Transcriptome profiling of two coffee varieties in response to infection with an endemic X. fastidiosa subsp. fastidiosa strain from Costa Rica

Xylella fastidiosa subsp. fastidiosa is endemic in Costa Rica. Since the 1990s, the presence, the broad genetic diversity of the isolates, and dissemination of the bacteria have been confirmed throughout the different coffee-producing regions of the country. Although the bacteria is prevalent and has great potential for disease, most of the colonized coffee plants are asymptomatic or to a major extent show mild symptoms that relate to “crespera” disease. The presence of X. fastidiosa does not represent a serious threat to the coffee industry in Costa Rica, a different scenario to other known crops. To understand the host-pathogen interaction of X. fastidiosa with coffee plants, we performed transcriptomic analysis on two varieties of coffee: Catuaí, a common variety used throughout the country, and CR95, a variety that has shown resistance to fungal pathogens. We assessed plant response to X. fastidiosa seven days post-infection. In vitro grown six-month-old coffee plants were inoculated with X. fastidiosa subsp. fastidiosa (ST33), previously isolated from coffee, or with PBS in case of the control groups (five plants per group). Seven days post-infection the presence of the bacteria was determined by qPCR. In addition, RNA sequencing was performed for each infected and control plant. Our results show that CR95 plants have a lower overall bacterial load seven days post-infection than Catuaí. The Principal component analysis (PCA) clustered healthy and infected replicates separately. CR95 showed twice differentially expressed genes than Catuaí. GO enrichment and network analyses revealed the involvement of several metabolic pathways in response to the exposure to the bacteria. Genes related to plant recognition and defense response were also identified. In conclusion, coffee plants recognize the presence of X. fastidiosa but do not induce a strong defense response, a window of opportunity that may favor plant colonization and persistence.