Revisiting the amalgaviral landscapes in plant transcriptomes expands the host range of plant amalgaviruses

Abstract

Abstract Plant amalgaviruses are monopartite, double-stranded RNA genome containing viruses, capable of vertical transmission through seeds. An attempt to revisit the plant transcriptome assembled contigs for amalgaviral sequences identified 40 putative novel amalgaviruses in 35 plant species, nearly doubling the number of known plant amalgaviruses. Of the 35 plant species, 33 species are reported to host amalgaviruses for the first time, including a pteridophytic and two gymnospermic species. Coding-complete genomes of all the identified viruses were recovered and the putative + 1 programmed ribosomal frameshift (PRF) sites were determined. The genomes of 35 identified amalgaviruses contained the conserved + 1 PRF motif ‘UUU_CGN’, while variant versions were predicted in five of the genomes. Phylogenetic analysis grouped pteridophyte- and gymnosperm-infecting amalgaviruses together in a divergent clade while few of the related angiosperm-infecting amalgaviruses infect members of the same plant family, reiterating the co-evolution of plant amalgaviruses and their hosts. The current study paves way for further studies on understanding the biological properties and developing detection assays of identified viruses.