goldfish metagenome
Frozen samples of liver and gill tissue were placed together in 600l of lysis buffer containing 0.5% foaming reagent (Reagent DX, Qiagen) and 1% of -mercaptoethanol (Sigma-Aldrich). Submerged tissue samples were homogenized with TissueRuptor (Qiagen) for one minute at 5000 rpm. To further homogenise tissue samples and remove tissue residues, the homogenate was centrifuged at full speed for three minutes. The homogenate was carefully removed and RNA from the clear supernatant was extracted using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) following the manufacturers protocol. Extracted RNA was quantified using NanoDrop (ThermoFisher) and RNA from each species was pooled corresponding to the site in which they were captured, resulting in 36 sample libraries (SI Table 2). RNA libraries were constructed using the Truseq Total RNA Library Preparation Protocol (Illumina). To enhance viral discovery and reduce the presence of non-viral reads, host ribosomal RNA (rRNA) was depleted using the Ribo-Zero-Gold Kit (Illumina)