Susanne von Bargen

High-throughput sequencing (HTS) was applied to investigate the virome of European beech (Fagus sylvatica) from asymptomatic leaves and symptomatic leaves exhibiting chlorosis, line patterns and malformation. Total RNA extracted from six samples, including herbarium material collected in 1967 and 1968 and contemporary samples from France, Germany, and The Netherlands, was subjected to Illumina sequencing followed by de novo assembly, sequence similarity searches and phylogenetic analyses. In each sample, contigs belonging to a previously undescribed virus within the genus Carlavirus were obtained. The virus was tentatively named beech carlavirus. No additional virus contigs were detected in the samples. The detection of the virus over more than five decades and in three European countries indicates its long-term and a probable wider occurrence and circulation. Moreover, its prolonged unnoticed presence suggests that it does not induce noticeable and acute disease outbreaks. These findings underscore the value of integrating historical and recent field samples through collaborative data sharing to improve insight into virus diversity and ecology in forest trees.

High-throughput sequencing (HTS) was applied to investigate the virome of European beech (Fagus sylvatica) from asymptomatic leaves and leaves exhibiting chlorosis, line patterns and malformation. Total RNA extracted from six samples, including herbarium material collected in 1967 and 1968 and contemporary samples from France, Germany, and the Netherlands, was subjected to Illumina sequencing followed by de novo assembly, sequence similarity searches and phylogenetic analyses. In each sample, contigs belonging to a previously undescribed virus within the genus Carlavirus were obtained. The virus was tentatively named beech carlavirus. The detection of the virus over more than five decades and in three European countries indicates its long-term and a probable wider occurrence and circulation. Moreover, its prolonged unnoticed presence suggests that it does not induce noticeable and acute disease outbreaks. These findings underscore the value of integrating historical and recent field samples through collaborative data sharing to improve insight into virus diversity and ecology in forest trees.

The defence-associated NDR1/HIN1-like (NHL) gene plays an important role in triggering plant defences in response to biotic stresses. The NHL gene is involved in gene-for-gene-mediated resistance mechanisms in response to attack by bacterial, fungal, and viral pathogens. Our study investigated the variation in 72 virus defence gene candidates annotated in the F. excelsior genome. Among all single nucleotide polymorphisms (SNPs) and indels detected in these candidates, one polymorphic site in the NDR1/HIN1-like protein-encoding gene was able to distinguish between common ash samples with different infection and symptomatic statuses. The SNP was a nonsynonymous substitution that would result in an amino acid change. The variation detected here may have an impact on pattern recognition and therefore affect the immune response, indicating tolerance/susceptibility to viruses of common ash. The identified marker may help in successfully identifying individuals with a low level of susceptibility to viral diseases.

In April 2024, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was expanded by 1 new order, 1 new family, 6 new subfamilies, 34 new genera and 270 new species. One class, two orders and six species were renamed. Seven families and 12 genera were moved; ten species were renamed and moved; and nine species were abolished. This article presents the updated taxonomy of Negarnaviricota as currently accepted by the ICTV, providing an essential annual update on the classification of members of this phylum that deepen understandings of their evolution, and supports critical public health measures for virus identification and tracking.

Ash shoestring-associated virus (ASaV; Emaravirus fraxini) is a five-segmented, negative-sense RNA virus associated with chlorosis and leaf deformation in Fraxinus species. This study investigated the genetic diversity and evolutionary dynamics of ASaV by analyzing nearly full-length RNA2–RNA5 and partial RNA1 sequences from isolates collected from different geographic regions and Fraxinus hosts. The sequence data uncovered that ASaV has a conserved genome, in which RNA3 and RNA5 showed more genetic divergence than other segments in the sequenced isolates. ASaV RNA3 and partial RNA1 were the most informative genomic regions for phylogenetic studies. There was a correlation between the clustering of the ASaV isolates and host species when the phylogenetic tree was constructed based on the RNA1 region. The ASaV genome is predominantly under purifying selection. Newly designed primers in this study facilitated robust amplification of genomic regions.

Across various European countries, Fraxinus excelsior L. is facing a decline caused by Hymenoscyphus fraxineus. The underlying mechanisms of the disease are still insufficiently understood in detail. Observations suggest that, in addition to the main pathogen, viral infections may also contribute to the decline of ash trees. We described homologues in the F. excelsior genome of formerly annotated virus resistance genes in model species and tested the applicability of primers on these gene fragments. Further, a prediction of cis-acting regulatory elements and transcription factor binding sites was accomplished, to determine the exact location of the promoters of these genes in the ash genome. After annotation and filtering the low-complexity regions, primers for use with genomic DNA were designed on sequences that showed a high degree of similarity and equality in length to translated regions and promoters of these regions. From the newly designed primers, those with the most favourable primer selection parameters were selected and tested on eight virus infected—four symptomatic and four asymptomatic—samples. The amplified products were analysed by agarose gel electrophoresis. From all producing one-band amplicons, 36 primer pairs amplifying translated, and 36 primers amplifying promoter regions were selected. Our study is the first step of a SNP discovery and marker development test. The further marker development on these sequences could be useful for the selection of ash individuals with various resistance to viral infections, providing a route for a more thorough understanding of the ash dieback–virus resistance interaction.

Plant diseases are mostly multicausal with several factors influencing the health status of affected hosts. Common ash (Fraxinus excelsior), a significant tree species of European forests, is currently mostly endangered by ash dieback, caused by the invasive fungus Hymenoscyphus fraxineus. However, contributing factors, including pathogenic viruses, are poorly understood. Here, we report the results of a virus screening conducted on selected special stands of F. excelsior. Over three consecutive years, ash trees from different origins were tested, including leaf material from mature seed trees, young trees and ash seedlings from the natural regeneration. Using RT-PCR, we screened for five viruses, including the generalist species ArMV (Nepovirus arabis) and CLRV (Nepovirus avii), as well as newly discovered viruses in ash, including the emaravirus ASaV (Emaravirus fraxini), the idaeovirus PrLBaV (Idaeovirus ligustri), and cytorhabdoviruses. The results revealed a high virus diversity in common ash. An association of ASaV detection with specific leaf symptoms, including shoestring, chlorotic ringspots, and vein yellowing, was documented. An analyses of relevant gene products of cytorhabdoviruses obtained from ashes of different sites revealed sequence diversities and two distinct phylogenetic groups present in ash populations. Signatures of novel viruses from different families have been identified by high-throughput sequencing. Together, our results provide insights into the virus diversity and distribution of viruses in ash and expand our knowledge about the virome of this endangered tree species.

In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.