Comprehensive Analysis of the First Complete Mitogenome and Plastome of a Traditional Chinese Medicine Viola Diffusa

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2024 Dec 2

PMID 39623304

Authors

Chenshuo Zhang

Aamir Rasool

Huilong Qi

Xu Zou

Yimeng Wang

Yahui Wang

Yang Wang

Yan Liu

Yuan Yu

Affiliations

Soon will be listed here.

Abstract

Background: Viola diffusa is used in the formulation of various Traditional Chinese Medicines (TCMs), including antiviral, antimicrobial, antitussive, and anti-inflammatory drugs, due to its richness in flavonoids and triterpenoids. The biosynthesis of these compounds is largely mediated by cytochrome P450 enzymes, which are primarily located in the membranes of mitochondria and the endoplasmic reticulum.

Results: This study presents the complete assembly of the mitogenome and plastome of Viola diffusa. The circular mitogenome spans 474,721 bp with a GC content of 44.17% and encodes 36 unique protein-coding genes, 21 tRNA, and 3 rRNA. Except for the RSCU values of 1 observed for the start codon (AUG) and tryptophan (UGG), the mitochondrial protein-coding genes exhibited a codon usage bias, with most estimates deviating from 1, similar to patterns observed in closely related species. Analysis of repetitive sequences in the mitogenome demonstrated potential homologous recombination mediated by these repeats. Sequence transfer analysis revealed 24 homologous sequences shared between the mitogenome and plastome, including nine full-length genes. Collinearity was observed among Viola diffusa species within the other members of Malpighiales order, indicated by the presence of homologous fragments. The length and arrangement of collinear blocks varied, and the mitogenome exhibited a high frequency of gene rearrangement.

Conclusions: We present the first complete assembly of the mitogenome and plastome of Viola diffusa, highlighting its implications for pharmacological, evolutionary, and taxonomic studies. Our research underscores the multifaceted importance of comprehensive mitogenome analysis.

References

Zhong Y, Yu R, Chen J, Liu Y, Zhou R . Highly active repeat-mediated recombination in the mitogenome of the holoparasitic plant . Front Plant Sci. 2022; 13:988368. PMC: 9532969. DOI: 10.3389/fpls.2022.988368. View

Choi K, Park S . Complete Plastid and Mitochondrial Genomes of Reveal Intracellular Gene Transfer (IGT), Horizontal Gene Transfer (HGT), and Cytoplasmic Male Sterility (CMS). Int J Mol Sci. 2021; 22(11). PMC: 8201098. DOI: 10.3390/ijms22116143. View

Lin B, Hui J, Mao H . Nanopore Technology and Its Applications in Gene Sequencing. Biosensors (Basel). 2021; 11(7). PMC: 8301755. DOI: 10.3390/bios11070214. View

Kurtz S, Choudhuri J, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R . REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 2001; 29(22):4633-42. PMC: 92531. DOI: 10.1093/nar/29.22.4633. View

Zhang X, Gu C, Zhang T, Tong B, Zhang H, Wu Y . Chloroplast (Cp) Transcriptome of P. davidiana Dode×P. bolleana Lauch provides insight into the Cp drought response and Populus Cp phylogeny. BMC Evol Biol. 2020; 20(1):51. PMC: 7201580. DOI: 10.1186/s12862-020-01622-7. View

Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones E, Fischer A, Bock R . GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017; 45(W1):W6-W11. PMC: 5570176. DOI: 10.1093/nar/gkx391. View

Wick R, Schultz M, Zobel J, Holt K . Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 2015; 31(20):3350-2. PMC: 4595904. DOI: 10.1093/bioinformatics/btv383. View

Li X, Lin C, Yang J, Yu W . assembling a complete mitochondrial genome of (Orobanchaceae) using GetOrganelle toolkit. Mitochondrial DNA B Resour. 2020; 5(1):1056-1057. PMC: 7748611. DOI: 10.1080/23802359.2020.1722038. View

Bi C, Qu Y, Hou J, Wu K, Ye N, Yin T . Deciphering the Multi-Chromosomal Mitochondrial Genome of . Front Plant Sci. 2022; 13:914635. PMC: 9240471. DOI: 10.3389/fpls.2022.914635. View

10.

Moon H, Kim S . A complete chloroplast genome sequence of Palibin 1899 (Violaceae), a member of VIOLA ALBIDA complex. Mitochondrial DNA B Resour. 2023; 8(6):673-677. PMC: 10281375. DOI: 10.1080/23802359.2023.2224462. View

11.

Komar A . The Yin and Yang of codon usage. Hum Mol Genet. 2016; 25(R2):R77-R85. PMC: 6372012. DOI: 10.1093/hmg/ddw207. View

12.

Sperisen C, Buchler U, Gugerli F, Matyas G, Geburek T, Vendramin G . Tandem repeats in plant mitochondrial genomes: application to the analysis of population differentiation in the conifer Norway spruce. Mol Ecol. 2001; 10(1):257-63. DOI: 10.1046/j.1365-294x.2001.01180.x. View

13.

Maas S, Rich A . Changing genetic information through RNA editing. Bioessays. 2000; 22(9):790-802. DOI: 10.1002/1521-1878(200009)22:9<790::AID-BIES4>3.0.CO;2-0. View

14.

Modi A, Vai S, Caramelli D, Lari M . The Illumina Sequencing Protocol and the NovaSeq 6000 System. Methods Mol Biol. 2021; 2242:15-42. DOI: 10.1007/978-1-0716-1099-2_2. View

15.

Dill K . Dominant forces in protein folding. Biochemistry. 1990; 29(31):7133-55. DOI: 10.1021/bi00483a001. View

16.

Jung J, Kim J, Jeong Y, Yi G . AGORA: organellar genome annotation from the amino acid and nucleotide references. Bioinformatics. 2018; 34(15):2661-2663. DOI: 10.1093/bioinformatics/bty196. View

17.

Khan A, Asaf S, Lee I, Al-Harrasi A, Al-Rawahi A . First chloroplast genomics study of Phoenix dactylifera (var. Naghal and Khanezi): A comparative analysis. PLoS One. 2018; 13(7):e0200104. PMC: 6067692. DOI: 10.1371/journal.pone.0200104. View

18.

Liu S, Ni Y, Li J, Zhang X, Yang H, Chen H . CPGView: A package for visualizing detailed chloroplast genome structures. Mol Ecol Resour. 2023; 23(3):694-704. DOI: 10.1111/1755-0998.13729. View

19.

Zhou S, Wei N, Jost M, Wanke S, Rees M, Liu Y . The Mitochondrial Genome of the Holoparasitic Plant Thonningia sanguinea Provides Insights into the Evolution of the Multichromosomal Structure. Genome Biol Evol. 2023; 15(9). PMC: 10476698. DOI: 10.1093/gbe/evad155. View

20.

Sheng W, Deng J, Wang C, Kuang Q . The garden asparagus ( L.) mitochondrial genome revealed rich sequence variation throughout whole sequencing data. Front Plant Sci. 2023; 14:1140043. PMC: 10084930. DOI: 10.3389/fpls.2023.1140043. View