Assembly and comparative analysis of the complete mitochondrial genome of Viburnum chinshanense

Viburnum chinshanense is an endemic species found exclusively in the North-Central and South-Central regions of China. This species is a lush garden ornamental tree and is extensively utilized for vegetation restoration in rocky desertification areas. In this study, we obtained 13.96 Gb of Oxford Na...

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Bibliographic Details
Published in:BMC plant biology 2023-10, Vol.23 (1), p.1-487, Article 487
Main Authors: Zhu, Haoxiang, Shan, Yuanyu, Li, Jingling, Zhang, Xue, Yu, Jie, Wang, Haiyang
Format: Article
Language:English
Subjects:
Analysis
Angiosperms
Annotations
Assembly
Botanical research
Cell division
Comparative analysis
Cytochrome
Desertification
Dipsacales
Ecological restoration
Endemic species
Genes
Genetic aspects
Genomes
Genomics
Lamiales
Medical research
Mitochondria
Mitochondrial DNA
Mitochondrial genome
Mutation
Natural history
Ornamental trees
Phylogenetics
Phylogeny
Proteins
RNA editing
RNA editing
MTPT
rRNA
Transfer RNA
tRNA
Viburnum
Viburnum chinshanense
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Summary:Viburnum chinshanense is an endemic species found exclusively in the North-Central and South-Central regions of China. This species is a lush garden ornamental tree and is extensively utilized for vegetation restoration in rocky desertification areas. In this study, we obtained 13.96 Gb of Oxford Nanopore data for the whole genome, and subsequently, by combining Illumina short-reads, we successfully assembled the complete mitochondrial genome (mitogenome) of the V. chinshanense using a hybrid assembly strategy. The assembled genome can be described as a circular genome. The total length of the V. chinshanense mitogenome measures 643,971 bp, with a GC content of 46.18%. Our annotation efforts have revealed a total of 39 protein-coding genes (PCGs), 28 tRNA genes, and 3 rRNA genes within the V. chinshanense mitogenome. The analysis of repeated elements has identified 212 SSRs, 19 long tandem repeat elements, and 325 pairs of dispersed repeats in the V. chinshanense mitogenome. Additionally, we have investigated mitochondrial plastid DNAs (MTPTs) and identified 21 MTPTs within the mitogenome and plastidial genome. These MTPTs collectively span a length of 9,902 bp, accounting for 1.54% of the mitogenome. Moreover, employing Deepred-mt, we have confidently predicted 623 C to U RNA editing sites across the 39 protein-coding genes. Furthermore, extensive genomic rearrangements have been observed between V. chinshanense and the mitogenomes of related species. Interestingly, we have also identified a bacterial-derived tRNA gene (trnC-GCA) in the V. chinshanense mitogenome. Lastly, we have inferred the phylogenetic relationships of V. chinshanense with other angiosperms based on mitochondrial PCGs. This study marks the first report of a mitogenome from the Viburnum genus, offering a valuable genomic resource for exploring the evolution of mitogenomes within the Dipsacales order.
ISSN:1471-2229
1471-2229
DOI:10.1186/s12870-023-04493-4