In total, approximately 2.5 M reads per replicate per feedstock treatment were functionally annotated (Additional file 1: Table S4B).
The lists of genes identified as differentially expressed during microsclerotia development were functionally annotated in-silico to identify genes encoding the different types of proteins that are potentially involved in microsclerotia biogenesis.
Eight genes were functionally annotated in the global test, and their major function was examined according to KEGG pathways (Table 3).
Homologues to more than 80 mRNA-tags were functionally annotated in the databases.
Among them, 42,583 were functionally annotated in the NCBI non-redundant database and 47,877 in the tomato genome reference.
Five hundred probes on the array represent 258 unique genes that are functionally annotated in Gene Ontology (http://www.geneontology.org) as members of the Wnt receptor signaling pathway.
These significantly differentially expressed CPE and NPE genes were functionally annotated in the Ingenuity Knowledge Base (Ingenuity® Systems, version 11631407, http://www.ingenuity.com; assessed at August 5, 2013).
Because only 6,996 detected transcripts were functionally annotated in VectorBase (genome version AaegL2.1, vectorbase.org) we performed a Blast2GO analysis of all predicted peptides annotated as 'conserved hypothetical protein' or 'hypothetical protein' in Vectorbase against the protein database Swissprot (Blastp, E-value < 10-3, annotation cut-off = 55, GO weight = 5).
In this study, about 2.5% of the whole transcriptome assembly was identified as rust-responsive genes and 85% of them were functionally annotated in P. monticola defense, but their putative contribution to host resistance to C. ribicola awaits verification by functional genomics studies or association studies focused on exploring gene variation in P. monticola populations.
These tools also allow us to assess the function of many genes in vivo, which is needed now more than ever as human geneticists discover disease-causing genes at an unprecedented pace, while <30% of the fly's genes are functionally annotated in vivo (St Pierre et al. 2014).
