Figure 7
The virus accumulation and copy number for each identified virus or viroid in each peach transcriptome. (a) The number of sequenced reads associated with the identified viruses and viroids in each peach transcriptome. We blasted all read sequences in each cultivar with E-value 1e−5 as a cutoff against the reference genome sequences of identified viruses and viroids and calculated the number of matched reads. (b) The portion of virus-associated reads in each transcriptome was calculated as the number of viral reads divided by all sequenced reads. (c) The portion of identified viruses and viroids based on the number of virus-associated reads in all six peach transcriptomes. In the case of APV1 and APV2 as well as PeVD and PcVT, their sequenced reads were combined due to their high sequence similarity. (d) The portion of the identified viruses and viroids based on their copy numbers. The copy number was calculated as the number of identified sequence reads multiplied by 101 bp, then divided by the size of the identified virus genomes. (e) The portion of the identified viruses and viroids in each transcriptome based on the viral reads. (f) The portion of identified viruses and viroids in each transcriptome based on their copy number. The portion of identified viruses and viroids in the BC cultivar was based on (g) the calculated expected read count and (h) FPKM values. The portion of identified viruses and viroids in the JH cultivar based on (i) the calculated expected read count and (j) FPKM values. The expected read count and FPKM values were calculated using the Trinity program, as described in the methods section.
