Abstract
BackgroundCoffee is one of the world's most important crops; it is consumed worldwide and plays a significant role in the economy of producing countries. Coffea arabica and C. canephora are responsible for 70 and 30% of commercial production, respectively. C. arabica is an allotetraploid from a recent hybridization of the diploid species, C. canephora and C. eugenioides. C. arabica has lower genetic diversity and results in a higher quality beverage than C. canephora. Research initiatives have been launched to produce genomic and transcriptomic data about Coffea spp. as a strategy to improve breeding efficiency.ResultsAssembling the expressed sequence tags (ESTs) of C. arabica and C. canephora produced by the Brazilian Coffee Genome Project and the Nestlé-Cornell Consortium revealed 32,007 clusters of C. arabica and 16,665 clusters of C. canephora. We detected different GC3 profiles between these species that are related to their genome structure and mating system. BLAST analysis revealed similarities between coffee and grape (Vitis vinifera) genes. Using KA/KS analysis, we identified coffee genes under purifying and positive selection. Protein domain and gene ontology analyses suggested differences between Coffea spp. data, mainly in relation to complex sugar synthases and nucleotide binding proteins. OrthoMCL was used to identify specific and prevalent coffee protein families when compared to five other plant species. Among the interesting families annotated are new cystatins, glycine-rich proteins and RALF-like peptides. Hierarchical clustering was used to independently group C. arabica and C. canephora expression clusters according to expression data extracted from EST libraries, resulting in the identification of differentially expressed genes. Based on these results, we emphasize gene annotation and discuss plant defenses, abiotic stress and cup quality-related functional categories.ConclusionWe present the first comprehensive genome-wide transcript profile study of C. arabica and C. canephora, which can be freely assessed by the scientific community at http://www.lge.ibi.unicamp.br/coffea. Our data reveal the presence of species-specific/prevalent genes in coffee that may help to explain particular characteristics of these two crops. The identification of differentially expressed transcripts offers a starting point for the correlation between gene expression profiles and Coffea spp. developmental traits, providing valuable insights for coffee breeding and biotechnology, especially concerning sugar metabolism and stress tolerance.
Highlights
Coffee is one of the world’s most important crops; it is consumed worldwide and plays a significant role in the economy of producing countries
expressed sequence tags (ESTs) libraries data To evaluate ESTs from Coffea spp. we collected 187,412 ESTs derived from 43 cDNA libraries produced by the Brazilian Coffee Genome Project initiative [21]
All ESTs were produced by the Sanger method, and cDNA clones were subjected only to 5’ sequencing
Summary
Coffee is one of the world’s most important crops; it is consumed worldwide and plays a significant role in the economy of producing countries. Coffea arabica and C. canephora are responsible for 70 and 30% of commercial production, respectively. Two species of the genus Coffea are responsible for almost all coffee bean production: C. arabica and C. canephora (approximately 70 and 30% of worldwide production, respectively). As a consequence of its autogamy and evolutionary history, “Arabica” coffee plants have a narrow genetic basis. This problem is amplified in the main cultivated genotypes (i.e., Mundo Novo, Catuai and Caturra), which were selected from only two base populations: Typica and Bourbon [4]. The introduction of a new trait into an elite coffee variety via conventional breeding techniques is a lengthy process due to the narrow genetic basis of C. arabica [4,10] and the long seedto-seed generation cycle
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