The virome of maize rough dwarf disease: Molecular genome diversification,phylogeny and selection

The main threat to maize production in the Mediterranean area is maize rough dwarf disease (MRDD) caused by Maize rough dwarf virus (MRDV). The analysis of virus diversification is necessary to assess the risk of MRDD outbreaks. We analysed the virome of MRDD by next-generation sequencing using pooled samples prepared from maize plants collected in Spain between 1999 and 2017. This yielded the sequences of all 10 genomic segments from six MRDV isolates plus an additional variant of S5 in one sample. Five of the genomes were 29,145 nucleotides (nt) in length, and the other was 3 nt longer. The six genomes were AT rich with low codon usage bias and the 13 open reading frames (ORFs) showed low potential expression levels. The highest expression levels were predicted for ORFs encoding the non-structural proteins P6, P5-1 and P9-1, and the structural protein P10. There was a strong correlation between higher level expression and T-ended codons, which were the most over-represented class. The concatenate and three individual segments (S3, S6 and S7) each formed a monophyletic group, whereas the remaining segments split into two groups with different clustering relationships relative to two other European MRDV isolates. The MRDV virome showed certain temporal and geographical diversification, but several proteins were highly conserved, especially P7-2. Three significant recombination hotspots were identified among genomic segments and four within segments. The ORFs encoding structural proteins appear under greater purifying selection.