Wipf-Scheibel, C. | Search bioRxiv

bioRxiv2026

Common molecular determinants underlie potyvirus host species jumps and resistance breakdown.

Given their rapid evolutionary dynamics, viruses offer a powerful system to investigate the mechanisms underlying host jumps. Here, we experimentally evolved endive necrotic mosaic virus (ENMV) in five plant hosts within the family Asteraceae: two putative ancestral hosts (Lactuca sativa and Tragopogon pratensis), and three alternative crop or weed species (Cichorium endivia, Zinnia elegans and Calendula arvensis). The resulting evolved viral populations, together with the ancestral strain, were then evaluated in a reciprocal cross-inoculation experiment across all five host species. ENMV exhibited clear adaptive responses in two hosts, Z. elegans and C. arvensis, with increased infection success and higher systemic viral accumulation compared to the ancestral virus. In contrast, no evidence of adaptation was detected in L. sativa, T. pratensis and C. endivia. Strikingly, strong cross-adaptation emerged between Z. elegans and C. arvensis: viral populations evolved in either host consistently outperformed those evolved in other hosts, as well as the ancestral strain, when infecting the reciprocal host. Sequencing of the VPg cistron in adapted populations revealed multiple nonsynonymous mutations, several of which arose independently across evolutionary lineages and in both Z. elegans and C. arvensis selection regimes. Functional assays using an infectious ENMV cDNA clone demonstrated that seven of these substitutions, individually or in combination, significantly increased the infection rate in both Z. elegans and C. arvensis. Notably, several of these substitutions also enhanced infectivity across four additional Asteraceae species among the eleven tested, without a clear relationship to host phylogenetic distance. Remarkably, all identified substitutions map to amino acid positions or adjacent residues in VPg previously implicated in the breakdown of recessive resistance genes against potyviruses in both crop and model plant systems. Together, these results suggest that adaptation to host resistance and host range expansion in potyviruses may rely, at least in part, on shared molecular pathways.

evolutionary biology↗

bioRxiv2017

High throughput amplicon sequencing to assess within- and between-host genetic diversity in plant viruses

Molecular epidemiology approaches at the landscape scale require to study the genetic diversity of viral populations from numerous hosts and to characterize mixed infections. In such a context, high-throughput amplicon sequencing (HTAS) techniques create interesting opportunities as they allow identifying distinct variants within a same host while simultaneously genotyping a high number of samples. Validating variants produced by HTAS may, however, remain difficult due to biases occurring at different steps of the data-generating process (e.g. environmental contaminations and sequencing error). Here, we focused on Endive necrotic mosaic virus (ENMV), a member of family Potyviridae, genus Potyvirus to develop an HTAS approach and to characterize the genetic diversity at the intra- and inter-host levels from 430 samples collected over an area of 1660 km2 located in south-eastern France. We demonstrated how it is possible, by incorporating various controls in the experimental design and by performing independent sample replicates, to estimate potential biases in HTAS results and to implement an automated and robust variant calling procedure.\n\nHighlightsO_LIHigh-throughput amplicon sequencing to assess plant virus genetic diversity\nC_LIO_LIEstimating bias in high throughput amplicon sequencing results\nC_LIO_LIAutomated variant calling procedure for robust high throughput amplicon sequencing\nC_LI

molecular biology↗