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1.
Nat Commun ; 12(1): 3276, 2021 06 02.
Artigo em Inglês | MEDLINE | ID: mdl-34078898

RESUMO

Chinese goldthread (Coptis chinensis Franch.), a member of the Ranunculales, represents an important early-diverging eudicot lineage with diverse medicinal applications. Here, we present a high-quality chromosome-scale genome assembly and annotation of C. chinensis. Phylogenetic and comparative genomic analyses reveal the phylogenetic placement of this species and identify a single round of ancient whole-genome duplication (WGD) shared by the Ranunculaceae. We characterize genes involved in the biosynthesis of protoberberine-type alkaloids in C. chinensis. In particular, local genomic tandem duplications contribute to member amplification of a Ranunculales clade-specific gene family of the cytochrome P450 (CYP) 719. The functional versatility of a key CYP719 gene that encodes the (S)-canadine synthase enzyme involved in the berberine biosynthesis pathway may play critical roles in the diversification of other berberine-related alkaloids in C. chinensis. Our study provides insights into the genomic landscape of early-diverging eudicots and provides a valuable model genome for genetic and applied studies of Ranunculales.


Assuntos
Alcaloides de Berberina/metabolismo , Coptis/genética , Sistema Enzimático do Citocromo P-450/genética , Genoma de Planta , Proteínas de Plantas/genética , Vias Biossintéticas/genética , Coptis/química , Coptis/metabolismo , Sistema Enzimático do Citocromo P-450/metabolismo , Medicamentos de Ervas Chinesas , Duplicação Gênica , Regulação da Expressão Gênica de Plantas , Ontologia Genética , Anotação de Sequência Molecular , Filogenia , Proteínas de Plantas/metabolismo , Plantas Medicinais
2.
Plant Mol Biol ; 102(4-5): 477-499, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31902069

RESUMO

KEY MESSAGE: The study carry out comprehensive transcriptome analysis of C. deltoidea and exploration of BIAs biosynthesis and accumulation based on UHPLC-MS/MS and combined sequencing platforms. Coptis deltoidea is an important medicinal plant with a long history of medicinal use, which is rich in benzylisoquinoline alkaloids (BIAs). In this study, Ultra performance liquid chromatography-electrospray ionization tandem mass spectrometry (UHPLC-ESI-MS/MS) and combined sequencing platforms were performed for exploration of BIAs biosynthesis, accumulation and comprehensive transcriptome analysis of C. deltoidea. By metabolism profiling, the accumulation of ten BIAs was analyzed using UHPLC-MS/MS and different contents were observed in different organs. From transcriptome sequencing result, we applied single-molecule real-time (SMRT) sequencing to C. deltoidea and generated a total of 75,438 full-length transcripts. We proposed the candidate biosynthetic pathway of tyrosine, precursor of BIAs, and identified 64 full length-transcripts encoding enzymes putatively involved in BIAs biosynthesis. RNA-Seq data indicated that the majority of genes exhibited relatively high expression level in roots. Transport of BIAs was also important for their accumulation. Here, 9 ABC transporters and 2 MATE transporters highly homologous to known alkaloid transporters related with BIAs transport in roots and rhizomes were identified. These findings based on the combined sequencing platforms provide valuable genetic information for C. deltoidea and the results of transcriptome combined with metabolome analysis can help us better understand BIAs biosynthesis and transport in this medicinal plant. The information will be critical for further characterization of C. deltoidea transcriptome and molecular-assisted breeding for this medicinal plant with scarce resources.


Assuntos
Alcaloides/biossíntese , Benzilisoquinolinas/química , Coptis/genética , Coptis/metabolismo , Transcriptoma , Cromatografia Líquida de Alta Pressão , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Filogenia , Folhas de Planta/metabolismo , Raízes de Plantas/metabolismo , Plantas Medicinais/metabolismo , Rizoma/metabolismo , Análise de Sequência de DNA , Espectrometria de Massas por Ionização por Electrospray , Espectrometria de Massas em Tandem
3.
Molecules ; 23(12)2018 Nov 27.
Artigo em Inglês | MEDLINE | ID: mdl-30486378

RESUMO

Coptis plants (Ranunculaceae) to have played an important role in the prevention and treatment human diseases in Chinese history. In this study, a multi-level strategy based on metabolic and molecular genetic methods was performed for the characterization of four Coptis herbs (C. chinensis, C. deltoidea, C. omeiensis and C. teeta) using high performance liquid chromatography-ultraviolet (HPLC-UV) and restriction site-associated DNA sequencing (RAD-seq) techniques. Protoberberine alkaloids including berberine, palmatine, coptisine, epiberberine, columbamine, jatrorrhizine, magnoflorine and groenlandicine in rhizomes were identified and determined based on the HPLC-UV method. Among them, berberine was demonstrated as the most abundant compound in these plants. RAD-seq was applied to discover single nucleotide polymorphisms (SNPs) data. A total of 44,747,016 reads were generated and 2,443,407 SNPs were identified in regarding to four plants. Additionally, with respect to complicated metabolic and SNP data, multivariable statistical methods of principal component analysis (PCA) and hierarchical cluster analysis (HCA) were successively applied to interpret the structure characteristics. The metabolic variation and genetic relationship among different Coptis plants were successfully illustrated based on data visualization. Summarily, this comprehensive strategy has been proven as a reliable and effective approach to characterize Coptis plants, which can provide additional information for their quality assessment.


Assuntos
Alcaloides de Berberina/análise , Coptis , Medicamentos de Ervas Chinesas/análise , Metabolômica , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA , Cromatografia Líquida de Alta Pressão , Coptis/química , Coptis/genética , Humanos
4.
Zhongguo Zhong Yao Za Zhi ; 42(3): 473-477, 2017 Feb.
Artigo em Chinês | MEDLINE | ID: mdl-28952251

RESUMO

The genetic diversity and genetic relationship among four medicinal species of Coptis were detected by the approach of sequence-related amplified polymorphism (SCoT). The associated genetic parameters were calculated by POPGENE1.31. The systematic diagram of genetic relationship were clustered by TREECONW. The results showed that a total of 434 bands were produced by using 28 primers, of which 430 were polymorphic loci. There was a high level of genetic diversity among species (PPB=99.1%,Na=1.990 6,Ne=1.329 3,H=0.212 2,I=0.337 8). However, genetic diversity was lower within species, the average of genetic parameters wasPPB=16.8%,Na=1.168 2, Ne=1.073 0,H=0.043 7,I=0.067 7. The Nei's genetic differentiation coefficient was 0.794 0, that indicated that most of the genetic variation existed among species. By clustering analysis, different individuals gathered in the same group. The results confirmed that SCoT marker can be used as one of the effective methods to reveal the genetic diversity and relationship among medicinal species of Coptis.


Assuntos
Coptis/genética , Variação Genética , Filogenia , China , Análise por Conglomerados , Coptis/classificação , Primers do DNA , Plantas Medicinais/classificação , Plantas Medicinais/genética , Polimorfismo Genético
5.
Biomed Res Int ; 2017: 8201836, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28698879

RESUMO

The Coptis chinensis Franch. is an important medicinal plant from the Ranunculales. We used next generation sequencing technology to determine the complete chloroplast genome of C. chinensis. This genome is 155,484 bp long with 38.17% GC content. Two 26,758 bp long inverted repeats separated the genome into a typical quadripartite structure. The C. chinensis chloroplast genome consists of 128 gene loci, including eight rRNA gene loci, 28 tRNA gene loci, and 92 protein-coding gene loci. Most of the SSRs in C. chinensis are poly-A/T. The numbers of mononucleotide SSRs in C. chinensis and other Ranunculaceae species are fewer than those in Berberidaceae species, while the number of dinucleotide SSRs is greater than that in the Berberidaceae. C. chinensis diverged from other Ranunculaceae species an estimated 81 million years ago (Mya). The divergence between Ranunculaceae and Berberidaceae was ~111 Mya, while the Ranunculales and Magnoliaceae shared a common ancestor during the Jurassic, ~153 Mya. Position 104 of the C. chinensis ndhG protein was identified as a positively selected site, indicating possible selection for the photosystem-chlororespiration system in C. chinensis. In summary, the complete sequencing and annotation of the C. chinensis chloroplast genome will facilitate future studies on this important medicinal species.


Assuntos
Coptis/genética , Evolução Molecular , Genoma de Cloroplastos , Anotação de Sequência Molecular
6.
PLoS One ; 11(4): e0153127, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27044035

RESUMO

Coptis (Ranunculaceae) contains 15 species and is one of the pharmaceutically most important plant genera in eastern Asia. Understanding of the evolution of morphological characters and phylogenetic relationships within the genus is very limited. Here, we present the first comprehensive phylogenetic analysis of the genus based on two plastid and one nuclear markers. The phylogeny was reconstructed using Bayesian inference, as well as maximum parsimony and maximum likelihood methods. The Swofford-Olsen-Waddell-Hillis and Bayesian tests were used to assess the strength of the conflicts between traditional taxonomic units and those suggested by the phylogenetic inferences. Evolution of morphological characters was inferred using Bayesian method to identify synapomorphies for the infrageneric lineages. Our data recognize two strongly supported clades within Coptis. The first clade contains subgenus Coptis and section Japonocoptis of subgenus Metacoptis, supported by morphological characters, such as traits of the central leaflet base, petal color, and petal shape. The second clade consists of section Japonocoptis of subgenus Metacoptis. Coptis morii is not united with C. quinquefolia, in contrast with the view that C. morii is a synonym of C. quinquefolia. Two varieties of C. chinensis do not cluster together. Coptis groenlandica and C. lutescens are reduced to C. trifolia and C. japonica, respectively. Central leaflet base, sepal shape, and petal blade carry a strong phylogenetic signal in Coptis, while leaf type, sepal and petal color, and petal shape exhibit relatively higher levels of evolutionary flexibility.


Assuntos
Evolução Biológica , Coptis/classificação , Coptis/genética , Filogenia , Código de Barras de DNA Taxonômico , Genes de Plantas , Fenótipo , Plantas Medicinais/classificação , Plantas Medicinais/genética
7.
Zhongguo Zhong Yao Za Zhi ; 35(14): 1789-94, 2010 Jul.
Artigo em Chinês | MEDLINE | ID: mdl-20939267

RESUMO

OBJECTIVE: To study the morphological and anatomical characteristics of Coptis deltoidea based on the research of its breeding system. METHOD: The flowering process of C. deltoidea was observed dynamically and the out-crossing index was estimated, using Motic BA200 microscope to observe the morphologic characteristics of the mixed bud, stolon and pollen was observed microscopically, and compared with those of C. chinensis. RESULT: The results showed that the breeding system of C. deltoidea was facultative hybridization, it could bloom normally and fruit while cannot form seeds. And there were no statistical differences in the number of stamens, pistils, ovules, pollens in a stamen, pollens in a flower, pollen-ovule ratio, and the pollen grain size between C. deltoidea and C. chinensis. However the pollen of C. deltoidea developed anomaly, most of the pollen grains in it were surface depression, the texture was unsharp or broken, the pollen could not germinate. The lateral bud on the lower side of the mixed bud formed in the bud stage. Pericyclic fibers in the stolon (the vegetative propagation branch) shaped like a cap, and all the shaped-caps nearly formed a ring. CONCLUSION: The abnormal development of the pollen could be the mainly cause to the no formation of seeds in C. deltoidea. The lateral bud forming in the bud stage then developing the stolon is the characteristics of the asexual propagation. Pericycle fibers in the stolon nearly forming a ring is a secondary character to accommodate the vegetative propagation of C. deltoidea.


Assuntos
Coptis/anatomia & histologia , Coptis/genética , Cruzamento , Coptis/crescimento & desenvolvimento , Flores/anatomia & histologia , Flores/genética , Flores/crescimento & desenvolvimento , Pólen/anatomia & histologia , Pólen/genética , Pólen/crescimento & desenvolvimento
8.
Zhongguo Zhong Yao Za Zhi ; 35(11): 1367-71, 2010 Jun.
Artigo em Chinês | MEDLINE | ID: mdl-20822000

RESUMO

In the present paper, three Coptis species, collected from Sichuan and Chongqing, China, were used for karyotypic analyses. The results indicated that both C. chinensis and C. omeinensis were diploid with chromosome 2n = 2x = 18, and C. deltoidea was an autotriploid with chromosomes 2n = 3x = 27, which explained why this species was morphologically so isolated from other species and its sterile and narrow distributing regions. The relationship between C. chinensis and C. omeinensis based on chromosome data was discussed. The probable origin of C. deltoidea was also suggested.


Assuntos
Cromossomos de Plantas/genética , Coptis/genética , China , Diploide , Cariotipagem
9.
Artigo em Inglês | MEDLINE | ID: mdl-20689233

RESUMO

O-Methyltransferases, which catalyze the production of small molecules in plants, play a crucial role in determining biosynthetic pathways in secondary metabolism because of their strict substrate specificity. Using three O-methyltransferase (OMT) cDNAs that are involved in berberine biosynthesis, we investigated the structure that was essential for this substrate specificity and the possibility of creating a chimeric enzyme with novel substrate specificity. Since each OMT has a relatively well-conserved C-terminal putative S-adenosyl-L-methionine-binding domain, we first exchanged the N-terminal halves of different OMTs. Among the 6 combinations that we tested for creating chimeric OMTs, 5 constructs produced detectable amounts of recombinant proteins, and only one of these with an N-terminal half of 6-OMT and a C-terminal half of 4'-OMT (64'-OMT) showed methylation activity with isoquinoline alkaloids as a substrate. Further enzymological analysis of 64'-OMT reaction product indicated that 64'-OMT retained the regio-specificity of 6-OMT. Further examination of the N-terminal region of 64'-OMT showed that about 90 amino acid residues in the N-terminal half were critical for reaction specificity. The creation of OMTs with novel reactivity is discussed.


Assuntos
Alcaloides/biossíntese , Coptis/enzimologia , Isoquinolinas/metabolismo , Metiltransferases/química , Metiltransferases/metabolismo , Alcaloides/química , Sequência de Aminoácidos , Berberina/metabolismo , Sítios de Ligação , Biocatálise , Coptis/genética , DNA Complementar/genética , DNA Complementar/metabolismo , Isoquinolinas/química , Metiltransferases/classificação , Metiltransferases/genética , Dados de Sequência Molecular , S-Adenosilmetionina/metabolismo , Homologia de Sequência de Aminoácidos , Especificidade por Substrato
10.
Zhongguo Zhong Yao Za Zhi ; 35(2): 138-41, 2010 Jan.
Artigo em Chinês | MEDLINE | ID: mdl-20394278

RESUMO

OBJECTIVE: To discuss the genetic diversity of Coptis omeiensis. METHOD: The genetic diversity of 110 individuals from 10 populations was analyzed by RAPD. RESULT: 14 primers were selected to produce highly reproducible RAPD bands. Among 132 amplified bands, 98 showed polymorphism, the percentage of polymorphic bands reached to 74.24%. Nei's gene diversity index (H) was 0.2863, Shannon's information index (I) was 0.3624, G(st) was 0.2305. The genetic distance coefficient and the similarity were 0.1931-0.5245 and 0.5016-0.8843, respectively. CONCLUSION: There exists a held high genetic diversity in C. omeiensis and the majority of genetic variation occurs in the populations. By cluster analysis, the geographical distribution is very obvious. The RAPD marker can be used for the analysis of the genetic diversity and genetic variation of C. omeiensis.


Assuntos
Coptis/genética , Variação Genética , Polimorfismo Genético , China , Coptis/classificação , Filogenia , Técnica de Amplificação ao Acaso de DNA Polimórfico
11.
Zhongguo Zhong Yao Za Zhi ; 34(24): 3176-9, 2009 Dec.
Artigo em Chinês | MEDLINE | ID: mdl-20352993

RESUMO

OBJECTIVE: To study the genetic diversity of Coptis deltoidea. METHOD: The genetic diversity of 90 individuals from 8 populations was analyzed by ISSR. RESULT: Twelve primers were selected to produce highly reproducible ISSR bands. Among 128 amplified bands, 94 showed polymorphism, the percentage of polymorphic bands reached 73.44%. Nei's gene diversity index (H) was 0.1925, Shannon's information index (I) was 0.3028, Gst was 0.7212. The genetic distance coefficient and similarity were 0.0858-0.2314 and 0.8046-0.9425, respectively. CONCLUSION: C. deltoidea held a high genetic diversity and the majority of genetic variation occurs among populations. By cluster analysis, the geographical distribution is very obvious. The ISSR marker can be used for the analysis of genetic diversity and genetic variation of C. deltoidea.


Assuntos
Coptis/classificação , Coptis/genética , Variação Genética/genética , Análise por Conglomerados , DNA de Plantas/genética , Genética Populacional , Filogenia , Polimorfismo Genético/genética
12.
Biosci Biotechnol Biochem ; 72(2): 398-405, 2008 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-18256493

RESUMO

Many plant secondary metabolites show strong biological activities and are potentially also toxic to plants, while plants producing such active compounds are usually insensitive to their own metabolites, suggesting that they have species-specific detoxification mechanisms. In order to clarify the detoxification mechanism of alkaloids, we used cultured cells of Coptis japonica, which are capable of producing a yellow benzylisoquinoline alkaloid, berberine, and accumulate it in the vacuole. Unlike other plant cells that do not produce berberine, C. japonica shows strong tolerance to this alkaloid. We established a fission yeast strain that was sensitive to berberine and performed functional screening using a C. japonica cDNA library. One cDNA clone, which conferred clear berberine tolerance, encoded galactinol synthase (CjGolS). The possible role of CjGolS in berberine tolerance is discussed.


Assuntos
Berberina/farmacologia , Coptis/enzimologia , Galactosiltransferases/genética , Sequência de Aminoácidos , Sequência de Bases , Coptis/classificação , Coptis/genética , Primers do DNA , DNA Complementar , Galactosiltransferases/química , Dados de Sequência Molecular , Filogenia , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Schizosaccharomyces/efeitos dos fármacos , Homologia de Sequência de Aminoácidos
13.
Zhongguo Zhong Yao Za Zhi ; 31(23): 1937-40, 2006 Dec.
Artigo em Chinês | MEDLINE | ID: mdl-17348182

RESUMO

OBJECTIVE: To detemine the genetic diversity of Coptis chinensis. METHOD: 32 germplasmic resources of C. chinensis were analyzed by ISSR molecular markers. To make up the systematic diagram of genetic relationship by TREECONW software and clustered by UPGMA method. RESULT: A total of 106 ISSR bands were scored, among which 51 were polymorphic bands. The average percentage of polymorphic bands was 48. 1%. Genetic similarity coefficient were changed from 0. 825 8 to 0. 935 1. By cluster analysis, the geographical distribution is not very obvious, but it was also showed some of the C. chinensis from the same region were in the same group which presented the law of geographical distribution in the tested materials. CONCLUSION: Different germplasms diversity of C. chinensis is low and the relationship of C. chinensis is close.


Assuntos
Coptis/genética , Variação Genética , Plantas Medicinais/genética , Sequências Repetitivas de Ácido Nucleico/genética , Biodiversidade , China , Análise por Conglomerados , Coptis/classificação , DNA de Plantas/genética , Folhas de Planta/genética , Plantas Medicinais/classificação
14.
Life Sci ; 77(9): 991-1002, 2005 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-15964315

RESUMO

It is difficult to understand precisely the physiological actions of herbs because they contain a complex array of constituent molecules. In the present study we used DNA microarray data for 12600 genes to examine the anti-proliferative activity of the herb Coptidis rhizoma and eight constituent molecules against eight human pancreatic cancer cell lines. We identified 27 genes showing strong correlation with the 50% inhibitory dose (ID50) of C. rhizoma after 72-h exposure. Hierarchical cluster analysis with correlation coefficients between expression levels of these 27 C. rhizoma-related genes and the ID50 of each constituent molecule classified these test molecules into two clusters, one consisting of C. rhizoma and berberine and the other consisting of the remaining seven molecules. Our results suggest that one molecule, berberine, can account for the majority of the anti-proliferative activity of C. rhizoma and that DNA microarray analyses can be used to improve our understanding of the actions of an intact herb.


Assuntos
Antineoplásicos Fitogênicos/análise , Coptis/genética , Medicamentos de Ervas Chinesas/análise , Análise de Sequência com Séries de Oligonucleotídeos , Neoplasias Pancreáticas/tratamento farmacológico , Alcaloides de Berberina/uso terapêutico , Linhagem Celular Tumoral , Coptis chinensis , Perfilação da Expressão Gênica , Humanos
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