# Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes
## 3 Results
### Results and Discussion  
#### 3.3.1 Genome Assembly  
To test our functional annotation workflow, we selected twelve arthropod genomes, four of which were community-curated. The genomes were selected to represent a range of assembly quality and a diverse set of arthropod species. These twelve genomes were supplemented with three well-studied arthropods (a reference set): _Drosophila melanogaster_ (fruit fly), _Apis mellifera_ (honeybee), and _Tribolium castaneum_ (red flour beetle) from the Orders Diptera, Hymenoptera, and Coleoptera, respectively. We note that all these species have been assembled, annotated, and the proteomes are considered mostly complete with BUSCO completeness scores ranging from 31 to 99% (Table 4). The genome assemblies for the selected species varied in contiguity and quality, with scaffold N50s ranging from 13.8 kb to 58.5 Mb (Table 3). Another metric of interest for quantifying the quality of the assembly before scaffolding is contig N50 that ranged from as low as 2.2 kb for genomes assembled with Illumina paired-end and mate-pair reads to 749.5 kb for genomes assembled with PacBio long-read technology (Table 3). Please note that assemblies with low contig N50, but comparatively high scaffold N50 can have large gaps filled with unknown (N) nucleotides.  
The proteome sets we used ranged from 12,318-33,019 proteins (Table 3). We examined the proportion of these proteins that were annotated with GO data, and were also interested in determining what BLAST-based analyses contributed to this GO annotation compared to the motif-based InterProScan annotation. Overall, GO annotation ranged from 30-60% of the protein set, with an average of 45%, including the reference genomes. Notably, other species achieved the same rates of GO annotation as the reference gene sets, indicating that the workflow performs as expected. We also wanted to evaluate if assembly contiguity (contig and scaffold N50) and gene space completeness corresponded to coverage of functional annotation for the proteome. This was not always the case as 44.6% of the proteins from _L. lunatus_ (caddisfly) were associated with GO terms, but the assembly only has a scaffold N50 of 54.6 kb and a contig N50 of 2.1 kb. The gene space for caddisfly is relatively incomplete at 42.4 with low duplication (Figure S1 and Table 4). On the other end of the spectrum, the hypenopteran C. _foridanum_ (parasitoid wasp) has a contig and scaffold N50 of 14.5 kb and 1 Mb, respectively, but only 34.1% of its proteins must GO terms associated with them. The other hypenopteran in the test set, _A. rose_ (turnip sawfly), has a better GO term coverage of 57.05%, but it also has a more contiguous genome with a contig and scaffold N50 of 51.4 kb and 1 Mb, respectively. Both _A. rose_ (turnip sawfly) and C. _foridanum_ (parasitoid wasp) have comparable BUSCO completeness metrics (99.7% and 93.7%), but duplication in the gene space is higher at 30.8% in _A. rose_ compared to only 1.2% in _C. floridanum_. It should be noted that highly curated reference genomes like _Drosophila melanogaster_ have multiple isoforms annotated per protein (46.6 of 99.9) that are reported as duplicates by BUSCO.