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Identification of virus-encoded microRNAs in divergent Papillomaviruses

Fig 7

FcPV1 miRNAs are detected in vivo during viral infection.

(A) DNA-seq coverage for FcPV1 genome in miDGE library is plotted on log10 scale on the y-axis. The x-axis corresponds to position in the genomic sequence. A schematic of the FcPV1 gene organization taken from NCBI reference sequence NC_004068 is provided at the top. (B) Small RNA-seq coverage for FcPV1 genome in miDGE library is plotted on log10 scale on the y-axis. Values above the x-axis correspond to the forward strand and those below correspond to the reverse strand. The x-axis corresponds to position in the genomic sequence. Peaks corresponding to the newly identified miRNA genes are labeled. (C) Plot of read coverage and start sites for reads mapping to the FcPV1 genome in library prepared with RNA from infected chaffinch leg lesion samples. On the y-axis, coverage is plotted with gray lines and read start counts are plotted with black impulses. Values above the x-axis represent the forward strand and those below represent reads mapping to the negative strand. Genomic position is indicated on the X-axis. Peaks corresponding to the newly identified miRNA genes (fcpv1-miRs-F1 & F2) are labeled as well as the lower expressed candidate miRNA “fcpv1-miR-F3”. The inset photograph is of one of the chaffinches with characteristic leg lesions used in preparation of the small RNA-seq libraries. (D) Plot of read coverage and start sites for reads mapping to the FcPV1 genome in library prepared with RNA from chaffinch pectoral muscle samples. On the y-axis, coverage is plotted with gray lines and read start counts are plotted with black impulses. Values above the x-axis represent the forward strand and those below represent reads mapping to the negative strand. Genomic position is indicated on the X-axis. Peaks corresponding to the newly identified miRNA genes are labeled.

Fig 7

doi: https://doi.org/10.1371/journal.ppat.1007156.g007