Biology subjects

Rotunno, S.

Publications and source records attributed to Rotunno, S..

5 recordsLinked to original sources

bioRxiv2026

Experimental characterization of zeta viruses and discovery of betaviroid-like RNAs expand the diversity of coding circular RNA replicons

Viroid-like RNAs (vdlRNAs) are infectious agents characterized by single-stranded circular genomes folding into compact secondary structures, often containing self-cleaving ribozymes involved in replication. Recent metatranscriptomic studies have expanded their diversity across multiple ecological niches and revealed novel vdlRNAs groups with protein-coding capacity, including zeta viruses, characterized by the potential to encode an endless tandem-repeat protein in each polarity strand. However, besides their in silico identification, no experimental evidence supported their existence and molecular features. Here, three new zeta viruses were identified and one of them was molecularly characterized from soil. In addition, a novel type of coding vdlRNAs, named betaviroid-like RNAs was discovered. Similar to zeta viruses, betaviroid-like RNAs are circular RNAs containing, in each polarity strand, one ribozyme and one open reading frame (ORF) encompassing the full-length genome. Unlike zeta viruses, betaviroid-like ORFs are not endless but longer than the unit-length genome. Existence of both circular RNA polarity strands, absence of DNA forms, and self-cleavage activity of ribozymes were experimentally confirmed for both zeta viruses and betaviroid-like RNAs, providing data consistent with symmetric rolling-circle replication. Additional zeta viruses and betaviroid-like RNAs were identified in publicly available metatranscriptomic datasets from wetlands of different geographic areas, supporting their broad distribution. Sixteen zeta viruses contain diverse self-cleaving ribozymes, including delta, type II and III hammerhead, twister, and hairpin ribozymes, expanding the known ribozyme diversity of this group. Altogether, our results provide the first experimental characterization of zeta viruses and betaviroid-like RNAs expanding the diversity of circular RNA replicons.

microbiology↗

bioRxiv2026

Vector-enabled metagenomics reveals the first detection of the geminivirus beet curly top Iran virus in Europe

2.Geminiviruses are among the most threatening emerging insect-borne viruses and are responsible for serious outbreaks. Climate change could further exacerbate their impact on crops, highlighting the need for new diagnostic approaches to manage potentially dangerous situations. Vector-Enabled Metagenomics (VEM) exploits the natural ability of highly mobile insects to accumulate viruses acquired from plants over time and space within an ecosystem; this approach is effectual in monitoring the presence of new invasive and indigenous viruses in large areas. Geminiviruses have circular single-stranded DNA genomes that can be readily targeted by Rolling Circle Amplification (RCA). The combination of RCA and VEM largely increases the chances of detecting geminiviruses. This approach enabled us to identify the becurtovirus beet curly top Iran virus (BCTIV, Becurtovirus betae) in insects collected in Europe. BCTIV is a major pathogen of sugar beet but can also infect plants of other families; it is transmitted by cicadellids and has been so far detected only in Iran and Anatolia (Turkey). We also show that two cucurbit species, watermelon (Citrullus lanatus) and zucchini (Cucurbita pepo) are both natural and experimental hosts for BCTIV. 3. Impact statementVirus infections account for almost 50% of emerging plant diseases globally and may produce high crop losses, resulting in huge economic and social impact worldwide. Geminiviruses, threatening both monocot and dicot plants, represent high risk for both staple food and industrial crops. A peculiar diagnostic approach combining a specific geminivirus enrichment reaction, the monitoring of the virome of highly mobile insects within agricultural areas and the sensitivity of high throughput sequencing (HTS) was effective in producing a first alert for a new polyphagous virus. The reduced cost of HTS methods further raises interest in this approach, making it suitable as a first step for monitoring large areas. 4. Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

molecular biology↗

bioRxiv2025

Oxford Nanopore Sequencing as a useful tool for investigating the population dynamics of invasive begomoviruses in Sicily

Tomato yellow leaf curl disease (TYLCD) is a major viral disease severely affecting tomato crops in the Mediterranean region, leading to reduced crop yield and significant economic losses. The disease is caused by monopartite begomoviruses belonging to the Geminiviridae family, primarily tomato yellow leaf curl Sardinia virus (TYLCSV) and tomato yellow leaf curl virus (TYLCV), which often co-infect tomato plants, promoting the emergence of recombinant viral genomes. To investigate the diversity and evolutionary dynamics of these viruses, symptomatic plants collected from agricultural sites in Sicily between 2020 and 2022, along with archived plant samples from 1994 to 1999, were analyzed. For each collection site, leaves from symptomatic plants were pooled to form representative samples. Total nucleic acids were extracted and subjected to rolling circle amplification to enrich circular viral genomes. The amplified products were sequenced using Oxford Nanopore Technologies (ONT) long-read sequencing to obtain full-length viral genomes. Bioinformatic analyses revealed that archived samples exclusively contained TYLCSV-related sequences, confirming its historical predominance in Sicilian agroecosystems. Recent samples, by contrast, no longer contained TYLCV or TYLCSV parental genomes but were dominated by TYLCV-derived recombinants such as TYLCV-IS141- and TYLCV-IS76-like variants, indicating a temporal shift in the structure of the viral population. Furthermore, a distinct group of newly emerged recombinants, provisionally referred to as TYLCV-IMS54, was identified in the most recent samples. Their genome comprises a TYLCV backbone, a 54-nucleotide segment from TYLCSV located downstream of the stem-loop region, and an 341-nucleotide region derived from TYLCV-Mild. These results demonstrate the importance of continuous viral population monitoring through ONT-based sequencing to detect emerging variants that may influence disease management strategies in tomato crops and highlight the central role of recombination in shaping begomovirus populations. IMPACT STATEMENTTomato yellow leaf curl disease (TYLCD) is one of the most damaging viral diseases affecting tomato crops in the Mediterranean basin, yet the long-term dynamics of its causal agents and the role of recombination remain challenging due to the genome plasticity of these viruses. This study provides an updated and comprehensive picture of the begomovirus population structure in Sicily, a key agricultural region for tomato production, by analyzing both contemporary and historical plant samples. Through the application of ONT long-read sequencing combined with RCA and bioinformatic analyses, this research identified persistent recombinant genotypes including a distinct group of newly emerged recombinants, named TYLCV-IMS54. These findings expand current knowledge on the genetic variability and evolutionary processes shaping begomovirus populations in Sicilian agroecosystems. The detection of recombinant genomes highlights the enduring role of recombination in begomovirus diversification. By integrating sequencing data with population and phylogenetic analysis, this work offers valuable insights into the epidemiology and management of TYLCD in regions heavily impacted or newly colonized by these viral pathogens. The study also underscores the importance of continuous molecular surveillance using ONT-based platforms to enable early detection of emerging recombinant variants, with significant implications for plant virology, crop protection and agricultural biosecurity strategies. DATA SUMMARYRaw reads are deposited in the Sequence Read Archive (SRA) of NCBI (https://www.ncbi.nlm.nih.gov/sra) with BioProjects ID PRJNA1226414 and PRJNA1273745; the recombinant TYLCV-IMS54 sequence is available in GenBank with Accession Number PQ873011. Parental TYLCV-strains used in this study could be retrieved in GenBank with the following Acc. Nos: DQ144621 for TYLCV, NC_003828 for TYLCSV, KJ913682 for TYLCV-Mild. Recombinant strains could be retrieved in GenBank with the following Acc. Nos.: LN846609 for TYLCV-IS76 and AF271234 for TYLCMaV. The authors confirm that all supporting data, code and protocols have been provided within the article or through supplementary data files.

plant biology↗

bioRxiv2025

The Freesia refracta virome analysis sheds new light on the phylogenetic relationships in the Konkoviridae and Yueviridae families

The necrosis syndrome of freesia, first described in 1970 in Northern Europe, is still jeopardizing freesia cultivation all over the world. Although several viruses have been listed as possible causal agents, the etiology of the disease is still not clear and is possibly linked to a combination of different factors. In this study, a high-throughput sequencing virome analysis was performed on total RNA extracts derived from symptomatic freesia leaves; a novel virus putatively belonging to the recently ratified Konkoviridae family in the Bunyaviricetes class has been identified and characterized, for which we propose the name of freesia konkovirus 1 (FreKV-1). This family, officially listing only one genus and two species, has been expanded by exploring publicly available metatranscriptomic datasets through the Serratus Project Database and reconstructing new viral entities; the phylogenetic position of the Konkoviridae family has been investigated and new genera belonging to the family have been proposed. Moreover, a further previously unknown virus, putatively belonging to the Yueviridae family was partially characterized and its phylogenetic position was discussed. Overall, the analysis increased our knowledge of the number of viral agents infecting freesia and possibly involved in freesia necrosis syndrome.

plant biology↗

bioRxiv2018

Impact of high phosphorous and sodium on productivity and stress tolerance of Arundo donax plants

Arundo donax L. is an invasive species recently employed for biomass production that emits large amounts of isoprene, a volatile compound having important defensive role. Here, the potential of A. donax to grow in degraded soils, characterized by poor fertility, eutrophication and/or salinization, has been evaluated at morphological, biochemical and transcriptional level. Our results highlight sensitivity of A. donax to P deficiency. Moreover, we show that A. donax response to salt stress (high sodium, Na+), which impaired plant performance causing detrimental effects on leaf cells ultrastructure, is characterized by enhanced biosynthesis of antioxidant carotenoids and sucrose. Differently from Na+, high phosphorous (P) supply did not hamper photosynthesis although it affected carbon metabolism through reduction of starch content and by lowering isoprene emission. In particular, we revealed on salt-stress leaves that high P enhanced the expression of genes involved in abiotic stress tolerance, but further increased diffusive limitations to photosynthesis and slowed-down sugar turnover without modifying isoprene emission. Therefore, despite limiting productivity, high P improved A. donax tolerance to salinity by favouring the accumulation of carbohydrates that protect cells and increase osmotic potential, and by stimulating the synthesis of antioxidants that improves photo-protection and avoids excessive accumulation of reactive oxygen species.\n\nHighlightsArundo donax is sensitive to elevated salinity. High phosphorous supply to salt-stressed A. donax enhances transcriptomic changesthat induce the onset of physiological mechanisms of stress tolerance but limits productivity.

physiology↗