Sequencing of coffee rust isolates from Brazil
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ABSTRACT:
PROVIDER: PRJEB51178 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:Coffee rust - race II- whole genome sequencing
| PRJEB50957 | ENA
Project description:With the aid of a biochip, carrying representative sequences from approximately 2200 sequences from the genome of isolate 9a5c from X. fastidiosa (Xf), microarray-based comparisons have been performed with 8 different Xf isolates obtained from coffee plants.
2013-12-31 | GSE41163 | GEO
Project description:The fungus Puccinia striiformis f.sp. tritici (PST) is the causal pathogen of stripe rust in wheat. New highly virulent PST races appeared at the beginning of this century and spread rapidly causing significant yield losses in wheat production worldwide. Race PST-08/21 was isolated in the UK in 2008 Yr1, Yr2, Yr3, Yr4, Yr6, Yr9, Yr17, Yr27, Yr32, YrRob, YrSol. We applied the RNAseq approach to refine the gene prediction in de novo assembled PST 08/21 contigs and to determine which genes are expressed during wheat infections. Total RNA was extracted from a pool of stripe rust infected wheat leaves and from two biological replicates of haustoria isolates.
2013-08-19 | E-GEOD-42496 | biostudies-arrayexpress
Project description:Eucalyptus rust is caused by the biotrophic fungus, Austropuccinia psidii, which affects commercial plantations of Eucalyptus, a major raw material for the pulp and paper industry in Brazil. Aiming to uncover the molecular mechanisms involved in rust resistance and susceptibility in Eucalyptus grandis, we used epifluorescence microscopy to follow the fungus development inside the leaves of two contrasting half-sibling genotypes (rust-resistance and rust-susceptible), to determine the time-course for comparative metabolomic and proteomic analyses in plantlets artificially inoculated with rust. Within 24 hours of complete fungal invasion, a total of 709 plant metabolites showed that the rust-resistant genotype suppressed many metabolites 6 hours after inoculation (hai), with responses being progressively induced after 12 hai. In contrast, the rust-susceptible genotype displayed an alternated metabolite response to infection, which culminated in a strong suppression at 24 hai. Multivariate analyses of genotypes and time points were used to select 16 differential metabolites chemically classified as flavonoids, benzenoids and other compounds. Applying the Weighted Gene Co-Expression Network Analysis (WGCNA), rust-resistant and rust-susceptible genotypes had, respectively, 871 and 852 proteins grouped into 14 and 13 modules, of which 10 and 7 protein modules were significantly correlated to the selected metabolites. Functional analyses revealed roles for oxidative-dependent responses leading to temporal activity of metabolites and proteins after 12 hai in rust-resistance, while the initial over-accumulation of metabolites and correlated proteins caused a lack of progressive response after 12 hai in rust-susceptible genotype. This study provides a brief understand on the temporal divergences of resistant and susceptible molecular responses of E. grandis plants to rust.
2021-09-09 | PXD021280 | Pride
Project description:With the aid of a biochip, carrying representative sequences from approximately 2200 sequences from the genome of isolate 9a5c from X. fastidiosa (Xf), microarray-based comparisons have been performed with 8 different Xf isolates obtained from coffee plants. DNA from the 9a5c isolate was used as a reference in competitive hybridization experiments against DNA from 8 different Xf isolates obtained from coffee plants. Equimolecular amounts of each DNA have been labelled with either Cy3- or Cy5-dCTP and hybridized with a 9a5c Xf biochip. Statistical validation of fold change variations was performed with the aid of the Significance Analysis of Microarrays (SAM) method Tusher and coworkers, using the software developed by B. Narasimham and available at http://www-stat.stanford.edu/~tibs/SAM/index.html. Spots that showed a Reference/Test ratio <1:2 were considered to be present in greater copy number in the test over the reference strain, as proposed by Smoot and coworkers, while spots that showed an average Reference/Test ratio >5:1 were considered to be missing in the test strain. The application of these criteria in a direct sequence comparison between strains 9a5c and Temecula-1, which have been completely sequenced, provided an estimated error rate below 0.3%
2013-12-31 | E-GEOD-41163 | biostudies-arrayexpress
Project description:Population genomic footprints of host adaptation, introgression and recombination in Coffee Leaf Rust
| PRJEB26471 | ENA
Project description:Population genomic footprints of host adaptation, introgression and recombination in Coffee Leaf Rust
| PRJEB26843 | ENA
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