The Expanding Menagerie of Prunus-Infecting Luteoviruses

Abstract

Members of the genus Luteovirus are responsible for economically destructive plant diseases worldwide. Over the past few years, three luteoviruses infecting Prunus trees have been characterized. However, the biological properties, prevalence, and genetic diversity of those viruses have not yet been studied. High throughput sequencing of samples of various wild, cultivated, and ornamental Prunus species enabled the identification of four novel species in the genus Luteovirus for which we obtained complete or nearly complete genomes. Besides, we identified another new putative species recovered from Sequence Read Archive data. Furthermore, we conducted a survey on peach-infecting luteoviruses in eight European countries. Analyses of 350 leaf samples collected from germplasm, production orchards, and private gardens showed that peach-associated luteovirus (PaLV), nectarine stem pitting-associated virus (NSPaV), and a novel luteovirus, peach-associated luteovirus 2 (PaLV2), are present in all countries, while the most prevalent virus was NSPaV, followed by PaLV. An analysis of the genetic diversity of these viruses was also conducted. Moreover, the biological indexing on GF305 peach indicator plants demonstrated that PaLV and PaLV2, like NSPaV, are transmitted by graft at relatively low rates. No clear viral symptoms have been observed either in graft-inoculated GF305 indicators, or in different peach tree varieties observed in an orchard. The data generated during this study provide a broader overview of the genetic diversity, geographical distribution and prevalence of peach-infecting luteoviruses, and suggest these viruses are likely asymptomatic in peach under most circumstances.

Genomic analyses of a widespread blueberry virus in the United States

“…The P3a-like protein was also not identified in BlVL, AlLV1, NSPaV, RCaV, or PmaLV. However, PmaLV does encode the P4 movement protein ( Khalili et al., 2023 ).

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“…Analyses included isolates of 19 genomes, with REFSEQ isolates used where available; the 13 luteoviruses accepted by ICTV and six putative unclassified members of the genus: almond luteovirus 1 (AlLV1), peach associated luteovirus (PaLV) and four Prunus -infecting species ( Khalili et al., 2023 ). NCBI ORFfinder and alignments to other luteoviruses was used to identify BlVL ORFs.…”

Diversity and pathobiology of an ilarvirus unexpectedly detected in diverse host plants and in global sequencing data

“…), usually through infected pollen (Bristow and Martin 1999). Ilarviruses pose persistent threats to fruit production such as for Prunus species (Pallas et al 2012;Khalili et al 2022) or blackberry (Rubus fruticosus) (Poudel et al 2014). In recent years, several ilarviruses were reported to cause problems in tomato production in the USA, such as tomato necrotic streak virus (TomNSV) (Badillo-Vargas et al 2016;Adkins et al 2015) and tomato necrotic spot virus (ToNSV) (Bratsch et al 2019(Bratsch et al , 2018.…”

“…Recently, mining of vast amounts of Arabidopsis thaliana publicly available sequence read archive (SRA) datasets uncovered a novel comovirus (family Secoviridae ), Arabidopsis latent virus 1, which was demonstrated to be mechanically and seed transmitted, but causes no symptoms in A. thaliana , (Verhoeven et al 2022). A recent study on Prunus -associated luteoviruses (family Luteoviridae ) also uncovered a new luteovirus through a search of SRA datasets (Khalili et al 2022). Many HTS-based discoveries of crop and non-crop viruses have also been reported (Gaafar et al 2020; Rivarez et al 2022; Ma et al 2019; Xu et al 2017), but only a small subset of these studies biologically characterized the identified viruses (Hou et al 2020; Rivarez et al 2021).…”

Complete genome sequences of three Prunus-infecting nepoviruses: apricot latent ringspot virus, myrobalan latent ringspot virus and a novel virus from smooth stone peach (Prunus mira Koehne)

“…The large contigs representing the two genomic RNAs of ALRSV and MLRSV missed only short terminal sequences. Both 5' and 3' genome ends were determined for each molecule by RACE experiments as described [7]. Full-length RNA1 were determined to be 7,690 nt (OR141117) and 7,678 nt (OR141115), excluding the polyA tail, for ALRSV and MLRSV respectively, while their RNA2 were respectively 5,686 nt (OR141118) and 5,736 nt (OR141116).…”