Single nucleotide resolution maps of Illumina mRNA-seq reads representing viral transcripts from susceptible (S) and Ty-1 resistant (R) tomato plants infected with TYLCV-IL, its recombinant derivative TYLCV-IS76 or their combination (IL+IS76) at 10 and 30 days post inoculation (dpi).

For each condition, Illumina 100 nt paired-end reads of the two biological replicates (1 and 2) were mapped onto the reference sequences of IL and IS76 using BWA and the resulting BAM files were analysed by MISIS-2 (Seguin et al. 2016 [60]) to generate tables of reads mapped to each reference sequence with zero mismatches. The reference sequences were extended at the 3-end by 99 nts from the 5’-terminal sequence to allow for mapping RNAs derived from the circular viral genome including the first and last nucleotide of the linear reference. In each table, the first column gives nucleotide positions of the corresponding viral genome sequence. In the next columns, the positions of 5′-terminal nucleotide of sense RNAs and 3′-terminal nucleotide of antisense RNAs along the reference sequence are indicated, and the read counts are given for each RNA mapped with zero mismatches to the forward (rightward) strand (columns fwd1 and fwd2) and the reverse (leftward) strand (columns rev1 and rev2), along with the total counts of reads mapped at the respective positions of the forward (rightward) and reverse (leftward) strands in the two replicates divided by 2 (i.e., average counts). In each table file on the right side, histograms of the average counts of rightward and leftward reads are inserted with the rightward reads colored in blue and the leftward reads colored in red. In the case of mixed infections (IL+IS76), the number of reads derived from each virus was counted at each SNP using MISIS-2 (Seguin et al. 2006 [60]) and a percentage of reads derived from each virus (or its selected region) was calculated. The average percentage at all SNPs of the viral genome (or its selected region) was applied on all parts of the genome (or its selected region) that contain no SNPs to estimate the number of reads derived from the entire genome of each virus (or its selected region) or each strand of the viral genome (or its selected region).
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