The genomic sequences of both the severe and mild isolate were determined using high-throughput sequencing (HTS). Total RNA was extracted using a Qiagen RNA plant mini kit (Germantown, MD), treated with RNase-free DNase (Ambion) and subjected to ribosomal RNA depletion before TruSeq RNA library preparation [27 ]. HTS was performed on a NextSeq 500 Illumina platform as single 75 bp reads.
Sequence reads were initially processed and assembled into contigs by CLC Workbench 11 (Qiagen USA). Genome assemblies were determined with Spades and Geneious 11 (Biomatters, New Zealand). Terminal sequences were obtained using 5’ RACE Kit (ThermoFisher) and an anchored oligo-dT primer for the 3’end. Primer design, genome assembly and open reading frame (ORF) prediction were conducted using Geneious Prime (Biomatters, New Zealand).
Sequence reads were initially processed and assembled into contigs by CLC Workbench 11 (Qiagen USA). Genome assemblies were determined with Spades and Geneious 11 (Biomatters, New Zealand). Terminal sequences were obtained using 5’ RACE Kit (ThermoFisher) and an anchored oligo-dT primer for the 3’end. Primer design, genome assembly and open reading frame (ORF) prediction were conducted using Geneious Prime (Biomatters, New Zealand).