during the process of population differentiation and ecological speciation (Neale and Antoine 2011). Moreover, we can develop conservation strategies easily when we understand the genetic information of P. tremula. In the present research, we constructed the whole chloroplast genome of P. tremula and understood many genome varition information about the species, which will provide beneficial help for population genetics studies of P. tremula

The fresh leaves of P. tremula were collected from Xin Jiang (88°31′N, 43°19′E). Fresh leaves were silica-dried and taken to the laboratory until DNA extraction. The voucher specimen (OZSY001) was laid in the Herbarium of China West Normal University and the extracted DNA was stored in the −80 °C refrigerator of the Key Laboratory of Southwest China Wildlife Resources Conservation. We extracted total genomic DNA from 25 mg silica-gel-dried leaf using a modified CTAB method (Doyle 1987). The whole-genome sequencing was then conducted by Biodata Biotechnologies Inc. (Hefei, China) with Illumina Hiseq platform. The Illumina HiSeq 2000 platform (Illumina,San Diego, CA) was used to perform the genome sequence. We used the software MITObim 1.8 (Hahn et al. 2013) and metaSPAdes (Nurk et al. 2017) to assemble chloroplast genomes. We used P. tremuloides (GenBank: MN561844) as a reference genome. We annotated the chloroplast genome with the software DOGMA (Wyman et al. 2004), and then corrected the results using Geneious 8.0.2 (Campos et al. 2016) and Sequin 15.50 (http://www.ncbi.nlm.nih.gov/Sequin/).

The complete chloroplast genome of P. tremula (National Genomics Data Center accession number GWHAMKC00000000) was characterized from Illumina pair-end sequencing. The complete chloroplast genome sequence of Populus tremula was characterized from Illumina pair-end sequencing. The chloroplast genome of P. tremula was 156,862 bp in length, containing a large single-copy region (LSC) of 84,971 bp, a small single-copy region (SSC) of 16,605 bp, and two inverted repeat (IR) regions of 27,640 bp. The overall GC content is 30.69%, while the correponding values of the LSC, SSC, and IR regions are 64.5%, 69.3%, and 60.1%, respectively. The genome contains 131 complete genes, including 86 protein-coding genes (62 protein-coding gene species), 37 tRNA genes (29 tRNA species) and 8 rRNA genes (4 rRNA species).

We used the complete chloroplast genomes sequence of P. tremula and 12 other related species of Populus and Salix interior as outgroup to construct phylogenetic tree. The 14 chloroplast genome sequences were aligned with MAFFT (Katoh and Standley 2013), and then the Neighbour-joining tree was constructed by MEGA 7.0 (Kumar et al. 2016). The results confirmed that P. tremula was clustered with P. davidiana (Figure 1).

Figure 1. Neighbour-joining (NJ) analysis of P. tremula and other related species based on the complete chloroplast genome sequence. Genbank accession numbers: P. davidiana (KP861984), P. koreana (MN864049), P. yunnanensis (KP729176), P. euphratica (KJ624919), P. adenopoda (NC032368), P. rotundifolia (KX425853), P. cathayana (KP929175), P. balsamifera (KJ664927), P. ilicifolia (NC031371), P. trichocarpa (EF489041), P. fremontii (KJ664926), P. tremuloides (MN561844) and Salix interior (NC024681).

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The data that support the findings of this study are openly available in National Genomics Data Center at https://bigd.big.ac.cn/gwh, accession number GWHAMKC00000000.

Additional information

Funding

Financial support for this research was provided by the Fundamental Research Funds of China West Normal University [Grant No. 19E044] and the Open Fund of State Key Laboratory of Tree Genetics and Breeding (Chinese Academy of Forestry) [Grant No. TGB2019002].