Bioinformatics analysis, libraries statistics and RPKM calculations

Low sequencing quality and adapter sequences were removed from the libraries using trimmomatic-0.32 and ribosomal contaminants were removed with SortMeRNA version 2.0⁴³. Sequencing reads were mapped to one or several of the following reference genome assemblies: (1) viral genome of SfAV (described above), (2) viral genome of TnAV (described above), (3) Spodoptera frugiperda genome, SF_CORN_1 assembly (NCBI accession GCA_900240015.1), (4) Trichoplusia ni genome (NCBI accession ASM360422v1⁴⁴ and bowtie2⁴⁵ and the splice-aware program hisat2⁴⁶ was used for all other genomes. Library statistics, read counts and RPKMs calculation were determined using the bedtools⁴⁷ intersectBed program in conjunction with custom written Perl scripts (available upon request). RPKM values were calculated for each replicate individually using the standard RPKM calculation formula⁴⁸. RPKM values from the three replicates were then averaged to obtain a single estimate of transcript expression. The TnAV-6a (previously TnAV-2c)²³ was used as a reference genome to refer to the ORFs order in our TnAV-6a1 variant. GraphPad Prism version 8.4.3 (GraphPad Software, San Diego, California, USA, www.graphpad.com) was used for Figs. 3, ​,4,4, ​,55 and Supplementary Fig. ^S1 generation and unpaired t-test was used to compare the statistical difference of the innate immunity genes expression level between the different tissues.