RA3a
Three datasets (T_k, T_o, and T_g) in paired-end format were first removed of sequence adapters and low quality reads using BBDuk of the BBTools packages (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user- guide/bbduk-guide/). QC reads were assembled into contigs using SPAdes V3.11.1 (1). All reads were then screened for potential contaminating sequences through MEGABLAST searches against the NCBI non-redundant database. Reads identified as bacterial and human sequences, as well low sequence coverage (e.g., <20) were removed. All contigs were then predicted for open reading frame and annotated using Funannotate (https://funannotate.readthedocs.io/en/latest/index.html).