Insertion of Badnaviral DNA in the Late Blight Resistance Gene (R1a) of Brinjal Eggplant (Solanum melongena)

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.

Contribution of historical herbarium small RNAs to the reconstruction of a cassava mosaic geminivirus evolutionary history

“…Although symptoms promoted by integrated viral sequences are theoretically possible, they wouldn't be expected for endogenous virus sequences, whose partial integration is unlikely to promote any infection 46 , even for the longest integrated EGSs described so far 45 . In addition, geminiviral endogenous elements have not so far been reported to give rise to episomal viruses 25 , 48 . Finally, our reconstructed ACMV genomes showed a very high pairwise genetic identity (>99%) with their modern counterparts, a value that we would predict to be smaller in case of non-functional geminivirus sequences integrated in plant genomes for long periods 49 .…”

Viroscope: Plant viral diagnosis from high-throughput sequencing data using biologically-informed genome assembly coverage

“…Read assignment can be prone to generate false positives in circumstances where the host has sequences derived from viral origin, such as endogenous viral elements (Massart et al, 2019). For instance, badnaviruses can integrate their reversetranscriptase domains/regions into the host plant genome, however their presence is not necessarily associated with infection (Bhat et al, 2016;Serfraz et al, 2021). It also should be mentioned that the majority of endogenous viral elements are replication-defective mainly because of sequence decay or host regulation mechanisms have co-evolved to suppress their expression.…”

“…It also should be mentioned that the majority of endogenous viral elements are replication-defective mainly because of sequence decay or host regulation mechanisms have co-evolved to suppress their expression. Only five infective elements, all originated from Caulimoviridae family viruses (which include Badnavirus genus), have been reported in plants (Serfraz et al, 2021). However, if a badnavirus replicase is detected in the dataset, it is highly likely to be functional, and thus represent a risk to provoke a potential systemic viral infection in certain 10.3389/fmicb.2022.967021…”

Identification of Cacao Mild Mosaic Virus (CaMMV) and Cacao Yellow Vein-Banding Virus (CYVBV) in Cocoa (Theobroma cacao) Germplasm

“…This finding raises the possibility that RIM 52 contains two CaMMV genomes, one of which was not detected in the previous genome discovery study. Endogenous viral elements (EVEs) have been widely reported in plant species [29][30][31][32], including cocoa [2]. It should be noted that neither the standard PCR methods used for CaMMV detection [24], nor the short-read sequencing employed in genome studies [3,6], can differentiate between free virus and EVEs; however, the significantly higher amplification from symptomatic than asymptomatic samples argues against the presence of such integrated elements.…”