Abstract
Salix sinopurpurea is a morphologically special shrubby willow characterizing opposite leaves. Here, we reported the complete chloroplast (cp) genome sequence of Salix sinopurpurea. The cp genome is 155,546 bp in length, including a large single-copy (LSC) region of 84,412 bp, a small single-copy (SSC) region of 16,216 bp, and a pair of inverted repeated regions of 27,459 bp. The cp genome of Salix sinopurpurea encodes 130 genes, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic tree showed that Salix sinopurpurea is closely related to Salix psammophila and Salix suchowensis.
Keywords: Salix sinopurpurea, complete chloroplast genome, phylogeny
Salix sinopurpurea C. Wang et C. Y. Yang is a shrubby willow that is always confused with S. purpurea L., S. linearistipularis (Franch.) Hao and S. suchowensis Cheng based on morphological features. Salix sinopurpurea is one of the unique species characterizing opposite leaves in genus Salix. Thus, S. sinopurpurea is an important species to shed light on the evolutionary and phylogenetic relation of genus Salix. In this study, we assembled and annotated the complete chloroplast (cp) genome of S. sinopurpurea (GenBank accession number: MW077725) to provide genomic and genetic sources for further research.
The fresh leaves of S. sinopurpurea were collected from Xian, Shaanxi province, China (N 108°48′49″, E 33°51′6″). The voucher specimens (collection number: HLCS19_18) were deposited in the Herbarium of Beijing Forestry University (BJFC). Genomic DNAs were extracted using CTAB method (Doyle and Doyle 1987), and 2 × 150 bp pair-end sequencing was performed on an Illumina HiSeq 4000 platform at Novogene (http://www.novogene.com, Beijing, China). The whole assembly process was conducted with Geneious 10.2 (Kearse et al. 2012), mainly following He et al. (2019), using S. babylonica (MF189167) as reference. The initial annotations of complete cp genome were performed using Plastid Genome Annotator (PGA) (Qu et al. 2019) with Amborella trichopoda (AJ506156) as reference, and verified manually using Unix program Plann 1.1.2 (Huang and Cronk 2015) and Geneious 10.2 (Kearse et al. 2012).
The cp genome of S. sinopurpurea was 155,546 bp in length, containing a large single-copy (LSC) region of 84,412 bp, a small single-copy (SSC) region of 16,216 bp, and a pair of inverted repeat (IR) regions of 27,459 bp. Genome annotation predicted 130 genes, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC-content of the cp genome was 36.7%, while the corresponding values in the LSC, SSC, and IR regions were 34.4%, 31.0%, and 41.9%, respectively.
Phylogenetic inference suggested that S. sinopurpurea is closely related to S. psammophila and S. suchowensis (Figure 1), which was conducted using the best-fit model K3Pu + F+R2 according to Bayesian Information Criterion in IQ-TREE 1.6.12 (Nguyen 2015) with 5000 bootstrap replicates. The 23 complete cp genomes were aligned using MAFFT (Katoh and Standley 2013). This study could lay a foundation for species delimitation and evolutionary relation of genus Salix in the future.
Figure 1.
Maximum likelihood tree with 5000 bootstrap replicates constructed using IQ-TREE based on chloroplast genomes of 23 Salicaceae species.
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 GenBank of NCBI at https://www.ncbi.nlm.nih.gov/, reference number MW077725.
References
- Doyle JJ, Doyle JL.. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 19:11–15. [Google Scholar]
- He J, Yao M, Lyu RD, Lin LL, Liu HJ, Pei LY, Yan SX, Xie L, Cheng J.. 2019. Structural variation of the complete chloroplast genome and plastid phylogenomics of the genus Asteropyrum (Ranunculaceae). Sci Rep. 9(1):15285. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Huang DI, Cronk QC.. 2015. Plann: a command-line application for annotating plastome sequences. Appl Plant Sci. 3(8):1500026. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Katoh K, Standley DM.. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28(12):1647–1649. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ.. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 32(1):268–274. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Qu XJ, Moore MJ, Li DZ, Yi TS.. 2019. PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes. Plant Methods. 15:50. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/, reference number MW077725.