Abstract
Salix triandra is a great willow for bees and an excellent choice for living willow structures. In this study, we assembled and annotated the complete chloroplast (cp) genome sequence of S. triandra. The whole cp genome is 155,821 base-pairs (bp) in size, which comprises one small single copy (SSC) region of 16,223 bp and one large single copy (LSC) region of 84,532 bp separated by a pair of inverted repeats (IRs) of 27,533 bp. There are 131 genes, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis with the Neighbour-joining method indicates that S. triandra is closely related to S. tetrasperma. The complete cp genome will facilitate the biological studies in the order Malpighiales in future.
Keywords: Salix triandra, chloroplast genome, phylogeny
Salix triandra (common names: almond willow, almond-leaved willow) is a species of willow native to Western and Central Asia and Europe. S. triandra has immense economic value because it provides bees with abundant pollen and nectar early in the year (Farkas and Zajácz 2007). Salix triandra belongs to flowering plants of Salicaceae family, which contains 56 genera and about 1220 species summarized by the Angiosperm Phylogeny Group (APG) (Christenhusz and Byng 2016). In this paper, the complete cp genome sequence of S. triandra is characterized for further phylogenetic studies of the family Salicaceae.
The total genomic DNA was extracted from fresh leaves of Salix triandra collected in Maoer Mountain (China; N45°19′40.60″, E127°37′9.03″) using TakaRa MiniBEST Plant Genomic DNA Extraction Kit (Tokyo, Japan). Voucher specimen was deposited in the Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University (DB447). Then, the whole-genome sequences were conducted on PacBio RS II Sequencing Instrument (Pacific Bioscience, USA) by Nextomics Biosciences (Wuhan, China). After controlling quality and correcting of 17.6 G raw data, the remaining high-quality reads were assembled with Falcon version 3.0 (Chin et al. 2016). There are many similar cp genomes of homologous species available, which usually as reference genomes to acquire the order of contigs (Wang et al. 2018). So we used BLASTN (Camacho et al. 2009) to isolate cp contigs of S. triandra based on S. suchowensis (NC_026462.1). The annotation of S. triandra cp genome was conducted with DOGMA (Wyman et al. 2004) with manual check and the physical map was drawn by OGDRAW (Lohse et al. 2007).
The complete cp genome of S. triandra (GenBank accession number: MK722343) is 155,821 bp, and shares the common feature of comprising an LSC region of 84,532 bp, an SSC region of 16,223 bp, and two IRs region of 27,533 bp. The total length of protein-coding genes is 91,877 bp, accounting for 58.96% of the complete cp genome and encoding 26,646 amino acids. The overall GC content is 36.65%, higher than those of LSC (34.39%) and SSC (30.94%) regions, but lower than those of IRs regions 41.79%). The cp genome possesses 131 functional genes, including 86 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. Among these genes, three genes (rps12, clpP, ycf3) have two introns, and other 17 genes have one intron each. There are 18 genes (7 protein-coding genes, 7 tRNA and 4 rRNA genes) duplicated in the IR regions.
To identify the phylogenetic position of S. triandra, 24 cp genomes (excluding S. triandra) of the family Salicaceae were downloaded from National Centre for Biotechnology Information (NCBI). These 25 cp genomes sequences were aligned with ClustalW (Thompson et al. 2002). The phylogenetic tree (Figure 1) based on 70 protein-coding genes using the neighbour-joining method was reconstructed by MEGA7 (Kumar et al. 2016). The phylogenetic analysis showed that S. triandra is evolutionarily closest to S. tetrasperma with 100% bootstrap value.
Figure 1.
Phylogenetic tree with neighbour-joining method was constructed by MEGA7. The 70 protein-coding genes of 25 cp genomes from the Salicaceae family were aligned by ClustalW. The bootstrap values (indicating on the branches) were based on 1000 replicates and the accession number is list after each species name.
Disclosure statement
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References
- Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. BLASTþ: architecture and applications. BMC Bioinformatics. 10(1):421. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chin C-S, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O'Malley R, Figueroa-Balderas R, Morales-Cruz A, et al. 2016. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods. 13(12):1050. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Christenhusz MJ, Byng JW. 2016. The number of known plants species in the world and its annual increase. Phytotaxa. 261(3):201–217. [Google Scholar]
- Farkas Á, Zajácz E. 2007. Nectar production for the Hungarian honey industry. Eur J Plant Sci Biotechnol. 1(2):125–151. [Google Scholar]
- Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 33(7):1870. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lohse M, Drechsel O, Bock R. 2007. OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet. 52(5–6):267–274. [DOI] [PubMed] [Google Scholar]
- Thompson JD, Gibson TJ, Higgins DG. 2002. Multiple sequence alignment using clustalW and clustalX. Current protocols in bioinformatics/editorial board, Andreas D. Baxevanis. [et al.], Chapter 2(Unit 2), Unit 2.3. [DOI] [PubMed] [Google Scholar]
- Wang X, Cheng F, Rohlsen D, Bi C, Wang C, Xu Y, Wei S, Ye Q, Yin T, Ye N, et al. 2018. Organellar genome assembly methods and comparative analysis of horticultural plants. Hortic Res. 5(1):3. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wyman SK, Jansen RK, Boore JL. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics. 20(17):3252–3255. [DOI] [PubMed] [Google Scholar]