Abstract

Abstract

Background: 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. 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.

Results: Assembling 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.

Conclusion: We 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.

Details

Title
An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora
Author
Mondego, Jorge MC; Vidal, Ramon O; Carazzolle, Marcelo F; Tokuda, Eric K; Parizzi, Lucas P; Costa, Gustavo GL; Pereira, Luiz FP; Andrade, Alan C; Colombo, Carlos A; Vieira, Luiz GE; Pereira, Gonçalo AG
Pages
30
Publication year
2011
Publication date
2011
Publisher
BioMed Central
e-ISSN
14712229
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
902059074
Copyright
© 2011 Mondego et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.