Transcriptome Analysis Uncovers the Gene Expression Profile of Hemileia vastatrix (Race XXXIII) during the Interactions with Resistant and Susceptible Coffee

Isabel Samila Lima Castro,Sávio De Siqueira Ferreira,Talles Eduardo Ferreira Maciel,Juan Carlos Florez,Eveline Teixeira Caixeta,Rejane Do Livramento Freitas-Lopes,Laércio Zambolim,Eunize Maciel Zambolim

doi:10.3390/agronomy12020444

Transcriptome Analysis Uncovers the Gene Expression Profile of Hemileia vastatrix (Race XXXIII) during the Interactions with Resistant and Susceptible Coffee

Isabel Samila Lima Castro, Sávio De Siqueira Ferreira + Show 6 more

Open Access

https://doi.org/10.3390/agronomy12020444

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Abstract

Coffee leaf rust is caused by Hemileia vastatrix Berk. and Broome and is the most important coffee disease in all regions where coffee is cultivated. Here, we sought to sequence the transcriptome of H. vastatrix race XXXIII to obtain a database for use as a reference in studies of the interaction between the fungus and coffee. In addition, we aimed to identify differentially expressed genes that have the potential to act as effector proteins during the interaction. Sequencing of cDNA libraries from uredospores and from compatible and incompatible interactions at different key time points generated about 162 million trimmed reads. We identified 3523 differentially expressed genes. The results suggested that the fungal transcriptome is dynamically altered over the course of infection and that the interaction with a susceptible plant upregulates a larger set of fungal genes than the interaction with a resistant plant. Co-expression network analysis allowed us to identify candidate genes with the same expression pattern as that of other effectors of H. vastatrix. Quantitative PCR analysis identified seven transcripts that may be effectors involved in the coffee–H. vastatrix interaction. This information provides a basis for obtaining new insights into the molecular mechanisms of infection in this pathosystem. Understanding gene expression during the infection process may contribute to elucidating the molecular mechanisms leading to the breakdown of resistance by new physiological races of the fungus.

Highlights

Hemileia vastatrix Berk. and Broome causes the most important coffee leaf rust disease in all regions where coffee is cultivated [1,2]
The transcriptome was obtained based on libraries from hydrated and germinated uredospores of H. vastatrix and from compatible and incompatible interactions at different key time points
In the susceptible leaves (Caturra CIFC 19/1), hypersensitive response (HR) responses were observed in about 30% of the infection sites from 17 to 96 hpi (Table 1)

Summary

Introduction

Hemileia vastatrix Berk. and Broome causes the most important coffee leaf rust disease in all regions where coffee is cultivated [1,2]. Broome causes the most important coffee leaf rust disease in all regions where coffee is cultivated [1,2]. The disease causes leaves to fall prematurely, which results in the death of branches and low photosynthesis rates, reducing the coffee yield in the following year by 27% to 50% [2,3]. Leaf rust negatively impacts coffee quality, affecting the chemical composition of the beans and the beverage [4]. In Brazil, a major producer, the fungus is widely distributed in all producing areas of Coffea arabica L. and C. canephora Pierre ex A. The discovery of H. vastatrix in Hawaii in late 2020 highlights that this disease colonizes all major coffee-growing regions of the world [6,7]

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