# Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes
## 3 Results
### Results and Discussion
#### 3.3.2 Gene Ontology Annotation
\begin{table}
\begin{tabular}{c c c c c c c} \hline \hline \multirow{2}{*}{**Species**} & \multirow{2}{*}{**Proteins**} & \multicolumn{2}{c}{**Proteins**} & \multicolumn{2}{c}{**GOanna (BLAST)**} & \multicolumn{2}{c}{**InterProScan (Motif Analysis)**} \\ \cline{3-7}  & & **Assigned GO** & **Proteins** & **Average GO** & **AOSigned GO** & **AOSigned GO** & **AOS** \\ \hline _Apis mellifera_ & & & & & & \\ (honey bee) & 15,314 & 39.91\% & 2.59\% & 164.796 & 39.32\% & 33.745 \\ _Drosophila melanogaster_ & & & & & & \\ (fruit fly) & & & & & & \\ _Tribolium castructom_ & & & & & \\ (red flour beetle) & 18,534 & 44.98\% & 2.64\% & 142.27 & 44.36\% & 33.585 \\ _Diphorina citri_ & & & & & & \\ (Asian citrus psyllid) & & & & & & \\ _Athalia rose_ & & & & & \\ (turnip sawfly) & & & & & & \\ _Varra destructor_ & & & & & \\ (parasitic mite) & & & & & & \\ _Aparis planipennis_ & & & & & \\ (emerald ash borer) & 15,497 & 51.07\% & 2.87\% & 179.869 & 41.27\% & 31.368 \\ _Certainitis capitata_ & & & & & & \\ (Mediterranean fruit fly) & 14,212 & 49.42\% & 7.94\% & 127.988 & 46.42\% & 32.504 \\ _Cimer lactatirius_ & & & & & & \\ (Cimicidae bed bug) & 14,212 & 49.26\% & 3.00\% & 177.746 & 48.33\% & 35.017 \\ _Limmipthins lunatus_ & & & & & & \\ (caddisfly) & 13,292 & 44.61\% & 4.09\% & 172.298 & 43.03\% & 31.353 \\ _Homalidisca vitripennis_ & & & & & & \\ (glassy-winged sharpshooter) & & & & & & \\ _Proceedus fascitus_ & & & & & \\ (large milkweed bug) & & & & & & \\ _Copidosoma floridanum_ & & & & & \\ (parasitoid wasp) & & & & & & \\ _Lartoclus hepers_ & & & & & \\ (Western black widow spider) & & & & & & \\ _Eurytemon affinis_ & & & & & \\ (calanoid copep) & & & & & & \\ \hline \hline \end{tabular}
\end{table} 
Table 5: GOanna and InterProScan results for arthropod genomes selected for this study. The test species are sorted by their GO term coverage. distance from \(D\). _melanogaster_, despite having a better contig and scaffold N50 of 5.7 kb and 862.6 kb, respectively. However, it had a poor BUSCO completeness metric with only 57.5% completeness and 22.5% missing orthologs. We found a common theme in our test set and related analysis, whereby the quality and depth of functional annotation were inversely proportional to the phylogenetic distance from the \(D\). _melanogaster_ model species (data not shown). There are two major approaches for associating GO with gene products--manual curation of published literature on gene function and sequence analysis. The former approach has been limited to less than 20 species, and it is unlikely that most species across the kingdom of life will get the benefit of the sustained manual curation based on experimental evidence from published literature. In response, GO curators have developed a method for transferring GO functions across species based upon phylogenetic analysis [3], but this method still relies on manual review by expert curators. While our GO annotation workflow provides a rapid method to associate GO function with proteomes, our results emphasize the need for the better annotation of non-model species in every major clade so that proteins from newly sequenced genomes can be assigned function more accurately. One approach to achieve this goal would be to combine the GO phylogenetic approach to identify genes not found in \(D\). _melanogaster_ and identify invertebrate species with existing functional literature for targeted GO curation by providing more direct evidence annotations for invertebrate gene products. This focused application of phylogenetics and targeted manual curation would likely provide GO annotation that would impact the annotation of invertebrate gene function. We note that this is also a limitation of our sequence-based approach as it is dependent on manual biocuration of published papers from reference species (e.g., _D. melanogaster_) to provide a useful level of functional detail. Another limitation of our workflow is that it is currently limited to proteins and does not provide information about ncRNA function.