10 research outputs found
An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora
Background: Coffee is one of the worldâs 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
Construction and characterization of a Coffea canephora BAC library to study the organization of sucrose biosynthesis genes
Corresponding author: E-mail: [email protected] audienceThe first bacterial artificial chromosome (BAC) library of Robusta coffee (Coffea canephora) was constructed, with the aim of developing molecular resources to study the genome structure and evolution of this perennial crop. Clone 126, which is highly productiveand confers good technological and organoleptic qualities of beverage, was chosen for development of this library. The BAC library contains 55,296 clones, with an average insert size of 135 Kb per plasmid, therefore representing theoretically nine haploid genome equivalents of C. canephora. Its validation was achieved with a set of 13 genetically anchored single-copy and 4 duplicated RFLP probes and yielded on average 9 BAC clones per probe. Screening of this BAC library was also carried out with partial cDNA probes coding for enzymes of sugar metabolism like invertases and sucrose synthase, with the aim of characterizing the organization and promoter structure of this important class of genes. It was shown that genes for both cell wall and vacuolar forms of invertases were probably unique in the Robusta genome whereas sucrose synthase was encoded by at least two genes. One of them (CcSUS1) was cloned and sequenced, showing that our BAC library is a valuable tool to rapidly identify genes of agronomic interest or linked to cup quality in C. canephora