Abstract
Populus davidiana plays an important ecological role in boreal and temperate forests, serving as wildlife habitats and watersheds. The complete chloroplast genome sequence of P. davidiana was characterized from Illumina pair-end sequencing. The chloroplast genome of P. davidiana was 155,325 bp in length, containing a large single-copy region (LSC) of 84,679 bp, a small single-copy region (SSC) of 16,862 bp, and two inverted repeat (IR) regions of 26,892 bp. The overall GC content is 36.80%, while the corresponding values of the LSC, SSC, and IR regions are 34.5%, 30.5%, and 42.5%, 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. davidiana and P. hopeiensis clustered together as sisters to other Populus species.
Introduction
Populus davidiana occurs in northern and central parts of China, plus Mongolia, Korea, and the Far East of Russia (Zheng et al. Citation2017; Hou et al. Citation2018). Populus davidiana is widely distributed in the Northern Hemisphere and plays an important ecological role in boreal and temperate forests, serving as wildlife habitats and watersheds; they can dominate riparian forests, but are ecologically adaptable. Populus davidiana has wide geographic distribution, high intraspecific polymorphism, adaptability to different environments, combined with a relatively small genome size. Consequently, P. davidiana 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 Citation2011). Moreover, we can develop conservation strategies easily when we understand the genetic information of P. davidiana. In the present research, we constructed the whole chloroplast genome of P. davidiana and understood many genome variation information about the species, which will provide beneficial help for population genetics studies of P. davidiana.
The fresh leaves of P. davidiana were collected from Lijiang city (100°23′N, 26°88′E). Fresh leaves were silica-dried and taken to the laboratory until DNA extraction. The voucher specimen (SY002) was laid in the Herbarium of Chongqing University of Arts and Sciences and the extracted DNA was stored in the –80 °C refrigerator of the Key Laboratory of College of Landscape Architecture and Life Science. We extracted total genomic DNA from 25 mg silica-gel-dried leaf using a modified CTAB method (Doyle Citation1987). 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 (Hahnet al. Citation2013) and metaSPAdes (Nurk et al. Citation2017) to assemble chloroplast genomes. We used P. tremula (GenBank: NC_027425) as a reference genome. We annotated the chloroplast genome with the software DOGMA (Wyman et al. Citation2004), and then corrected the results using Geneious 8.0.2 (Campos et al., Citation2016) and Sequin 15.50 (http://www.ncbi.nlm.nih.gov/Sequin/).
The complete chloroplast genome of P. davidiana (National Genomics Data Center accession number GWHAMJQ01000000) was characterized from Illumina pair-end sequencing. The complete chloroplast genome sequence of P. davidiana was characterized from Illumina pair-end sequencing. The chloroplast genome of P. davidiana was 155,325 bp in length, containing a large single-copy region (LSC) of 84,679 bp, a small single-copy region (SSC) of 16,862 bp, and two inverted repeat (IR) regions of 26,892 bp. The overall GC content is 36.80%, while the correponding values of the LSC, SSC, and IR regions are 34.5%, 30.5%, and 42.5%, 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).
To confirm the phylogenetic location of P. davidiana within the family of Populus, we used the complete chloroplast genomes sequence of P. davidiana and 21 other related species of Populus and Salix babylonica and Salix arbutifolia as outgroup to construct phylogenetic tree. The 22 chloroplast genome sequences were aligned with MAFFT (Katoh and Standley Citation2013), and then the neighbour-joining tree was constructed by MEGA 7.0 (Kumar et al. Citation2016). The results confirmed that P. davidiana was clustered with P. hopeiensis ().
Figure 1. Neighbour-joining (NJ) analysis of P. davidiana and other related species based on the complete chloroplast genome sequence.
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 National Genomics Data Center at https://bigd.big.ac.cn/search?dbId=gwh&q=GWHAMJQ01000000, accession number GWHAMJQ01000000.
Additional information
Funding
References
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