## 2 Results
were insufficient to confirm the presence of these pathogens. A closer examination of the predicted proteins from the virus scaffolds indicated that only seven were assigned as \"high-quality\" viral genomes, and 25 scaffolds were determined to be viral genomes of \"medium-quality\" as determined by CheckV (Ref. [51] File S4). Although many shorter scaffolds were not aligned to the IIV6 genome, many of the predicted genes in these scaffolds were annotated as viral. Therefore, these scaffolds are likely to be viral and quality may be affected by the database integrity, sequence read quality, or assembly artifacts. These sequences also may represent new viruses. Other sequences were classified as low-quality matches or undetermined genomes. Interestingly, one medium quality scaffold (Scaffold_4233) was similar to a circular virus (DTR_035638) from the metagenome in the reduced digestive system of an oligochaete, _Olavius albidis_, a marine gutless worm related to another _Olavius_ spp. with a symbiont metaproteome that evidently contributes to nutrient metabolism [52]. This scaffold was longer (8979 bp) than that of the circular virus (5878 bp). Regarding immunity genes, conserved sequences involved in insect immunity were used to identify orthologs in the _A. domestic_ genome assembly. Genes related to conserved cercropins and defensins were not found in the assembly and have not been identified in the literature from any orthopteran insect to date. However, there were two genes identified as peptidoglycan recognition protein (PGRP) (File S5). Three transcripts found in a previous transcriptome assembly [22] corresponded to these PGRP genes (Figure 2). Only one PGRP transcript appears to be expressed at low levels in the embryo. Expression of all PGRPs, especially ci_142522_1, ramps up during the 1 st week of development, and gradually decreases throughout the nymphal stages. PGRPs are expressed at higher levels in female compared to male adult _A. domesticus_. Figure 1: Link density histogram of the _A. domesticus_ Hi-C scaffolded assembly (**left**) and scaffold name and length of the 11 largest scaffolds in the assembly (**right**). Eleven genes were identified as encoding gram negative binding proteins (GNBP, File S5). These GNBP genes corresponded to 27 transcripts from the transcriptome assembly [22], some which were apparent isoforms of ANN05691-RA (5), ANN05692-RA (3), ANN05929-RA (4), and ANN16377-RA (3). Most of the GNBP transcripts were expressed at low levels in the _A. domesticus_ adult (Figure 3A). However, cl_1105989_1 and _2 isoforms of ANN16377-RA were more highly expressed in all life stages except for embryos, as well as male and female adults. Figure 3: _Cont._  
Figure 2: Expression profiles of three potential PGRP transcripts from _A. domesticus_ developmental stages or male and female adults. The figure legend has the identification of transcripts from a previous transcriptome assembly [22]. There were four genes annotated as lysozyme in the _A. domesticus_ assembly (File S5). Contigs cl_658063 (five isoforms) and cl_660380_1 (two isoforms) corresponding to ANN24139-RA and ANN24140-RA/ANN24139-RA, respectively, were the most highly expressed putative lysozyme transcripts in the transcriptome assembly [22]; ANN19980-RA transcripts were expressed at low levels (Figure 3B). Lysozyme transcripts were expressed higher in 1 and 2 week nymphs and male and female adults. Figure 3: Expression profiles of transcripts tentatively identified as immune-related genes in _A. domesticus_ developmental stages or male and female adults (as indicated in the legend). Transcripts were identified in a previous transcriptome assembly [22]. (**A**) GNBP; (**B**) Lysoszymes; (**C**) PPO. The _A. domesticus_ genome assembly contained nine genes annotated as PPO (File S5). Contig cl_93919 (nine isoforms), corresponding to all nine genes, was more highly expressed throughout life stages (Figure 3C).