Ontology highlight
ABSTRACT:
PROVIDER: PRJNA783534 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17037610_1.fastq.gz | Fastqsanger.gz | |||
| SRR17037610_2.fastq.gz | Fastqsanger.gz | |||
| SRR17037611_1.fastq.gz | Fastqsanger.gz | |||
| SRR17037611_2.fastq.gz | Fastqsanger.gz | |||
| SRR17037612_1.fastq.gz | Fastqsanger.gz |
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Project description:The closely related Coffea arabica cultivars ‘Tall Mokka’ and ‘Typica’, with excellent flavor, but differing distinctively in the size of aerial organs, branching pattern and branch numbers. Differential gene expression analysis of shoot tips of arabica coffee cultivars 'Tall Mokka' and 'Typica' were done using Potato cDNA microarray as cross-species platform. Using cross-species microarray hybridization, we identified a prolyl oligopeptidase (CaPOP) gene as differentially expressed between the shoot tips of ‘Tall Mokka’ and ‘Typica’. Isolation and sequencing of POP genes from coffee identified three paralogs, CaPOP1, CaPOP2 and CaPOP3. All three genes were present in both cultivars, which suggest that differences in the expression of CaPOP are caused by factor(s) regulating the transcription of CaPOPs. CaPOP1 differs in sequence from CaPOP2 primarily in having two large deletions in the promoter region. CaPOP genes are homologous to arabidopsis At1g20380, encoding a post-proline cleaving enzyme that acts on substrates shorter than 30 amino acids. Ectopic expression of CaPOP1 under its native promoter in transgenic arabidopsis resulted in more secondary branches than in the wild type. This is the first study to successfully isolate CaPOP genes and characterize their expression in the developing tissues of coffee. This study also identified a novel role for prolyl oligopeptidase in control of branching.
2011-08-04 | GSE31179 | GEO
Project description:The closely related Coffea arabica cultivars ‘Tall Mokka’ and ‘Typica’, with excellent flavor, but differing distinctively in the size of aerial organs, branching pattern and branch numbers. Differential gene expression analysis of shoot tips of arabica coffee cultivars 'Tall Mokka' and 'Typica' were done using Potato cDNA microarray as cross-species platform. Using cross-species microarray hybridization, we identified a prolyl oligopeptidase (CaPOP) gene as differentially expressed between the shoot tips of ‘Tall Mokka’ and ‘Typica’. Isolation and sequencing of POP genes from coffee identified three paralogs, CaPOP1, CaPOP2 and CaPOP3. All three genes were present in both cultivars, which suggest that differences in the expression of CaPOP are caused by factor(s) regulating the transcription of CaPOPs. CaPOP1 differs in sequence from CaPOP2 primarily in having two large deletions in the promoter region. CaPOP genes are homologous to arabidopsis At1g20380, encoding a post-proline cleaving enzyme that acts on substrates shorter than 30 amino acids. Ectopic expression of CaPOP1 under its native promoter in transgenic arabidopsis resulted in more secondary branches than in the wild type. This is the first study to successfully isolate CaPOP genes and characterize their expression in the developing tissues of coffee. This study also identified a novel role for prolyl oligopeptidase in control of branching. Eight coffee trees of 'Typica' ('K') and six trees of 'Tall Mokka' ('M') cultivar were used in this study. The trees were equally divided into two groups 'A' and 'B' for each cultivar ('MA','MB', 'KA' and 'KB') and treated as biological replicates. Eight two channel microarray hybridizations were done in following pairs: MA x KA, MA x KB, MB x KA, MB x KB and dye swap replicate of each pair. Summary: Two-sample experiment: Tall Mokka vs. Typica . 8 Hybridizations. 2 Biological replicates per sample. 1 Dye swap per array.
2011-08-03 | E-GEOD-31179 | biostudies-arrayexpress
Project description:Coffee is one of the most important commodities cultivated worldwide and has great economic impact in producing countries. Although 130 different species belonging to the coffea gender have been described, only two of them are commercially exploited: Coffea arabica and Coffea canephora. C. arabica is responsible for 61% of the world production (Van der Vossen et al., 2015). However, due to the narrow genetic back ground, classical genetic breeding is time consuming and takes around 30 years (Santana-Buzzy et al., 2007; Hendre et al., 2014). Several genetic engineering and biotechnological tools have been successfully applied in coffee breeding. Somatic embryogenesis (SE) is a process in which new viable embryos are produced from somatic tissues. It is one of the most promising production processes (Santana-Buzzy et al, 2007; Marsoni et al., 2008). A better understanding of the molecular basis related to somatic embryogenesis will give insight into the process of embryo formation and totipotency and will allow the development of new in vitro culture strategies for the propagation and genetic manipulation of elite cultivars (Marsoni et al., 2008). High throughput proteomics in coffee is limited so far to 2D gel based proteomics techniques. Although really useful and the most common technique for plants, 2DE is limited in throughput and a gel free technique allow to go a step further (Carpentier & America, 2014; Vanhove et al., 2015). To improve the knowledge about somatic embryogenesis, we present the first high throughput proteome profile (1051 confident protein identifications) of coffee embryogenic cell suspensions developed from leaves of Coffea arabica cultivar Catuaí.
2016-02-03 | PXD002963 | Pride
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:MS/MS fragmentation data of coffee arabica samples acquired on QTOF with chromatographic separation on a phenomenex polar C18 column
2025-03-12 | MSV000097299 | MassIVE
Project description:The intermediate seed category was defined in the early 1990s using coffee (Coffea arabica) as a model. In contrast to orthodox seeds, intermediate seeds cannot survive complete drying, which is a major constraint for seed storage, for both biodiversity conservation and agricultural purposes. However, intermediate seeds are considerably more tolerant to drying than recalcitrant seeds, which are highly sensitive to desiccation. To gain insight into the mechanisms governing such differences, changes in desiccation tolerance (DT), hormone content and the transcriptome were analysed in developing coffee seeds. Acquisition of DT coincided with a dramatic transcriptional switch characterised by the repression of primary metabolism, photosynthesis and respiration, and the upregulation of genes coding for late embryogenesis abundant (LEA) proteins, heat shock proteins (HSP) and antioxidant enzymes. Analysis of heat-stable proteome in the mature coffee seed confirmed the accumulation of LEA proteins identified at the transcript level. Transcriptome analysis also suggests a major role for ABA and for the transcription factors CaHSFA9, CaDREB2G, CaANAC029, CaPLATZ and CaDOG-like in DT acquisition. The ability of CaHSFA9 and CaDREB2G to trigger HSP gene transcription was validated by Agrobacterium-mediated transformation of coffee somatic embryos.
2017-12-13 | GSE107949 | GEO
Project description:MS/MS fragmentation data of coffee arabica samples acquired on QTOF with chromatographic separation on a phenomenex polar C18 column
2025-03-12 | MSV000097299 | GNPS