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Analysis of Chenopodium-virus interactions using Chenopodium quinoa reference genome

Nourolah Soltani: University of Tennessee, Department of Entomology and Plant Pathology

<div>Local lesion hosts prevent systemic spread of viruses, but little is known about the molecular basis of the response. Publicly available RNA-Seq transcriptomic data, previously used for analyses of <em>Chenopodium amaranticolor</em> in response to <em>Cucumber mosaic virus</em> and <em>Tobacco mosaic virus</em>, were re-examined against a recent annotated reference genome of <em>C. quinoa</em>. Star was used to map reads, and HTSeq and DESeq were used to count, normalize and analyze differentially expressed genes (DEGs). Sequences of DEGs with adjusted <em>P</em> values < 0.1 were submitted to Blast2GO to annotate functional classification and assign KEGG and GO terms. Use of a reference genome from a related species was effective for read mapping, with 94% of reads mapping to the <em>C. quinoa</em> genome; 32% mapped to multiple loci and were not considered further. With this new analysis, 789 DEGs were obtained, which contrasts to 47,346 DEGs in the original paper. Discrepancy may be due to increased resolution provided by mapping to full gene models of <em>C. quinoa</em> genome instead of a <em>de novo</em> assembly, or use of stringent statistics that penalize absence of biological replicates. Our re-analysis with the new pipeline revealed DEGs with similar GO terms as the original article, but some regulatory pathways differed. Application of a reference genome from related species of <em>Chenopodium</em> facilitated re-analysis of transcriptome-based viral response and allowed identification of molecular pathways in virus-host interaction.</div>