Abstract
The availability of a representative Gene Ontology (GO) database is a prerequisite for a successful functional genomics study. Using the online Blast2GO tool we constructed a GO database of Aspergillus flavus, a plant and human pathogen. Of the predicted total 13,485 A. flavus genes 8,987 were annotated with GO terms. The mean GO level was 5.64. Using a low stringency setting of a sequence cut-off number of 10 and a node score of 20, we obtained 1,177 GO terms associated with biological process, 388 GO terms associated with molecular function and 200 GO terms associated with cellular component. Of the 8,987 annotated genes 4,232 were mapped to 129 reference pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The utility of the GO database was evaluated with published transcriptomic data by assessing physiological states in relation to the metabolic capacity of A. flavus growing at 30°C and 37°C. Results showed that growth at 30°C favored degradation of amino acids with nonpolar side chains, such as valine, leucine, isoleucine, phenylalanine and tryptophan. In contrast, growth at 37°C favored the degradation of arginine and histidine (basic), aspartate and glutamate (acidic), and serine and threonine (uncharged but polar) but biosynthesis of the aforementioned nonpolar-side-chain amino acids. KEGG pathways of amino acid degradation contributing to acetyl-CoA production, (saturated) fatty acid biosynthesis and degradation as well as biosynthesis of unsaturated fatty acids were active at 30°C, which suggests a requirement that A. flavus maintain a high content of unsaturated fatty acids at the optimal growth temperature. The proposition was supported by the finding that the GO cellular component involved at 30°C growth was mainly a fatty acid synthase complex. The constructed A. flavus GO database was proven to be useful in our functional genomics study. We also outlined the procedures for future update and refinement of the current A. flavus GO database, which can be achieved by concerted efforts of the Aspergillus research community.
Highlights
Aspergillus flavus is predominately a saprophytic fungus in the soil that grows on dead plant, agricultural debris, and animal tissue
Genome-wide investigations using EST or whole-genome microarray assays have been performed to examine genes differentially expressed in degenerated A. flavus strains after serial transfers [5], in a 70S-derived strain that is defective in the veA regulatory gene [6], in NRRL3357 that examined tryptophan supplementation on aflatoxin biosynthesis [7], in the simulated conditions of A. flavus-host interactions [8] and in the process of A. flavus-seed colonization [9]
The overall analysis resulted in 8,987 A. flavus sequences annotated with 37,139 Gene Ontology (GO) terms
Summary
Aspergillus flavus is predominately a saprophytic fungus in the soil that grows on dead plant, agricultural debris, and animal tissue. It can infect many crops such as corn, cotton, peanuts, and nut trees and the infection often leads to contamination with aflatoxin B1, a toxic and potent carcinogenic compound. Genome-wide investigations using EST or whole-genome microarray assays have been performed to examine genes differentially expressed in degenerated A. flavus strains after serial transfers [5], in a 70S-derived strain that is defective in the veA regulatory gene [6], in NRRL3357 that examined tryptophan supplementation on aflatoxin biosynthesis [7], in the simulated conditions of A. flavus-host interactions [8] and in the process of A. flavus-seed colonization [9]. The inability to pertinently interpret the results is mainly due to the lack of knowledge in network interactions among the differentially expressed genes examined
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