## 5 Materials and Methods
The resulting alignment files were processed by the scripts with RepeatMasker pipeline and our in-house scripts ([[https://github.com/kataksk/repeatlandscape_parser.git](https://github.com/kataksk/repeatlandscape_parser.git)]([https://github.com/kataksk/repeatlandscape_parser.git](https://github.com/kataksk/repeatlandscape_parser.git))). To analyze correlation between the repetitive elements and intron lengths, R packages GenomicFeatures [100] was used to obtain gene structures of gene models. To extract virus sequences from the genome, blastn of potential viral scaffolds were compared to _Clirolo iridescent_ virus (GenBank: AF303741.1). Quality assessment of the extracted virus-like scaffolds was performed by CheckV (v1.0.1) [51]. CRISPR target gene for knock-out/in. We chose the 5\({}^{\prime}\) of the Ad vermilion gene as our CRISPR target site for knock-in experiments. We identified the Ad vermilion gene from the _A. domesticus_ genome assembly using a transcriptome mRNA sequence (not complete, missing 3\({}^{\prime}\)) by Blastation (TM Software, Inc., Arcadia, CA, USA). We were able to identify eight exons, including the first exon (Figure 5a). We then used the second exon (around 150 bp) to select three target CRISPR targeting sites for designing sgRNAs (Table S8) using GGP sgRNA designer ([[https://portals.broadinstitute.org/gpp/public/analysis-tools/sgra-design](https://portals.broadinstitute.org/gpp/public/analysis-tools/sgra-design)]([https://portals.broadinstitute.org/gpp/public/analysis-tools/sgra-design](https://portals.broadinstitute.org/gpp/public/analysis-tools/sgra-design))). The target sgRNA sequences were ordered from Synthego (Redwood City, CA, USA). To verify the knock-out sequence in _A. domesticus_, genomic DNA extraction was using a ZymoResearch Quick-DNA insect miniprep kit (Irvine, CA, USA), forward primer \"GAGCAGTAGGCGCAGAAGAG\" and reverse primer \"TCCAAACGCAGAAGAGAGAC\" to amplify gDNA. After PCR, we used primer \"TGTAGTGAGTGTTACGCCA\" to sequence the PCR product using the Oklahoma Medical Research Foundation sequencing service facility (OMRF DNA sequencing, [[https://omrf.org/](https://omrf.org/)]([https://omrf.org/](https://omrf.org/))). Using these data, we compared the gRNA sequence to wild type sequence to determine the indel(s) generated by our knock-out and knock-in experiments (Table 3). Knock-in DNA construct design. For knock-in construct design, we used the Ad muscle actin gene promoter to express the marker gene, enhanced green florescent protein (EGPF) via CRISPR/Cas9. We utilized the muscle actin gene from _T. castaneum_ and _D. melanogaster_ to conduct a BLAST search of the _A. domesticus_ transcriptome data and used the mRNA sequence from that search to identify the Ad muscle actin gene in the genome assembly. We searched for a promoter region 1.5 kb upstream from the start codon of the Ad muscle actin genomic sequence using the Neural Network Promoter Prediction tool ([[https://frutify.org/seq_tools/promoter.html](https://frutify.org/seq_tools/promoter.html)]([https://frutify.org/seq_tools/promoter.html](https://frutify.org/seq_tools/promoter.html))). To design the DNA construct, 455 bp of the Ad muscle actin promoter sequence with its 5'UTR were placed upstream of the EGFP coding sequence along with a sv40 polyadenylation signal 3' of EGFP as the marker gene. A section of 86 bp of gDNA included CRISPR knock-in site(s) placed on both sides of the marker gene as the final knock-in DNA construct, Ad-actin-EGFP-KI. This DNA sequence was synthesized by GeneScript (Piscataway, NJ, USA) in their pUC57 vector plasmid as the final product. Microinjection solution preparation. The concentrations of the components of knock-out or knock-in microinjection solutions were: 100 ng/\(\,\)uL of DNA construct Ad-actin-EGFP-KI (only for knock-in treatment), 10 pmol/\(\,\)uL of sgRNA, 1 ug/\(\,\)uL of TrueCut Cas9 protein V2 (ThermoFisher, Waltham, MA, USA), and 20% phenol red buffer (Sigma Aldrich, St. Louis, MO, USA).