Short read coffee bean ripening transcriptome of the lower canopy
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ABSTRACT:
PROVIDER: PRJEB24850 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2286362.fastq.gz | Fastqsanger.gz | |||
| ERR2286362_1.fastq.gz | Fastqsanger.gz | |||
| ERR2286362_2.fastq.gz | Fastqsanger.gz | |||
| ERR2286363.fastq.gz | Fastqsanger.gz | |||
| ERR2286363_1.fastq.gz | Fastqsanger.gz |
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Project description:Short read coffee bean ripening transcriptome of the upper canopy
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Project description:Coffee leaf miner is an important plague in coffee crops. Using subtracted cDNA libraries and nylon filter arrays, we analyzed the expression profile of 1536 expressed sequence tags (ESTs) of coffee plants from an hybrid progeny (C. arabica x C. racemosa), containg resistant (R) and susceptible plants (S) to the infestation of coffee leaf miner. Leaf discs were collected from non-infested plants (R control - RC; S control - SC), infested plants after moth oviposition (R oviposition - Ro; S oviposition - So) and infested after larvar eclosion (R eclosion - Re; S eclosion - Se). Isolation and characterization of Coffea genes induced during coffee leaf miner (Leucoptera coffeella) infestation. Plant Science 169(2):351-360 Keywords: ordered
2005-08-15 | GSE2045 | GEO
Project description:Coffee leaf miner is an important plague in coffee crops. Using subtracted cDNA libraries and nylon filter arrays, we analyzed the expression profile of 1536 expressed sequence tags (ESTs) of coffee plants from an hybrid progeny (C. arabica x C. racemosa), containg resistant (R) and susceptible plants (S) to the infestation of coffee leaf miner. Leaf discs were collected from non-infested plants (R control - RC; S control - SC), infested plants after moth oviposition (R oviposition - Ro; S oviposition - So) and infested after larvar eclosion (R eclosion - Re; S eclosion - Se). Isolation and characterization of Coffea genes induced during coffee leaf miner (Leucoptera coffeella) infestation. Plant Science 169(2):351-360
2010-06-09 | E-GEOD-2045 | biostudies-arrayexpress
Project description:Background: Understanding the genetic elements that contribute to key aspects of coffee biology will impact future agronomical improvements for this economically important tree. The past years, EST collections were generated in Coffee, opening the possibility to create new tools for functional genomics. Results: The project PUCE CAFE, set up by the scientific consortium NESTLE/IRD/CIRAD has developed of long oligonucleotide coffee array using public coffee EST sequences mainly obtained from different stages during fruit development and leaves in Coffea canephora (Robusta). We have performed a validation experiment in order to check the array usability and the reproducibility of hybridizations. Conclusion: We have generated the first 15K Coffee array during this three years project PUCE CAFE, granted by The French National Research Agency (ANR, Programme Génoplante) . This new tool was dedicated to large scale transcriptomic analysis during grain development of Coffea canephora grown in different countries . Furthermore, other analysis have been also initiated by the different partners like analysis of polyploidy or drought resistance. In any case, at the end of the project, the generated arrays will be available to the international scientific community. three biological replicates were made for each tissue analyzed (i.e. leaves, flowers and mature beans). The following comparisons were made: Bean-Flower, Leaf-Flower and Leaf-Bean. In all, we performed microarray analyses on 18 slides [3 (replicates) x 2 (dyes) x 3 (organs)]
2011-11-01 | E-GEOD-24754 | biostudies-arrayexpress
Project description:The composition of the maturing coffee bean determines the processing performance and ultimate quality of the coffee produced from the bean. Analysis of differences in gene expression during bean maturation may explain the basis of genetic and environmental variation in coffee quality. The transcriptome of the coffee bean was analyzed at three stages of development, immature (green), intermediate (yellow) and mature (red). A total of more than 120 million 150?bp paired-end reads were collected by sequencing of transcripts of triplicate samples at each developmental stage. A greater number of transcripts were expressed at the yellow stage. As the beans matured the types of highly expressed transcripts changed from transcripts predominantly associated with galactomannan, triacylglycerol (TAG), TAG lipase, 11?S and 7S-like storage protein and Fasciclin-like arabinogalactan protein 17 (FLA17) in green beans to transcripts related to FLA1 at the yellow stage and TAG storage lipase SDP1, and SDP1-like in red beans. This study provides a genomic resource that can be used to investigate the impact of environment and genotype on the bean transcriptome and develop coffee varieties and production systems that are better adapted to deliver quality coffee despite climate variations.
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Project description:The production of high-quality coffee is being challenged by changing climates in coffee-growing regions. The coffee beans from the upper and lower canopy at different development stages of the same plants were analyzed to investigate the impact of the microenvironment on gene expression and coffee quality. Compared with coffee beans from the upper canopy, lower canopy beans displayed more intense aroma with higher caffeine, trigonelline, and sucrose contents, associated with greater gene expression in the representative metabolic pathways. Global gene expression indicated a longer ripening in the lower canopy, resulting from higher expression of genes relating to growth inhibition and suppression of chlorophyll degradation during early bean ripening. Selection of genotypes or environments that enhance expression of the genes slowing bean development may produce higher quality coffee beans, allowing coffee production in a broader range of available future environments.
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Project description:Lipids play an important role in coffee bean development, coffee brew and in the effects of coffee on human health. They account for around 17% of the dry bean weight and encompass different classes and subclasses, mostly triacylglycerols (TAG) and a minor quantity of phospholipids (PL) and βN-alkanoyl-5-hydroxytryptamides (C-5HT). To comprehensive profile these different lipids, it is important to evaluate extraction methods that provide high lipid coverage and to analyze the lipids in high-resolution techniques. In this work, liquid chromatography-high resolution tandem mass spectrometry (LC-HRMS/MS) was employed to comprehensive profile lipids from green Arabica coffee beans and to evaluate the extraction efficiency and lipid coverage of three methods: Bligh-Dyer (BD), Folch (FO), and Matyash (MA). The MA method yielded the greatest number of annotated compounds (131 lipids) compared to the other methods. In the positive electrospray ionization (ESI) mode, the main difference among extraction methods was observed for TAG and diacylglycerols, whereas for the negative ESI it was observed differences for phosphatidylinositol (PI), lysophosphatidylinositol and phosphatidic acid (p < 0.05). The analysis of coffees from different maturation stages and/or post-harvest processes were also performed using the MA method. Immature beans were discriminated from mature and overripe beans by its lower levels of C-5HT, PI, phosphatidylcholine, lysophosphatidylcholine, phosphatidyletanolamine, and lysophosphatidylethanolamine. These results can help to better understand the coffee lipid composition and its association with coffee quality.
2021-11-19 | MTBLS1972 | MetaboLights
Project description:The present study was conducted to evaluate the effects of the intake of three types of coffee (caffeinated, decaffeinated, and green unroasted coffee) on the livers of C57BL/6J mice fed a high-fat diet, and to extensively elucidate the physiological responses to coffee intake by analysing the findings obtained from a comprehensive transcriptomic analysis using DNA microarrays. The present study was conducted to evaluate the effects of the intake of three types of coffee (caffeinated, decaffeinated, and green unroasted coffee) on the livers of C57BL/6J mice fed a high-fat diet, and to extensively elucidate the physiological responses to coffee intake by analysing the findings obtained from a comprehensive transcriptomic analysis using DNA microarrays.
2013-12-10 | GSE53131 | GEO
Project description:wet coffee fermentation
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Project description:wet coffee fermentation
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