Cinchona calisaya
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA222472 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1021741_1.fastq.gz | Fastqsanger.gz | |||
| SRR1021741_2.fastq.gz | Fastqsanger.gz | |||
| SRR1023176.fastq.gz | Fastqsanger.gz |
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Project description:Cinchona pubescens Genome sequencing and assembly
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Project description:Considerable inter- and intraspecific variation with respect to the quantity and composition of plant natural products exists. The processes that drive this variation remain largely unknown. Understanding which factors determine chemical diversity has the potential to shed light on plant defenses against herbivores and diseases and accelerate drug discovery. For centuries, Cinchona alkaloids were the primary treatment of malaria. Using Cinchona calisaya as a model, we generated genetic profiles of leaf samples from four plastid (trnL-F, matK, rps16, and ndhF) and one nuclear (ITS) DNA regions from twenty-two C. calisaya stands sampled in the Yungas region of Bolivia. Climatic and soil parameters were characterized and bark samples were analyzed for content of the four major alkaloids using HPLC-UV to explore the utility of evolutionary history (phylogeny) in determining variation within species of these compounds under natural conditions. A significant phylogenetic signal was found for the content of two out of four major Cinchona alkaloids (quinine and cinchonidine) and their total content. Climatic parameters, primarily driven by changing altitude, predicted 20.2% of the overall alkaloid variation, and geographical separation accounted for a further 9.7%. A clade of high alkaloid producing trees was identified that spanned a narrow range of altitudes, from 1,100 to 1,350 m. However, climate expressed by altitude was not a significant driver when accounting for phylogeny, suggesting that the chemical diversity is primarily driven by phylogeny. Comparisons of the relative effects of both environmental and genetic variability in determining plant chemical diversity have scarcely been performed at the genotypic level. In this study we demonstrate there is an essential need to do so if the extensive genotypic variation in plant biochemistry is to be fully understood.
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Project description:Rubiaceae plants are globally widespread and possess significant economic and medicinal value. Such as the globally important crop of coffee, and Cinchona calisaya Wedd., which is rich in alkaloids, is an important medicinal resource for treating malaria. In recent years, several genome resources of Rubiaceae have been reported. However, the comprehensive phylogenetic relationships of Rubiaceae are still unknown. In this study, we present a nearly complete diploid genome assembly of C. calisaya, characterized by a genome size of 869.93 Mb, and contig N50 length of 44.34 Mb. Notably, 99.75% of the sequences have been successfully anchored to 17 chromosomes, with only 12 gaps remaining. BUSCO assessment indicates that 97.40% of complete core genes are present in the assembly. We identified a total of 42,741 protein-coding genes, among which 38,022 (89.00%) have received functional annotation. The high continuity and integrity of the C. calisaya genome provide a robust foundation for functional genomics research, varietal improvement, and the conservation of genomic resources in medicinal plants.
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Project description:Nucleophilic catalysts for a 1,6 addition/Nazarov cyclization/elimination sequence were evaluated for their ability to induce enantioselectivity in the electrocyclization step. Of the tertiary amines examined, it was found that a cinchona alkaloid derivative was able to generate substituted 5-hydroxy γ-methylene cyclopentenones with excellent enantioselectivity. The study results suggest that successful cyclization depends upon the ability of the dienyl diketone substrate to readily adopt an s-cis conformation.
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Project description:A spectroscopic study of an organocatalytic Henry reaction between nitroalkanes and aldehydes catalyzed by a quinidine-derived Cinchona alkaloid is described. The binding modes of the reaction substrates are investigated using electronic absorption and fluorescence spectroscopy and further corroborated by nuclear magnetic resonance measurements. Aldehydes are shown to associate with both the 6'-OH group and the basic quinuclidine nitrogen of the catalyst, whereas nitroalkanes do not exhibit a clear binding mode. Reaction progress kinetic analysis reveals that the reaction is first-order in both of the substrates and the catalyst. Second, the reaction proceeds approximately five times faster in the excess of the nitroalkanes than in the excess of the aldehydes, suggesting that binding of the aldehydes results in the inhibition of the catalyst. Aldehydes deactivate the basic quinuclidine site, thus suppressing the deprotonation of the nitroalkanes which is the proposed initial step in the reaction cycle.
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Project description:Cinchona pubescens isolate:P90104 Genome sequencing and assembly
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Project description:The development of highly enantioselective and general catalytic nitroaldol (Henry) reactions with ketones is a challenging yet desirable task in organic synthesis. In this communication, we report an asymmetric nitroaldol reaction with alpha-ketoesters catalyzed by a new C6'-OH cinchona alkaloid catalyst. This is the first highly efficient organocatalytic asymmetric Henry reaction with ketones. This reaction is operationally simple and affords high enantioselectivity as well as good to excellent yield for a broad range of alpha-ketoesters.
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