In silico analysis of the coffee transcriptome: identification of SNPs and inference of mechanisms of gene expression regulation

Author(s)

Ramon Oliveira Vidal

• Document type: Doctoral Thesis
• Press: Campinas, SP.
• Institution: Universidade Estadual de Campinas (UNICAMP). Instituto de Biologia
• Defense date: 2010-12-16

Examining board members

Gonçalo Amarante Guimarães Pereira; Pierre Marraccini; Marcelo Mendes Brandão; Paulo Mazzafera; Michel Eduardo Beleza Yamagishi

• Advisor: Gonçalo Amarante Guimarães Pereira

Abstract

Coffee is one of the most important crops in the world, being worldwide consumed and having significant participation in under development economies. Coffea arabica and Coffea canephora are responsible for 70% and 30% of commercial production, respectively. Cytogenetic analysis established that C. arabica is an autogamous alotetraploid formed by a recent (1 mya) hybridization between the diploids C. canephora and Coffea eugenioides. C. eugenioides is a wild species which grows in higher altitudes near forest edges, and produces few berries with small beans of low caffeine content. On the other hand, C. canephora is alogamous and grows better in lowlands. It is also characterized by higher productivity, more tolerance to pests, and higher caffeine content, but it has an inferior beverage compared with C. arabica. During the last decade, research initiatives have been launched to produce genomic and transcriptomic data about Coffea spp. This EST collection represents a good overview of C. arabica and C. canephora transcriptome, being appropriate as a resource for Coffea molecular analysis. This work aimed to obtain further information about Coffea spp. gene structure and expression and to identify genes that are specific or expanded in coffee plants. Moreover, it also intended to study the homeologous gene expression regulation in the alotetraploid C. arabica. In order to investigate these data two different EST assemblies were performed: (i) with each species individually, aiming the comparative analysis between the C. arabica, C. canephora and other crops; and (ii) with both coffee species together, allowing the identification of SNPs between C. arabica and one of its direct ancestors C. canephora and the examination of evolutive issues in C. arabica. The identification of differentially expressed transcrip ts and new gene families offered a starting point for the correlation of gene expression profil es and Coffea sp. development traits. Protein domain and Gene Ontology analyzes suggested significant differences between the data of coffee species analyzed, mainly in relation to complex sugar synthases, nucleotide binding proteins, retrotransposons and stress response. OrthoMCL tool identified specific or prevalent coffee protein families when compared with other five plant species. Using the high quality discrepancies, found in overlapped ESTs from C. arabica and C. canephora, sequence diversity profiles were evaluated within both species and used to deduce the transcript contribution of the C. canephora and C. eugenioides ancestors in the C. arabica. The assignment of the C. arabica homeologous genes to the ancestral genomes allowed us to analyze gene expression contributions of each subgenome. We suggest that this phenomenon has an important issue in Coffea gene expression and physiology. (AU)