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Updated: Jun 28, 2025

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
Published on: June 17, 2012
Gene ontology functional annotation datasets for the ITAG3.2 and ITAG4.0 tomato (Solanum lycopersicum) genome
Ricardo Rivera-Silva1, Ricardo A Chávez Montes2, Fabiola Jaimes-Miranda3
1División de Biología Molecular, IPICYT, San Luis Potosí, 78216, Mexico.
Abstract:
Functional annotation based on Gene Ontology has provided a structured and comprehensive system to access the current knowledge about the function of genes. For model plants such as Arabidopsis thaliana, there is a constant updating and restructuring of the functional annotation that increases the reliability of the analyses that use it. For tomato (Solanum lycopersicum), a crop widely used as a model plant for the study of fleshy fruits, there is no functional annotation, at least not freely accessible, even though its genome has long been sequenced and annotated. In this work, we generated, using a simplified version of the maize GAMER pipeline, a tomato Gene Ontology functional annotation with 72.42% (ITAG3.2) and 74.2% (ITAG4.0) of protein-coding genes with at least one GO term association. With this dataset, we share a reliable and easy-to-use tool with the tomato community.
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