COFFEA
RUST
Equipo 2:
Ximena Raigosa
Greecia Alejandra Campos
Jorge Americo Flores Valenzuela
Marcelo Gomez Palacio JAcobo
INtroduction
Coffea arabica is an allotetraploid hybrid
resulting from a natural hybridization between
Coffea canephora and Coffea eugenioides.
Nowadays, it is the source of approximately
60% of coffee products with an estimated
production of 10 million metric tons per year.
Cultivate C. arabica harbors a particularly low
genetic diversity and is susceptible to many
plant diseases and pests, such as coffee leaf
rust, as a result of a narrow genetic variation
caused by several bottlenecks.
(Salojärvi, 2024)
Methodology
Genoma de
referencia
FastQC Trimmonatic FastQC HISAT2
Genoma gtf
RNA >90 Feature
counts
RNA FNA
HISAT 2
PIPELINE 2
CD HIT
PIPELINE 1
Salmon
Methodology
Filter of genes
Import our data with no Normalization of MDS Selection of
expression data groups
Heatmap Contrast Dispersion
Enrichement Diferential genes
Results AnD Discussion
Multidimensional scaling (MDS) plot of all samples. Samples that cluster together
indicate similar transcriptomic patterns.
Heatmap
Generated from normalized counts.
Visualizes expression patterns across
biological samples.
Clear contrast between groups.
Several transcripts show reciprocal
expression:
↓ in Group 1→↑ in Group 2.
Suggests distinct transcriptional
responses under experimental
conditions.
Heatmap of normalized and variance-stabilized expression values
for selected genes across all samples. Colors represent relative
expression levels, where blue is the lowest expression level and red is
the highest.
Pathways
The photosynthesis–antenna proteins pathway with the
transcripts differentially expressed by the infection. Light- The metabolic pathway of photosynthesis with the transcripts
harvesting chlorophyll protein complexes (LHC) show a clear downregulated by the infection. Where PSI, PSII, F-type
downregulation, suggesting reduced efficiency in capturing light ATPase and photosynthetic electron transport present a
energy during stress conditions. downregulation.
The α-linolenic acid metabolism pathway showed a significant Phenylpropanoid biosynthesis shows an upregulation on
upregulation of phospholipases, responsible for the release of the α- shikimate O-hydroxycinnamoyltransferase and F5H, which are
linolenic precursor, as well as of 13S-lipoxygenase and 12- enzymes related to the biosynthesis of lignin, flavonoids and
oxophytodienoate reductase, which are key enzymes in jasmonate phenolic compounds. On the other hand, a downregulation at
biosynthesis. Simultaneously, downregulation of allene oxide synthase cinnamoyl-CoA reductase, it is a key rate-limiting enzyme for
and multifunctional proteins was observed. the production of lignin.
KEGG pathway map of starch and sucrose metabolism in Coffea arabica infected with
Hemileia vastatrix. Enzymes involved in starch and sucrose degradation (e.g., β-
glucosidases, trehalases, amylases) are predominantly upregulated, while several nodes
linked to cellulose and storage carbohydrate biosynthesis are downregulated.
CYTOCHROME P450
2.5.1.18
METHAD
ONE
1.1.1.1
FELBAM
ATE Aldophosphamide
1.1.1.1
3-Carbamoyl-2-
phenyl-
propionaldehyde
1.1.1.1
Cytochrome P450 metabolism presents a down and upregulation at the same type of alcohol
dehydrogenase and glutathione S-transferase; this could be for different variants of a same transcript
with opposite regulation, or different isoforms.
Plants present a sense system which allows them to activate immune responses against pathogens. In this pathway
a downregulation on protein kinase G (PKG) is shown, suggesting an alteration in cGMP-mediated signaling. In
contrast, calmodulin (CaM) was upregulated, which is related to the activation of calcium-dependent signaling
cascades.
Conclusion
At 24 hours post-infection of Coffea arabica with H. vastatrix,
defense pathways are upregulated while photosynthesis is
reduced. Reactive oxygen species (ROS) production may also be
triggered, acting both as defense signals and direct antimicrobial
agents. The plant shows dual regulation, with early lignin
biosynthesis enzymes upregulated but key regulators
downregulated, suggesting a defense response that remains
incomplete. Despite the severe economic impact of coffee rust,
the molecular mechanisms of this interaction are still not fully
understood due to the pathogen’s adaptability. This study
provides a transcriptomic snapshot of the plant’s early defense,
highlighting complex molecular responses and the need for
further functional validation.
PERSPECTIVES
Further research is needed to clarify and understand the interaction between the pathogen and
coffee, validate the functional role of the identified gene, its quantification and explore additional
perspectives
RT-qPCR → To confirm and quantify gene expression changes detected in RNA-seq.
ROS assays (DAB/NBT, quantitative) →
To evaluate oxidative burst as an early plant defense
response.
Fungal load quantification (qPCR) → To measure pathogen biomass and correlate infection level
with host response.
Phenylpropanoids / Lignin assays → To assess reinforcement of the cell wall as a structural
defense mechanism.
Calcium signaling measurements → To monitor Ca²⁺ fluxes as key second messengers in plant
resistance.
Acknowledgments
Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change and dispersion for RNA-
seq data with DESeq2 Genome Biology 15(12):550 (2014)
Chen Y, Chen L, Lun ATL, Baldoni PL, Smyth GK (2025). edgeR v4: powerful differential analysis
of sequencing data with expanded functionality and improved support for small counts and
larger datasets. Nucleic Acids Research 53(2), gkaf018.
The computational analyses were performed using the European Galaxy server
(https://usegalaxy.eu ). We acknowledge the Galaxy Project and its contributors for providing
open and accessible bioinformatics resources. In this work, we specifically employed the
following tools: FastQC, Trimmomatic, HISAT2, featureCounts, and Salmon for sequence quality
control, preprocessing, alignment, read quantification, and transcript abundance estimation.
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