# Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes
## 3 Results
### Results and Discussion
#### 3.3.2 Gene Ontology Annotation  
While metrics for assessing genome assembly and annotation are well-established, less work has been done on determining metrics for functional annotation. We measured the value of the GO terms assigned to gene products using the GO Annotation Quality (GAQ) Score [9; 19]. The GAQ Score incorporates the breadth of annotation, the depth (or detail) of assigned GO terms, and the evidence for these assertions [9; 19] to provide a quantitative score. A limitation of the GAQ Score is that it is relative and is best interpreted by determining improvements in the functional annotation of the same gene set over time with increasing GO annotation. To address this limitation of the GAQ Score, we provide the GAQ Score for _D. melanogaster_ to compare a well-annotated reference gene set. BLAST-based GO annotation assigned markedly fewer GO terms (accounting for at most only 4.09% of assigned annotations in caddisfly) (Table 5). However, the value of the GO annotations added by BLAST-based tools like GOanna is disproportional to the quantity of GO added by these tools. The average GAQ score for GO terms assigned by BLAST using GOanna was 142.02, while the average GAQ score of GO terms assigned by InterProScan based on motif search was 34.84. The GAQ score of the _D. melanogaster_ functional annotation downloaded from the European Bioinformatics Institute (EBI) [45], which included manual annotation, had a much higher GAQ score of 243.68 as it included evidence codes for manual functional annotation, which are weighted higher than sequence similarity-based GO term assignment. In addition to measuring how the assembly quality and proteome completeness influenced the GO term annotation, another question of interest was the potential influence of the phylogenetic distance from the model species, specifically _Drosophila melanogaster_. Among the reference genomes, _D. melanogaster_ is by far the best annotated and curated. Since GOanna uses a database of experimentally validated GO terms wherein _D. melanogaster_ was the model system used, 14.8% of _D. melanogaster_ proteins were annotated with GO terms by GOanna compared to 2.5% and 2.6% for the honeybee and red flour beetle, respectively (Table 5). Both _D. citri_ (Asian citrus psyllid) and _V. destructor_ (parasitic mite) showed overall annotation comparable to the selected references making the case that good quality genomes and annotation provide the best foundation for successful functional annotation. Surprisingly, the hypmepteran _A. rose_ (turnip sawfly) with a 99.7 BUSCO completeness, but lower contig NS0 (51.4 kb) and scaffold NS0 (1.3 Mb) than _D. citri_ and _V. destructor_ also fared well for overall annotation. The contiguous _D. citri_ and _V. destructor_ genomes did not have the highest BUSCO completeness scores (87.1% and 95.9%). The BUSCO ortholog set is computed based on a set of conserved genes in a clade, and the hemipteran clade is relatively under-sampled among arthropods, so this score might change in the future as more hemipteran genomes are sequenced. _C. capitata_ (Mediterranean fruit fly) had the highest percentage of proteins annotated by GOanna (7.9%), but that is somewhat expected considering its phylogenetic closeness to the reference species, _D. melanogaster_. The _L. lunatus_ (caddisfly) and _L. hesperus_ (Western black widow spider) genomes have the lowest contig N50, scaffold N50 metrics, and BUSCO completeness scores, but 44.6% of _L. lunatus_ proteins were annotated compared to 31.17% of _L. hesperus_ proteins. _E. affinis_ (calanoid copep) scored the poorest on GO annotation among our test species with only 30% of proteins annotated, possibly due to its phylogenetic