Department of Animal Biology/Centro de Investigação das Ferrugens do Cafeeiro
Campo Grande, Building C2, Floor 3
Abstracts (first author)
Analysis of Illumina RNA-seq data from a susceptible vs resistant coffee - Colletotrichum kahawae interactionPDF
Coffee berry disease (CBD), caused by the fungus Colletotrichum kahawae, is considered one of the biggest threats to Arabica coffee production in Africa at high altitude. Some coffee genotypes are known to be resistant to CBD, but the molecular genetic basis of coffee resistance is still unknown. With the purpose of gaining some insights on this process, a RNA Illumina sequencing approach was used to characterize the defense response of two coffee genotypes, respectively resistant and susceptible to C. kahawae, during the early stages of the infection process. Three inoculation time-points were selected (24, 48 and 72 hpi) and two biological replicates were collected. Twenty four independent cDNA libraries were sequenced and data is being analyzed to assess differential gene expression when comparing inoculated with control samples. The data was trimmed, and two assemblies were made: one with the control libraries and the other with the inoculated libraries. The first was used in expression quantification for both gene and isoform, by using statistical methods. Particular attention was paid to data normalization, using FPKM algorithm in gene quantification, and a Maximum Likelihood statistical model in isoform quantification. The other assembly is being used to discover C. kahawae genes by codon usage frequency (ECLAT). Although fungal transcripts are weakly represented in the samples, we expect to detect new and unknown genes of C. kahawae. The identification and characterization of expression differences between these contrasting situations will allow us to understand which genes are potentially involved in the resistance response of coffee to C. kahawae. The subsequent identification of the predicted proteins and their location in the metabolic networks could provide new relevant knowledge able to support and improve coffee breeding for resistance to CBD.
Funded by FCT (project PTDC/AGR-GPL/112217/2009)