Abstract
Viburnum dilatatum Thunb. is a large deciduous tree of Adoxaceae. In this study, the chloroplast genome sequence of V. dilatatum is 158,392 bp, consisting of a large single-copy (LSC) region with 87,070 bp, a small single-copy (SSC) region with 18,242 bp , and two inverted repeat (IR) regions with 26,540 bp. The GC content in the chloroplast genome of C. julianae is 38.1%. The chloroplast genome of V. dilatatum contains 126 genes, including 83 protein-coding genes, 39 tRNA genes, and 4 rRNA genes. Phylogenetic tree showed that V. dilatatum was clustered with V. utile.
Keywords: Viburnum dilatatum, chloroplast genome, Illumina sequencing, phylogenetic tree
Viburnum is a genus of Adoxaceae, including more than 200 species, and widely distributed in temperate and subtropical regions of the world. It has been reported that the solvent extracts of Viburnum dilatatum Thunb. could be used as an anti-irritation ingredient (Kwon et al. 2010). And its fruit has the alpha-glucosidase inhibitory activities and the antihyperglycemic action (Kunihisal et al. 2006). It is closely related to Viburnum erosum Thunb. and Viburnum wrightii Miq., meanwhile its intermediate forms are often found, resulting in taxonomic confusions (Jongsun 2019). So our complete Chloroplast genome data of V. dilatatum can contribute to a better understanding of the evolution of Viburnum.
The fresh leaf samples of V. dilatatum were collected in Botanical Garden, Zhengzhou, China (N34449.1680; E1133211.7960). The voucher specimen was deposited at the Herbarium of Henan Agricultural University (voucher number:VD-20-0915). The total genomic DNA was extracted from fresh leaves of V. dilatatum using a modified CTAB method (Doyle and Doyle 1987). Sequencing was performed with the Illumina HiSeq2500 Platform (San Diego, CA). The raw reads were generated by Illumina paired-end sequencing after removing adapters. The low-quality sequences of raw reads used Fastp (https://github.com/OpenGene/Fastp) for quality control. Resultant clean reads were assembled by GetOrganelle pipeline version 1.6.3a (https://github.com/Kinggerm/GetOrganelle) with the gene from Viburnum utile (GenBank accession no. NC_032296) as the reference sequence. The genome was automatically annotated by using the CpGAVAS2 pipeline (http://www.herbalgenomics.org/cpgavas) (Shi et al. 2019) and start/stop codons and intron/exon boundaries were adjusted in Geneious 20.2.2 (https://www.geneious.com/).
The chloroplast genome sequences of V. dilatatum were submitted to NCBI, and the accession number was MW346666. The genome sequences of V. dilatatum is 158,392 bp, consisting of a large single-copy (LSC) region with 87,070 bp, a small single-copy (SSC) region with 18,242 bp, and two inverted repeat (IR) regions with 26,540 bp. The GC content in the chloroplast genome of V. dilatatum is 38.1%. The chloroplast genome of V. dilatatum contained 126 genes, including 83 protein-coding genes, 39 tRNA genes, and 4 rRNA genes.
The phylogenetic tree was constructed based on the genome sequences of V. dilatatum in RAxML version 8.2 (Stamatakis 2006) with 1000 bootstrap replicates. As shown in the phylogenetic tree (Figure 1), the sixteen Adoxaceae species were grouped into four clusters. One of the clusters was comprised of four genus Viburnum species, which V. dilatatum was closely related to V. utile. This result was similar to the previous phylogenetic trees based on chloroplast genome sequences of Adoxaceae (Wang et al. 2020; Zhao et al. 2020).
Figure 1.
Maximum likelihood (ML) phylogenetic tree inferred from 16 plant chloroplast genomes. Numbers next to the branches are bootstrap support percentages.
Funding Statement
This work was supported by High-level talents scientific research project of North China University of Water Resources and Electric Power [201629].
Disclosure statement
No potential conflict of interest was reported by the author(s).
Data availability statement
The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/) under the accession no. MW346666. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA670186, SRA: SRS7893946, and SAMN17100625, respectively.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/) under the accession no. MW346666. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA670186, SRA: SRS7893946, and SAMN17100625, respectively.