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1.
Arch Virol ; 168(4): 107, 2023 Mar 11.
Article in English | MEDLINE | ID: mdl-36899282

ABSTRACT

Burdock (Arctium lappa L.) is not only a popular vegetable crop but also an important medicinal plant. In burdock plants with symptoms of leaf mosaic, a novel torradovirus tentatively named "burdock mosaic virus" (BdMV) was identified by high-throughput sequencing. The complete genomic sequence of BdMV was further determined using RT-PCR and the rapid amplification of cDNA ends (RACE) method. The genome is composed of two positive-sense single-stranded RNAs. RNA1 (6991 nt) encodes a polyprotein of 2186 aa, and RNA2 (4700 nt) encodes a protein of 201 aa and a polyprotein of 1212 aa that is predicted to be processed into one movement protein (MP) and three coat proteins (CPs). The Pro-Pol region of RNA1 and the CP region of RNA2 shared the highest amino acid sequence identity of 74.0% and 70.6%, respectively, with the corresponding sequences of lettuce necrotic leaf curl virus (LNLCV) isolate JG3. Phylogenetic analysis based on the amino acid sequences of the Pro-Pol and CP regions showed that BdMV clustered with other non-tomato-infecting torradoviruses. Taken together, these results suggest that BdMV is a new member of the genus Torradovirus.


Subject(s)
Arctium , Mosaic Viruses , Secoviridae , Arctium/genetics , Phylogeny , Genome, Viral , Secoviridae/genetics , Genomics , Mosaic Viruses/genetics , Polyproteins/genetics , Plant Diseases
2.
BMC Plant Biol ; 23(1): 86, 2023 Feb 09.
Article in English | MEDLINE | ID: mdl-36759759

ABSTRACT

BACKGROUND: Burdock is a biennial herb of Asteraceae found in Northern Europe, Eurasia, Siberia, and China. Its mature dry fruits, called Niu Bang Zi, are recorded in various traditional Chinese medicine books. With the development of sequencing technology, the mitochondrial, chloroplast, and nuclear genomes, transcriptome, and sequence-related amplified polymorphism (SRAP) fingerprints of burdock have all been reported. To make better use of this data for further research and analysis, a burdock database was constructed. RESULTS: This burdock multi-omics database contains two burdock genome datasets, two transcriptome datasets, eight burdock chloroplast genomes, one burdock mitochondrial genome, one A. tomentosum chloroplast genome, one A. tomentosum mitochondrial genome, 26 phenotypes of burdock varieties, burdock rhizosphere-associated microorganisms, and chemical constituents of burdock fruit, pericarp, and kernel at different growth stages (using UPLC-Q-TOF-MS). The wild and cultivation distribution of burdock in China was summarized, and the main active components and pharmacological effects of burdock currently reported were concluded. The database contains ten central functional modules: Home, Genome, Transcriptome, Jbrowse, Search, Tools, SRAP fingerprints, Associated microorganisms, Chemical, and Publications. Among these, the "Tools" module can be used to perform sequence homology alignment (Blast), multiple sequence alignment analysis (Muscle), homologous protein prediction (Genewise), primer design (Primer), large-scale genome analysis (Lastz), and GO and KEGG enrichment analyses (GO Enrichment and KEGG Enrichment). CONCLUSIONS: The database URL is http://210.22.121.250:41352/ . This burdock database integrates molecular and chemical data to provide a comprehensive information and analysis platform for interested researchers and can be of immense help to the cultivation, breeding, and molecular pharmacognosy research of burdock.


Subject(s)
Arctium , Plants, Medicinal , Plants, Medicinal/genetics , Arctium/genetics , Arctium/chemistry , Multiomics , Plant Breeding , Medicine, Chinese Traditional , Plant Extracts/chemistry
3.
Genome ; 63(1): 53-60, 2020 Jan.
Article in English | MEDLINE | ID: mdl-31580739

ABSTRACT

Arctium lappa, commonly called burdock, has a long medicinal and edible history. It has recently gained increasing attention because of its economic value. In this study, we obtained the complete chloroplast genome of A. lappa by Illumina Hiseq. The complete chloroplast genome of A. lappa is a typical circular structure with 152 708 bp in length. The GC content in the whole chloroplast genome of A. lappa is 37.7%. A total of 37 tRNA genes, 8 rRNA genes, and 87 protein-coding genes were successfully annotated. And the chloroplast genome contains 113 unique genes, 19 of which are duplicated in the inverted repeat. The distribution of 39 simple sequence repeats was analysed, and most of them are in the large single-copy (LSC) sequence. An inversion comprising 16 genes was found in the LSC region, which is 26 283 bp long. We performed multiple sequence alignments using 72 common protein-coding genes of 29 species and constructed a Maximum Parsimony (MP) tree. The MP phylogenetic result shows that A. lappa grouped together with Carthamus tinctorius, Centaurea diffusa, and Saussurea involucrata. The chloroplast genome of A. lappa is a valuable resource for further studies in Asteraceae.


Subject(s)
Arctium/genetics , Genome, Chloroplast , Arctium/classification , Codon Usage , DNA, Plant/chemistry , Genes, Plant , Inverted Repeat Sequences , Microsatellite Repeats , Phylogeny , Plants, Medicinal/genetics , Repetitive Sequences, Nucleic Acid
4.
J Agric Food Chem ; 60(16): 4067-75, 2012 Apr 25.
Article in English | MEDLINE | ID: mdl-22497441

ABSTRACT

Caffeoylquinic acids and lignans in the crude extracts of both roots and seeds from different burdock ( Arctium lappa L.) genotypes were simultaneously characterized and systematically compared by LC-MS and matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometry (MALDI-QIT-TOF MS), and their antioxidant activities were also investigated. A total of 14 lignans were identified in burdock seeds and 12 caffeoylquinic acids in burdock roots. High levels of caffeoylquinic acids were also detected in burdock seeds, but only trace amounts of lignans were found in burdock roots. Burdock seeds contained higher concentrations of lignans and caffeoylquinic acids than burdock roots. Quantitative analysis of caffeoylquinic acids and lignans in roots and seeds of various burdock genotypes was reported for the first time. Great variations in contents of both individual and total phenolic compounds as well as antioxidant activities were found among different genotypes. Burdock as a root vegetable or medicinal plants possessed considerably stronger antioxidant activity than common vegetables and fruits.


Subject(s)
Antioxidants/analysis , Arctium/chemistry , Lignans/analysis , Plant Extracts/analysis , Plant Roots/chemistry , Quinic Acid/analogs & derivatives , Seeds/chemistry , Antioxidants/metabolism , Arctium/genetics , Arctium/metabolism , Genotype , Lignans/metabolism , Plant Extracts/metabolism , Plant Roots/genetics , Plant Roots/metabolism , Quinic Acid/analysis , Quinic Acid/metabolism , Seeds/genetics , Seeds/metabolism
5.
Zhongguo Zhong Yao Za Zhi ; 36(14): 1931-5, 2011 Jul.
Article in Chinese | MEDLINE | ID: mdl-22016962

ABSTRACT

OBJECTIVE: To study the correlation between ITS sequence of Arctium lappa and Fructus Arctii quality of different origin. METHOD: The samples of Fructu arctii materials were collected from 26 different producing areas. Their ITS sequence were determined after polymerase chain reaction (PCR) and quality were evaluated through the determination of arctiin content by HPLC. Genetic diversity, genotype and correlation were analyzed by ClustalX (1.81), Mage 4.0, SPSS 13.0 statistical software. RESULT: ITS sequence of A. was obtained from 26 samples, and was registered in the GenBank. Corresponding arctiin content of Fructus arctii and 1000-grain weight were determined. A. lappa genotype correlated with Fructus arctii quality by statistical analysis. CONCLUSION: The research provided a foundation for revealing the molecular mechanism of Fructus arctii geoherbs.


Subject(s)
Arctium/genetics , Computational Biology , DNA, Ribosomal Spacer/genetics , Drugs, Chinese Herbal/standards , Arctium/chemistry , Furans/analysis , Genotype , Glucosides/analysis , Polymorphism, Genetic/genetics , Quality Control , Sequence Analysis, DNA , Software
6.
Zhongguo Zhong Yao Za Zhi ; 36(3): 338-41, 2011 Feb.
Article in Chinese | MEDLINE | ID: mdl-21585039

ABSTRACT

OBJECTIVE: To identify the traditional medicine Fructus Arctii from its adulterants by ITS. METHOD: Twenty-six samples of the different Fructus Arctii materials and 10 samples of the adulterants of the fruits of A. tomentosum, Onopordum acantium, Silybum marianum, and Amorpha fruticosa were collected. The total DNA of the samples were extracted, amplified cloned and sequenced. RESULT: ITS sequences were obtained from 26 samples respectively, there were Fructus Arctii 641 bp, A. tomentosum 641 bp, Onopordum acantium 639 bp, Silybum marianum 630-631 bp, Amorpha fruticosa 625-626 bp, which were registered in the GenBank. The similarity in ITS sequences between Fructus Arctii and the adulterants was less than 95%. In contrast, the similarity between any pair of Fructus Arctii was greater than 99%. The similarity was 98.29%-99.22% between Fructus Arctii and A. tomentosum. Phylogeny tree reconstruction using UPGMA analysis based on ITS nucleotide sequences can effectively distinguish Fructus Arctii from adulterants. CONCLUSION: ITS sequences can be used as a reliable molecular marker for the identification of Fructus Arctii.


Subject(s)
Arctium/genetics , Cell Nucleus/genetics , DNA, Ribosomal Spacer , Drug Contamination/prevention & control , Genetic Markers , Phylogeny , Sequence Analysis, DNA , Sequence Homology, Nucleic Acid
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