In Silico Discovery of Mycoviral Sequences

RNA-Seq raw reads from nine avcr2 isolates and a negative control (healthy P. monticola stems without C. ribicola infection) from previous studies [29 (link), 31 ] were used for in silico discovery of mycoviral sequences (Table 1). These RNA-Seq raw reads are accessible in GenBank under SRA numbers SRR1574690-SRR15774692, SRR1583540, SRR1583545, SRR1583552, SRR15835557-SRR1583559, and SRR3273235-SRR3273237. After trimming of adaptor and low-quality sequences, deep mRNA sequencing reads were de novo assembled using CLC Genomics Workbench version 5.5 with graph parameters of automatic word size and automatic bubble size (CLC bio, QIAgen, Aarhus, Denmark). Putative viral sequences were identified from the C. ribicola transcriptomes by BLASTx analysis against a data set of the Viral RefSeq (viral.1.protein.faa.gz) downloaded from the National Center for Biotechnology Information (NCBI, Bethesda, Maryland, USA). Possible overlapping contigs from different fungal isolates were re-assembled into longer consensus sequences using the CAP3 program with default settings [32 (link)].