Response of bitter and sweet Chenopodium quinoa varieties to cucumber mosaic virus: Transcriptome and small RNASeq perspective

Figures

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  Fig 1. Virus-induced Symptoms on Varieties of Chenopodium quinoa inoculated leaves and accumulation of viral RNA sequences from deep sequencing data. (A) Cucumber mosaic virus (CMV)-induced symptoms on C. quinoa varieties at 11 days post inoculation (dpi): ‘Jessie’ (low saponin level = sweet variety); ‘QQ74’ (moderate saponin level = sweet variety); ‘Red Head’ (high saponin level = bitter variety). (B) Number of viral reads across quinoa varieties over time. J, Q, and R are initials of the varieties, and the 1,4 are days post infection.

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  Fig 2. Relative expression (log2 fold change) of triterpene saponin biosynthesis activating regulator-like1 (TSARL1) gene at 1 and 4 days after inoculation with cucumber mosaic virus. The red and blue colors indicates up and down regulation patterns, respectively. Abbreviations are combinations of cultivars (J,Q, or R) and days-post-inoculation (1 or 4). Varieiteis tested were: Jessie (J), QQ74 (Q), and Red Head (R).

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  Fig 3. Nucleotide size distribution of endogenous siRNA. This graph depicts data from quinoa varieties (J, Q, R) with two treatments (C,T) at two time periods (days after inoculation [1,4]). J, Q, and R are initials of the varieties, and C and T are mock- and virus-inoculated, respectively.

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  Fig 4. Cucumber mosaic virus (CMV)-derived small interfering RNA (vsiRNA). (A) Nucleotide size distribution of vsiRNA. (B) Enrichment of 5’ terminal base across the varieties and days post inoculation. The graph depicts data from quinoa varieties (J,Q,R), and time (days after inoculation).

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  Fig 5. Distribution of virus-derived siRNA (vsiRNA) across cucumber mosaic virus (CMV) RNAs. The consensus vsiRNA distribution across three CMV RNA1, RNA2, and RNA3. The inner rectangles show reads mapped to respective viral RNA. Outer rectangles relate genome coordinates of consensus reads mapped to CMV RNAs.

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  Fig 6. Validation of expression pattern of genes selected from RNASeq (blue) using RT-qPCR (green). CqEF1α was used for gene normalization purpose. Gene function is shown on top of the plot.

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  Fig 7. Validation of detected known and predicted novel miRNAs by PCR. From left to right the samples are as follows: (A) Known miRNAs 1) DNA marker, 2) miR166b, 3) miR166m, 4) miR393, 5) miR395, 6) miR156, 7) miR399. (B) Novel miRNAs (nmiR) 1) DNA marker, 2) nmiR2, 3) nmiR5, 4) nmiR6, 5) nmiR9, 6) DNA marker, 7) nmiR3, 8) nmiR4, 9) DNA marker, 10) nmiR1, 11) nmiR7, 12) DNA marker, 13) nmiR8. The DNA marker is O’range Ruler 50bp ThermoFisher with the range of 50 to 200 with 50bp increments.