Michela Chiumenti

Italian National Research Council | CNR · Institute for Plant Sustainable Protection

The EFSA Panel on Plant Health conducted a pest categorisation of Capsicum chlorosis virus (CaCV) for the EU territory. The identity of CaCV, a member of the genus Orthotospovirus (family Tospoviridae), is established and reliable detection and identification methods are available. The pathogen is not included in the EU Commission Implementing Regu...

The European Commission requested the EFSA Panel on Plant Health to prepare and deliver risk assessments for commodities listed in Commission Implementing Regulation (EU) 2018/2019 as 'High risk plants, plant products and other objects'. This Scientific Opinion covers plant health risks posed by dormant grafted plants, rootstocks, budwood and scion...

The EFSA Panel on Plant Health conducted a pest categorisation of High Plains wheat mosaic virus (HPWMoV) for the EU territory. The identity of HPWMoV, a member of the genus Emaravirus (family Fimoviridae), is well established and reliable identification methods are available. The pathogen is not included in the EU Commission Implementing Regulatio...

Abstract The European Commission requested the EFSA Panel on Plant Health to prepare and deliver risk assessments for commodities listed in Commission Implementing Regulation (EU) 2018/2019 as ‘High risk plants, plant products and other objects’. This Scientific Opinion covers plant health risks posed by defoliated and in dormant phase, grafted bar...

Some plants of Jasminum officinale were selected in a nursery for investigation of sanitary status of candidate mother plants before vegetative propagation. The presence of yellow spots and leaf discoloration symptoms pushed for a generic diagnosis through deep sequencing to discover systemic pathogens. Either dsRNA or total RNA were extracted and...

Following a request from the EU Commission, the EFSA Panel on Plant Health conducted a pest categorisation of Apium virus Y (ApVY) for the EU territory. The identity of the ApVY, a member of the genus Potyvirus (family Potyviridae), is well established and reliable detection methods are available. The pathogen is not included in EU Commission Imple...

The widespread use of High-Throughput Sequencing (HTS) for detection of plant viruses and sequencing of plant virus genomes has led to the generation of large amounts of data and of bioinformatics challenges to process them. Many bioinformatics pipelines for virus detection are available, making the choice of a suitable one difficult. A robust benc...

Abstract Following a request from the EU Commission, the EFSA Panel on Plant Health conducted a pest categorisation of carrot thin leaf virus (CTLV) for the EU territory. The identity of CTLV, a member of the genus Potyvirus (family Potyviridae), is well established and reliable detection methods are available. The pathogen is not included in the E...

Citrus concave gum-associated virus (CCGaV) is a negative-stranded RNA virus, first reported a few years ago in citrus trees from Italy. It has been reported in apple trees in the USA and in Brazil, suggesting a wider host range and geographic distribution. Here, an anti-CCGaV polyclonal antiserum to specifically detect the virus has been developed...

The European Commission requested the EFSA Panel on Plant Health to prepare and deliver risk assessments for commodities listed in Commission Implementing Regulation (EU) 2018/2019 as 'High risk plants, plant products and other objects'). This Scientific Opinion covers plant health risks posed by 1- to 3-year-old dormant grafted plants and rootstoc...

Multi-locus sequence typing (MLST) is a widely used methodology for typing strains of Xylella fastidiosa (Xf) (Yuan et al., 2010; EPPO 7/24(4)). This approach is based on the sequence analyses of 7 housekeeping genes, on which the allelic profile and the sequence type (ST) is determined. Given the difficulties to isolate and culture Xf, the MLST an...

High-throughput sequencing (HTS) technologies have become indispensable tools assisting plant virus diagnostics and research thanks to their ability to detect any plant virus in a sample without prior knowledge. As HTS technologies are heavily relying on bioinformatics analysis of the huge amount of generated sequences, it is of utmost importance t...

Viroids are infectious non-coding RNAs that infect plants. During infection, viroid RNAs are targeted by Dicer-like proteins, generating viroid-derived small RNAs (vd-sRNAs) that can guide the sequence specific cleavage of cognate host mRNAs via an RNA silencing mechanism. To assess the involvement of these pathways in pathogenesis associated with...

Background Citrus industry is worldwide dramatically affected by outbreaks of Citrus tristeza virus (CTV). Controls should be applied to nurseries, which could act as diversity hotspots for CTV. Early detection and characterization of dangerous or emerging strains of this virus greatly help to prevent outbreaks of disease. This is particularly rele...

In 2014, high-throughput sequencing of libraries of total DNA from olive trees allowed the identification of two geminivirus-like contigs. After conventional resequencing of the two genomic DNAs, their analysis revealed they belonged to the same viral entity, for which the provisional name of Olea europaea geminivirus (OEGV) was proposed. Although...

With a small, circular and non-protein coding RNA genome, viroids are the smallest infectious agents. They invade plants, which in turn may develop symptoms. Since their discovery about fifty years ago, more than thirty viroids have been reported and classified using as species demarcation less than 90% sequence identity on the overall genome and e...

p>In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted...

Following a request from the European Commission, the EFSA Panel on Plant Health performed a pest categorisation of four phytoplasmas of tuber-forming Solanum spp. known to occur only outside the EU or having a limited presence in the EU. The only tuber-forming species of Solanum reported to be phytoplasma infected is S. tuberosum. This opinion cov...

Following a request from the European Commission, the EFSA Panel on Plant Health prepared a list of non-EU phytoplasmas of tuber-forming Solanum spp. A systematic literature review and search of databases identified 12 phytoplasmas infecting S. tuberosum. These phytoplasmas were assigned to three categories. The first group (a) consists of seven no...

Sixty years from the first disease description, a novel badnavirus associated with chestnut mosaic disease

Although the chestnut mosaic disease (ChMD) was described several decades ago, its etiology is still not elucidated. Here, using classical approaches in combination with high throughput sequencing (HTS) techniques, we identify a novel Badnavirus that is a strong etiological candidate for ChMD. Two disease sources from Italy and France were submitte...

Abstract The Panel on Plant Health of EFSA conducted a pest categorisation of 17 viruses of Rubus L. that were previously classified as either non‐EU or of undetermined standing in a previous opinion. These infectious agents belong to different genera and are heterogeneous in their biology. Blackberry virus X, blackberry virus Z and wineberry laten...

Abstract Following a request from the European Commission, the EFSA Panel on Plant Health performed a pest categorisation of nine phytoplasmas of Cydonia Mill., Fragaria L., Malus Mill., Prunus L., Pyrus L., Ribes L., Rubus L. and Vitis L. (hereafter “host plants”) known to occur only outside the EU or having a limited presence in the EU. This opin...

Abstract Following a request from the European Commission, the EFSA Panel on Plant Health prepared a list of non‐EU phytoplasmas of Cydonia Mill., Fragaria L., Malus Mill., Prunus L., Pyrus L., Ribes L., Rubus L. and Vitis L. A systematic literature review and search of databases identified 27 phytoplasmas infecting one or more of the host genera u...

In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted,...

Abstract Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses of Ribes L. determined as being either non‐EU or of undetermined standing in a previous EFSA opinion. These infectious agents belong to different genera and are heterogeneous in their biology. Alaska vitivirus 1 and Ribes...

Abstract Following a request from the EU Commission, the Panel on Plant Health performed a pest categorisation of 17 viruses and viroids, herein called viruses, of Cydonia Mill., Malus Mill. and Pyrus L. determined as being either non‐EU or of undetermined standing in a previous EFSA opinion. These viruses belong to different genera and are heterog...

Abstract Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses and viroids of Prunus L. determined as being either non‐EU or of undetermined standing in a previous EFSA opinion. These infectious agents belong to different genera and are heterogeneous in their biology. With the exclusi...

Abstract Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses and viroids of Fragaria L. determined as being either non‐EU or of undetermined standing in a previous EFSA opinion. These infectious agents belong to different genera and are heterogeneous in their biology. With the exclu...

Abstract Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses and viroids of Vitis L. determined as being either non‐EU or of undetermined standing in a previous EFSA opinion. These infectious agents belong to different genera and are heterogeneous in their biology. With the exclusio...

Abstract The Panel on Plant Health performed a listing of non‐EU viruses and viroids (reported hereinafter as viruses) of Cydonia Mill., Fragaria L., Malus Mill., Prunus L., Pyrus L., Ribes L., Rubus L. and Vitis L. A systematic literature review identified 197 viruses infecting one or more of the host genera under consideration. Viruses were alloc...

In the absence of protein-coding ability, viroid RNAs rely on direct interactions with host factors for their infectivity. RNA structural elements are likely involved in these interactions. Therefore, preservation of a structural element, despite the sequence variability existing between the variants of a viroid population, is considered a solid ev...

Understanding how viruses and subviral agents initiate disease is central to plant pathology. Whether RNA silencing mediates the primary lesion triggered by viroids (small non-protein-coding RNAs), or just intermediate-late steps of a signaling cascade, remains unsolved. While most variants of the plastid-replicating peach latent mosaic viroid (PLM...

High throughput sequencing was performed on total pooled RNA from six Turkish trees of Pistacia showing different viral symptoms. The analysis produced some contigs showing similarity with RNAs of emaraviruses. Seven distinct negative–sense, single-stranded RNAs were identified as belonging to a new putative virus infecting pistachio. The amino aci...

A new gemycircularvirus sequence was obtained from total DNAs extracted from olive leaves and twigs tissues. Its complete genome consists of a single-stranded circular DNA of 2,145 nt, whose sequence was obtained by rolling circle amplification (RCA). Genome analysis identified three open reading frames, sharing homologies with the coat and replica...

Armenian grapevine germplasm represents a valuable resource for national wine industry and still to be explored for phytosanitary and genetic applications. Indeed, the knowledge about virus infections is scarce. In 2017, in the frame of a COST DIVAS Short term study mission, a small scale dsRNA purification was done on ten leaf samples of the widel...

Phylogenetic trees showing the evolutionary history of selected gene families targeted by conserved miRNAs in Solanum lycopersicum. (A) EPlGT00140000000465 evolutionary history for HAP genes; (B) EPlGT00850000106226 evolutionary history for ARF genes; (C) EPlGT00140000000795 evolutionary history for HD ZIPIII genes; (D) EPlGT00850000106232 evolutio...

Diversity of selected functional conserved miRNAs (expression profile in sRNA datasets from mock-inoculated and TYLCSV-infected tomato plants). Bold characters indicate nucleotides differing from the canonical miRNA sequence.

In silico analysis of miRNA targets among the selected gene families, validated by PARE analysis.

Oligonucleotides used for quantitative reverse transcription PCR experiments of selected transcripts in TYLCSV-infected vs. mock-inoculated tissues.

Impact of the functional indels on the secondary structures of the transcript. (A,B) Global-free energy of the indel-containing region (positions 360–622, Solyc05g008070) and of the indel-lacking region (positions 360–638, Solyc07g049700), respectively. (C) Impact of the artificial insertion of the indel in the indel-lacking region.

Statistics of Solanum lycopersicum genomic and non-genomic siRNAs in tomato yellow leaf curl sardinia virus-infected and mock-inoculated plant tissues.

Output of PAREsnp listing 5′ RNA remnants of cDNA targeted by 21-nt-long secondary siRNAs in tomato TYLCSV-infected plant tissues.

Output of PAREsnp listing 5′ RNA remnants of cDNA targeted by 22-nt-long secondary siRNAs in tomato TYLCSV-infected plant tissues.

Plant viruses modify gene expression in infected tissues by altering the micro (mi)RNA-mediated regulation of genes. Among conserved miRNA targets there are transcripts coding for transcription factors, RNA silencing core and disease resistance proteins. Paralogs in these gene families are widely present in plant genomes and are known to respond di...

Recent developments in high-throughput sequencing (HTS), also called next-generation sequencing (NGS), technologies and bioinformatics have drastically changed research on viral pathogens and spurred growing interest in the field of virus diagnostics. However, the reliability of HTS-based virus detection protocols must be evaluated before adopting...

Quick decline caused by Citrus tristeza virus (CTV) destroyed citrus on sour orange rootstock in southern California during the 1930’s -40’s. However, use of resistant/tolerant CTV rootstocks, certified pathogen-free budwood, and quarantines have limited further economic damage from CTV. Multi-locus marker profiles of California CTV isolates reveal...

Strain differentiating marker profiles of citrus tristeza virus (CTV) isolates from California have shown the presence of multiple genotypes. To better define the genetic diversity involved, full-length genome sequences from four California CTV isolates were determined by small-interfering RNA sequencing. Phylogenetic analysis and nucleotide sequen...

This volume explores the use of viral metagenomics to diagnose known viruses for plant and food production, human and animal health, and identifying viral vectors like insects. The chapters in this book cover topics, such as sRNAs isolation from tissues of grapevines and woody plants, high-resolution screening of arthropod and plant viral communiti...

Preface

A protocol is described to purify small (s)RNA molecules from tissues of grapevine and other woody plants. The protocol has been specifically developed to analyze sRNA populations by high-throughput sequencing. It has been widely used on species of the genera Prunus and Vitis particularly rich in polyphenols and other enzyme-inhibiting compounds. T...

In Italy, grapevine certification system requires the status of “virus controlled” for multiplication and commercialization. This system entails free plant propagation material from Grapevine virus A (GVA), Grapevine virus B (GVB), Grapevine leafroll-associated virus 1, 2, 3 (GLRaV-1, -2, -3), Grapevine fanleaf virus (GFLV), Grapevine fleck virus (...

In Italy, grapevine certification system requires the status of “virus controlled” for multiplication and commercialization. This system entails free plant propagation material from Grapevine virus A (GVA), Grapevine virus B (GVB), Grapevine leafroll-associated virus 1, 2, 3 (GLRaV-1, -2, -3), Grapevine fanleaf virus (GFLV), Grapevine fleck virus (...

A devastating outbreak of a strain of Xylella fastidiosa is ravaging the olive trees of southern Puglia, Italy (Saponari et al., 2015). The bacterium, discovered in 2013, causes the Olive Quick Decline Syndrome (OQDS), a destructive disease characterized by apical and marginal leaf scorching, extensive branch and twig dieback, followed by death of...

A strain of Xylella fastidiosa is ravaging the olive trees of Southern Apulia, Italy (Saponari et al., 2013). The bacterium causes the Olive Quick Decline Syndrome (OQDS), a disease showing symptoms of apical and marginal leaf scorching, extensive branch and twig dieback and death of the trees (Martelli et al., 2016). Transmission tests demonstrate...

Stone fruits rank third among the most important crop species in Chile, after grapevine and apple. Specifically, cherry (Prunus avium L.) cultivation have increased during the last 10 years, making of Chile the most important exporter in the Southern hemisphere. Nineteen cherry samples collected in the spring of 2016 were subjected to high-throughp...

Most Citrus tristeza virus (CTV) isolates in California are biologically mild and symptomless in commercial cultivars on CTV tolerant rootstocks. However, to better define California CTV isolates showing divergent serological and genetic profiles, selected isolates were subjected to deep sequencing of small RNAs. Full-length sequences were assemble...

The CoDiRO strain of Xylella fastidiosa (Xf), which is devastating olive trees in the Apulia Region (southern Italy), represents the first documented establishment of this plant pathogenic bacterium in Europe. Diseases induced by Xf have no chemical cure and its pathogenic mechanism(s) are not completely understood. Nevertheless, profiles and relat...

Olive Quick Decline Syndrome (OQDS) is a destructive disease of olive (Olea europaea) described in Apulia (Italy), to which the CoDiRO strain of Xylella fastidiosa subsp. pauca (Xfp) is associated. Differently from the severely affected cv. Ogliarola salentina, Xfp-infected plants of the cv. Leccino develop reduced symptoms, which are compatible wi...

Following the introduction and establishment of the plant pathogenic bacterium Xylella fastidiosa (Xf) in the Apulia Region (southern Italy), olive turned to be the main host of the Salentinian bacterial strain and the majorly devastated crop. The mechanism of pathogenicity of Xf is still not completely understood and no means to cure the bacterium...

The CoDiRO strain of Xylella fastidiosa subsp. pauca (Xfp) is ravaging olive (Olea europaea) groves in southern Italy, causing a destructive disease denoted Olive Quick Decline Syndrome (OQDS). Field observations show that the Xfp-infected plants of the cv. Ogliarola salentina develop more severe symptoms than that of cv. Leccino. A global transcri...