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对传统中药白花地丁首个完整线粒体基因组和叶绿体基因组的综合分析。

Comprehensive analysis of the first complete mitogenome and plastome of a traditional Chinese medicine Viola diffusa.

作者信息

Zhang Chenshuo, Rasool Aamir, Qi Huilong, Zou Xu, Wang Yimeng, Wang Yahui, Wang Yang, Liu Yan, Yu Yuan

机构信息

College of Life Sciences, North China University of Science and Technology, 21 Bo Hai Road, Tangshan, People's Republic of China.

Institute of Biochemistry, University of Balochistan, Quetta, 87300, Pakistan.

出版信息

BMC Genomics. 2024 Dec 2;25(1):1162. doi: 10.1186/s12864-024-11086-4.

DOI:10.1186/s12864-024-11086-4
PMID:39623304
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11610153/
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.

摘要

背景

白花地丁用于多种中药配方，包括抗病毒、抗菌、镇咳和抗炎药物，因其富含黄酮类化合物和三萜类化合物。这些化合物的生物合成主要由细胞色素P450酶介导，这些酶主要位于线粒体和内质网的膜上。

结果

本研究展示了白花地丁有丝分裂基因组和质体基因组的完整组装。环状有丝分裂基因组跨度为474,721 bp，GC含量为44.17%，编码36个独特的蛋白质编码基因、21个tRNA和3个rRNA。除起始密码子（AUG）和色氨酸（UGG）的相对同义密码子使用值（RSCU）为1外，线粒体蛋白质编码基因表现出密码子使用偏好，大多数估计值偏离1，这与在密切相关物种中观察到的模式相似。对有丝分裂基因组中重复序列的分析表明，这些重复序列介导了潜在的同源重组。序列转移分析揭示了有丝分裂基因组和质体基因组之间共享24个同源序列，包括9个全长基因。在金虎尾目其他成员中的白花地丁物种间观察到共线性，这由同源片段的存在表明。共线块的长度和排列各不相同，有丝分裂基因组表现出高频的基因重排。

结论

我们展示了白花地丁有丝分裂基因组和质体基因组的首次完整组装，突出了其在药理学、进化和分类学研究中的意义。我们的研究强调了全面有丝分裂基因组分析的多方面重要性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/262d/11610153/c7369c31b480/12864_2024_11086_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/262d/11610153/1cbf24f0639b/12864_2024_11086_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/262d/11610153/50eecc62a434/12864_2024_11086_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/262d/11610153/40a04d588aff/12864_2024_11086_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/262d/11610153/be70d9e82c7f/12864_2024_11086_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/262d/11610153/2db234100655/12864_2024_11086_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/262d/11610153/5483a955d794/12864_2024_11086_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/262d/11610153/c7369c31b480/12864_2024_11086_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/262d/11610153/1cbf24f0639b/12864_2024_11086_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/262d/11610153/50eecc62a434/12864_2024_11086_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/262d/11610153/40a04d588aff/12864_2024_11086_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/262d/11610153/be70d9e82c7f/12864_2024_11086_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/262d/11610153/2db234100655/12864_2024_11086_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/262d/11610153/5483a955d794/12864_2024_11086_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/262d/11610153/c7369c31b480/12864_2024_11086_Fig7_HTML.jpg

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