Functional annotation of insecta transcriptomes: A cautionary tale from Lepidoptera

Functional annotation is a critical step in the analysis of genomic data, as it provides insight into the function of individual genes and the pathways in which they participate. Currently, there is no consensus on the best computational approach for assigning functional annotation. This study compares three functional annotation methods (BLAST, eggNOG-Mapper, and InterProScan) in their ability to assign Gene Ontology terms in two species of Insecta with differing levels of annotation, Bombyx mori and Manduca sexta. The methods were compared for their annotation coverage, number of term assignments, term agreement and non-overlapping terms. Here we show that there are large discrepancies in gene ontology term assignment among the three computational methods, which could lead to confounding interpretations of data and non-comparable results. This study provide insight into the strengths and weaknesses of each computational method and highlight the need for more standardized methods of functional annotation.