## 2 Results  
Genome assembly. The size of the _A. domesticus_ genome was measured by flow cytometry as described in [49]. The genome of female _A. domesticus_ was larger than males (2378.8 \(\pm\) 9.7 Mb vs. 2149.6 \(\pm\) 11.2 Mb, respectively, Table S1). The size of the X-chromosome was estimated as 387 Mb, the difference between the 2C genome size measurement of the XX female and the XO male. The average size of autosomal chromosomes was 177 Mb. Genomic DNA was extracted from a single _A. domesticus_ adult male for long read sequencing, and nuclear DNA from the same adult male was used for long range data in scaffolding. The draft assembly of long read data contained 28,340 contigs with an N\({}_{50}\) of 321,088 bases (Table 1). The final assembly with long range (Chicago and Hi-C) data contained 16,290 scaffolds originally with an N\({}_{50}\) of 221.839 Mb and a BUSCO score of 94.8%. After contaminant scaffolds (metagenome, mitochondrial, duplicate, and vector) were removed, the final _A. domesticus_ genome assembly contained 9964 scaffolds consisting of 2,346,604,983 bp. The final assembly had 11 larger chromosomes that totaled 2,137,583,504 bp, presumably representing the 10 autosomal chromosomes and single X sex chromosome predicted for males (Figure 1). The longest scaffold in the assembly was 304 Mb (scaffold_14394) and may represent a portion of the X chromosome. An in silico genome annotation revealed 29,304 predicted genes in 1064 scaffolds, concentrated in the 11 large scaffolds (84%). We compared the length of the BUSCO reference genes from _A. domesticus_ to those from a model coleopteran genome, _Tribolium castaneum_ (Figure S2). We found that 84% of the reference genes in _A. domesticus_ were longer than those in _T. castaneum_, some more than 80-fold longer. The longer length of _A. domesticus_ genes was due mostly to longer introns. There were 6246 scaffolds in the _A. domesticus_ genome assembly that were identified as metagenome sequences using multiple automated and manual annotations. Metagenomic scaffolds were from 1013 to 512,394 bp, and one larger scaffold, Ado_Mffpo_scaffold_8829, with 3,776,750 bases and 218 genes was identified as _Acinetobacter humanini_; these scaffolds were submitted to NCBI as _A. domesticus_-associated metagenome data. Approximately 83% of the metagenome scaffolds had similarity to Invertebrate Iridescent Virus 6 (IIV6, File S3, \"Ado_metagenome_Kraken2\"). Bacterial scaffolds were mostly from the classes \begin{table}
\begin{tabular}{c c c} \hline \hline
**Metric** & **PacBio Draft Assembly** & **Chicago/Hi-C Scaffolded** \\ \hline PB coverage & 27.3x (Sequel I) & - \\ \hline \#Contigs & 28,340 & - \\ \hline ContigN\({}_{50}\) & 321,088 bp & - \\ \hline Chicago/HiRise coverage & - & 10.37x \\ \hline HiC coverage & - & 11,358.72x \\ \hline Number of scaffolds & - & 16,290 \\ \hline N\({}_{50}\) (Mb) & - & 221.839 Mb \\ \hline Longest Scaffold & - & 303,995,810 bp \\ \hline L\({}_{50}\) (\#scaffolds) & - & 5 \\ \hline Busco (Insecta) & - & 94.8\% \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Metrics of the _A. domesticus_ genome assembly. Data included the CANU draft assembly from PacBio long read data, and the scaffolded assembly from Chicago and Hi-C long range data. Gammaproteobacteriaobacteria, Flavobacteria, Sphingobacteria, Fusobacteria, Betaproteobacteriaobacteria, Alphaproteobacteria, Actinomyctia, and Bacilli. However, follow-up screening of unclassified reads using blastn [50] and NCBInr found an additional 913 potential metagenome scaffolds (File S3, \"Blastn_unclassified\"). The final scaffolds were identified as mostly IIV6 and bacteria, but also a smaller number of scaffolds were fungi, protozoa, and nematode (File S3, \"Metagenome_summary\"). Of note, there were 27 scaffolds from _Wolbachia_ similar to those described from other insects. In our analysis, we did not find evidence of common foodborne pathogens, such as _Salmonella_ spp., and the few scaffolds aligning to _Listeria_ sp., _Escherichia coli_ or _Staphylococcus_ sp.