A comparative template-switching cDNA approach for the HTS-based multiplex detection of three viruses and one viroid commonly found in apple trees

Following a template-switching cDNA amplification protocol, seven cDNA synthesis treatments (reverse primers, oligo d(T)23-VN, random hexamers, and their combinations) were used to test simultaneously the relative abundance and coverage of the three most commonly latent RNA viruses (ACLSV, ASGV, ASPV) and one viroid (AHVd) found in apples. Amplified dscDNAs were subjected to library preparation using Nanopore SQK-DCS109 and Illumina Nextera XT, and sequenced with MinION and NextSeq2000, respectively.