## 5 Materials and Methods
The version described in this paper is version JAHLJT010000000. To determine scaffolds that were from the metagenome, we used multiple tools to screen the scaffolds, including BBSketch and NCBI Refseq ([[https://www.biostars.org/p/234837/](https://www.biostars.org/p/234837/)]([https://www.biostars.org/p/234837/](https://www.biostars.org/p/234837/))) and Kraken2 [92] in Omicsboxs (Biobam, Valencia, Spain, version 2.1.2, database RefSeq 2021.04, 2022.02). The scaffolds also were used in beta testing for GX, a screening tool for microbial contamination at NCBI ([[https://github.com/ncbi/fcs](https://github.com/ncbi/fcs)]([https://github.com/ncbi/fcs](https://github.com/ncbi/fcs))). We combined results from all three datasets (BBtools, Kraken2, GX) and manually annotated unclassified scaffolds with blastn [50], further using read depth to assign as insect or microbial. After this process, 80 scaffolds were removed as a result of NCBI screening tools to identify vector or duplicates, and 6245 metagenomic scaffolds were submitted to NCBI MIMS as a metagenome/environmental, host-associated sample (accession number PRJNA908265). Annotation and analysis. Annotation of the _A. domesticicus_ genome assembly was by Dovetail Genomics. Repeat families found in the genome assemblies of _A. domesticicus_ were identified de novo and classified using RepeatModeler (version 2.0.1) [93]. RepeatModeler depends on RECON (version 1.08) and RepeatScout (version 1.0.6) for the de novo identification of repeats within the genome. The custom repeat library obtained from RepeatModeler was used to discover, identify, and mask the repeats in the assembly file using RepeatMasker (version 4.1.0) [94]. Coding sequences from _Locusta migratoria, Teleogryllus occipitalis, Laupala kohalensis_, and _Xenocatantops brachycerus_ were used to train the initial ab initio model for _A. domesticus_ using AUGUSTUS (version 2.5.5) [95], with six rounds of prediction optimization. The same coding sequences also were used to train a separate ab initio model for _A. domesticus_ using SNAP (version 2006-07-28) [89]. RNAseq reads were mapped to the genome using STAR aligner (version 2.7) [96]. and intron hints were generated with the bam2 hints tools within AUGUSTUS. MAXER and SNAP (intron-exon boundary hints provided from RNA-Seq) were then used to predict genes in the repeat-masked reference genome. Swiss-Prot peptide sequences from the UniProt database were downloaded and used in conjunction with the protein sequences from the same training species to generate peptide evidence in Maker [97]. Only genes that were predicted by both SNAP and AUGUSTUS were retained in the final gene sets. AED scores were generated for each of the predicted genes as part of the MAXER pipeline to assess the quality of the gene prediction. Genes were further characterized for putative function by performing a BLAST [50] search of the peptide sequences against the UniProt database. tRNA were predicted using the software tRNAscan-SE (version 2.05) [98]. Predicted genes were analyzed by BUSCO (v.2.0) [99], using the lineage dataset insecta_odb9 (creation date: 2016-10-21, number of species: 42, number of BUSCOs: 1658). Predicted genes and sequence information are in supplemental files (Files S9 and S10). We annotated repetitive elements against the publicly available genomes consisting of six crickets and one locust. The sources of the genomes used in the analysis were: _Apteronembius asahinai_, GCA_019974035.1; _Gryllus bimaculatus_, GCA_017312745.1; _Laupala kohalensis_, GCA_002313205.1; _Telecogryllus ocanicus_, www.chirpbase.org, _Telecogryllus occipitalis_, GCA_01170035.1; _Locusta migratoria_, GCA_000516895.1. Libraries of repetitive elements were compiled by RepeatModeler-2.0.3 [93] for each species. Resulting libraries were classified using reference-based similarity search in RepBase (20170127 edition). RepeatMasker-4.1.2-p1 [94] was used with alignment option 'a' to annotate the repetitive elements in the genome assemblies.