NGS of EACMV-UG isolated from Nile Tulip tree in western Kenya
Virus DNA was amplified using rolling circle amplification. RCA products were fragmented to approximately 500 bp using an ultrasonicator (COVARIS, USA). The fragmented DNA was then end-repaired and adaptor-ligated per the NEBNext ultra II DNA library prep kit for Illumina (New England Biolabs, USA). Library concentration was measured using the NEBnext Library Quant kit (New England Biolabs, USA) and quality was validated using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA). The samples were pooled in equimolar concentrations and diluted to 4 nM based on library concentration and calculated library fragment size. The library pool was sequenced using a MiSeq sequencer (Illumina, USA) using the MiSeq Reagent Kit V3 (600 cycles) (Illumina, USA). The final pooled library was at 10 pM with 10% PhiX as control. Data produced were 2X300 bp paired end reads.