HiSeq of viral cDNA: Manatee Springs macrophytes
Virus particles were purified from macrophyte tissues through homogenization (bead-beating) followed by filtration (0.22 um) and nuclease treatment. Viral RNA was extracted with the RNeasy kit (Qiagen).  RNA was reverse-transcribed using the SuperScript IV First Strand Synthesis System (Invitrogen) with random hexamers. cDNA second-strand synthesis was performed using the Klenow Fragment DNA polymerase (New England Biolabs). Double-stranded products were cleaned using the AMPure XP Purification system and sheared using a Covaris instrument.  NGS libraries were prepared using the Accel-NGS 1S Plus DNA Library Kit for Illumina Platforms (Swift Biosciences) and pair-end sequenced on a HiSeq platform. Raw sequence files were trimmed with Trimmomatic version 0.36.0. We noticed that libraries were contaminated with Turtlegrass virus X (TVX; accession number MH077559). Therefore, TVX sequences were removed from all analyses.