NextSeq of viral DNA and cDNA: Blue Springs macrophytes
Virus particles were purified from macrophyte tissues through homogenization (bead-beating) followed by filtration (0.22 um) and nuclease treatment. Viral DNA and RNA were extracted with the MinElute Virus Spin kit (Qiagen).  Extracted nucleic acids were reverse-transcribed using the SuperScript IV First Strand Synthesis System (Invitrogen) with random hexamers. Second-strand synthesis was performed on the resulting cDNA/DNA 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 NextSeq platform. Raw sequence files were trimmed with Trimmomatic version 0.36.0.