Abstract
Endogenous viral elements (EVEs) are widespread in plant genomes. They result from the random integration of viral sequences into host plant genomes by horizontal DNA transfer and have the potential to alter host gene expression. We performed a large-scale search for co-transcripts including caulimovirid and plant sequences in 1,678 plant and 230 algal species and characterized 50 co-transcripts in 45 distinct plant species belonging to lycophytes, ferns, gymnosperms and angiosperms. We found that insertion of badnavirus EVEs along with Ty-1 copia mobile elements occurred into a late blight resistance gene (R1) of brinjal eggplant (Solanum melongena) and wild relatives in genus Solanum and disrupted R1 orthologs. EVEs of two previously unreported badnaviruses were identified in the genome of S. melongena, whereas EVEs from an additional novel badnavirus were identified in the genome of S. aethiopicum, the cultivated scarlet eggplant. Insertion of these viruses in the ancestral lineages of the direct wild relatives of the eggplant would have occurred during the last 3 Myr, further supporting the distinctiveness of the group of the eggplant within the giant genus Solanum.
Highlights
Endogenous viral elements (EVEs) originate from viruses with RNA or DNA genomes
The contribution of EVEs to the biology of their hosts through structural and/or functional modifications of their genomes is well documented in mammals (Feschotte and Gilbert, 2012) but it is more limited in plants
We identified 50 such co-transcripts in 45 plant species belonging to 31 distinct families of vascular plants, providing evidence that fused open reading frame (ORF) including caulimovirid sequences are present in plant genomes
Summary
Endogenous viral elements (EVEs) originate from viruses with RNA or DNA genomes. They are widespread in eukaryotic genomes (Holmes, 2011; Feschotte and Gilbert, 2012) and may comprise large portions of these genomes: it is estimated that 5–8% of the human genome is composed of endogenous retroviruses (ERVs; Holmes, 2011). They showed that several of the MP-like coding genes experience positive selection at the codon level, suggesting these genes might be expressed and serve a function in plants (Mushegian and Elena, 2015). They provided evidence that functional EGV-expressed replication-associated protein (Rep) were expressed in yams for extended periods following endogenization and that some of them are possibly still functionally expressed in several species of the Enantiophyllum clade (Filloux et al, 2015)
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