Simona Abbà

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

Researcher

About

67
Publications
9,289
Reads
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Citations
Introduction
My lab research is currently focused on: - de novo genome assembly and RNA-seq analysis of phytoplasmas; - in silico study of the grapevine/phytoplasma interactions through a system biology approach; I am also an advocate of Open Research Data. We are building an open access repository, named “V2P2 repository”, designed to preserve and share data on plant-virus interactions. http://v2p2arch.to.cnr.it/
Additional affiliations
September 2011 - present
Institute for Sustainable Plant Protection (IPSP) - National Research Council of Italy (CNR)
Position
  • Researcher
April 2006 - September 2006
University of Nottingham
Position
  • Visiting Ph. D.
January 2006 - September 2011
Università degli Studi di Torino
Position
  • PostDoc Position
Education
November 2003 - January 2006
Università degli Studi di Torino
Field of study
  • Biology and biotechnology of fungi
January 2002 - June 2002
Università degli Studi di Torino
Field of study
  • Bioinformatics
September 1995 - July 2001
Università degli Studi di Torino
Field of study
  • Molecular biology

Publications

Publications (67)
Article
Full-text available
Phytoplasmas are insect-borne pathogenic bacteria that cause major economic losses to several crops worldwide. The dynamic microbial community associated with insect vectors influences several aspects of their biology, including their vector competence for pathogens. Unraveling the diversity of the microbiome of phytoplasma insect vectors is gainin...
Article
Full-text available
Scaphoideus titanus (Hemiptera: Cicadellidae) is the natural vector of Flavescence dorée phytoplasma, a quarantine pest of grapevine with severe impact on European viticulture. RNA interference (RNAi) machinery components are present in S. titanus transcriptome and injection of ATP synthase β dsRNAs into adults caused gene silencing, starting three...
Article
Full-text available
Background Hazelnut allergy, which is characterized by symptoms that range from mild to severe, is one of the most common allergies in children throughout Europe, and an accurate diagnosis of this allergy is therefore essential. However, lipophilic allergens, such as oleosins, are generally underrepresented in diagnostic tests. We therefore sought...
Article
Full-text available
Insect vectors transmit viruses and bacteria that can cause severe diseases in plants and economic losses due to a decrease in crop production. Insect vectors, like all other organisms, are colonized by a community of various microorganisms, which can influence their physiology, ecology, evolution, and also their competence as vectors. The importan...
Article
Full-text available
The leafhopper Euscelidius variegatus is a natural vector of the chrysanthemum yellows phytoplasma (CYp) and a laboratory vector of the Flavescence dorée phytoplasma (FDp). Previous studies indicated a crucial role for insect ATP synthase α and β subunits during phytoplasma infection of the vector species. Gene silencing of ATP synthase β was obtai...
Preprint
Full-text available
The leafhopper Euscelidius variegatus is a natural vector of the chrysanthemum yellows phytoplasma (CYp) and a laboratory vector of the Flavescence dorée phytoplasma (FDp). Previous studies indicated a crucial role for insect ATP synthase α and β subunits during phytoplasma infection of the vector species. Gene silencing of ATP synthase β was obtai...
Article
Full-text available
Molecular changes associated with response to powdery mildew (PM) caused by Erysiphe necator have been largely explored in Vitis vinifera cultivars, but little is known on transcriptional and metabolic modifications following application of resistance elicitors against this disease. In this study, the whole transcriptome sequencing, and hormone and...
Article
Virus-based biocontrol technologies represent sustainable alternatives to pesticides and insecticides. Phytoplasmas are prokaryotic plant pathogens causing severe losses to crops worldwide. Novel approaches are needed since insecticides against their insect vectors and rogueing of infected plants are the only available strategies to counteract phyt...
Preprint
Full-text available
Virus-based biocontrol technologies are gaining attention as sustainable alternatives to pesticides and insecticides. Phytoplasmas are prokaryotic plant pathogens causing severe losses to crops worldwide. Novel approaches are needed since insecticide treatments against their insect vectors and rogueing of infected plants are the only available stra...
Article
Full-text available
The leafhopper Scaphoideus titanus is the primary vector of Flavescence dorée phytoplasma (FDp) in European vineyards. Flavescence dorée is one of the most severely damaging diseases of Vitis vinifera and, consequently, a major threat to grape and wine production in several European countries. Control measures are compulsory, but they mainly involv...
Article
Caleosins are involved in several cellular and biological processes that are closely associated with the synthesis, degradation, and stability of oil bodies (OBs). Because of the importance and the multiple roles of these OB‐associated proteins, in silico identification of sequences corresponding to putative caleosins in the hazelnut genome has bee...
Article
To study the role of wild areas around the vineyards in the epidemiology of flavescence dorée (FD) and track the origin of new foci, two phytoplasma genetic markers, dnaK and malG, were developed for FD phytoplasma (FDp) characterization. The two genes and the vmpA locus were used to genetically characterize FDp populations at seven agroecosystems...
Chapter
Transcriptomic analyses addressed to study phytoplasma gene expression may present few difficulties due to the uncultivable nature of these intracellular, obligate pathogens. While RNA extraction from insect vectors does not imply any particular adaptation of the protocols used in most commercial kits, RNA isolation from phytoplasma-infected plants...
Article
The biological bases of recovery of two grapevine cultivars, Nebbiolo and Barbera, showing different susceptibility and recovery ability to “flavescence dorée” (FD) phytoplasma infection were investigated. The expression over one vegetative season, in FD-recovered and healthy grapevines, of 18 genes involved in defence, hydrogen peroxide and hormon...
Article
BACKGROUND: RNA interference (RNAi) techniques have emerged as powerful tools to develop novel management strategies for the control of insect pests. The leafhopper Euscelidius variegatus is a natural vector of chrysanthemum yellows phytoplasma and a laboratory vector of flavescence dorée phytoplasma. Phytoplasmas are insect-borne bacterial plant p...
Article
Full-text available
Micro(mi)RNAs play crucial roles in plant developmental processes and in defense responses to biotic and abiotic stresses. In the last years, many works on small RNAs in grapevine (Vitis spp.) were published, and several conserved and putative novel grapevine-specific miRNAs were identified. In order to reorganize the high quantity of available dat...
Article
Phytoplasmas are plant pathogenic bacteria transmitted by hemipteran insects. The leafhopper Euscelidius variegatus is a natural vector of chrysanthemum yellows phytoplasma (CYp) and a laboratory vector of Flavescence dorée phytoplasma (FDp). The two phytoplasmas induce different effects on this species: CYp slightly improves, while FDp negatively...
Article
Molecular mechanisms underlying phytoplasma interactions with host plants are largely unknown. In this study attempts were made to identify effectors of three phytoplasma strains related to ‘Ca. P. aurantifolia’, crotalaria phyllody (CrP), faba bean phyllody (FBP), and witches’ broom disease of lime (WBDL), using information from draft genome of pe...
Article
Full-text available
The leafhopper Euscelidius variegatus is a natural vector of chrysanthemum yellows phytoplasma (CY) and an efficient vector of flavescence dorée phytoplasma (FD) under laboratory conditions. During a transcriptome sequencing (RNA-seq) project aimed at investigating the interactions between the insect and the two phytoplasmas, a 10,616-nucleotide-lo...
Article
Full-text available
Transcriptomics and genomics data recently obtained from the arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis have offered new opportunities to decipher the contribution of the fungal partner to the establishment of the symbiotic association. The large number of genes which do not show similarity to known proteins witnesses the uniqueness...
Article
Full-text available
A great number of flavored grape varieties, of significant oenological potential, are traditionally cultivated in north-western Italy, besides the renowned “Moscato bianco” (syn. “Muscat à petits grains blancs”). Understanding their origin, besides its historical and scientific interest, would help to increase market appeal and consequently facilit...
Article
Full-text available
Two bacterial symbionts of the European pest leafhopper, Macrosteles quadripunctulatus (Hemiptera: Cicadellidae), were fully sequenced. “ Candidatus Sulcia muelleri” and “ Ca . Nasuia deltocephalinicola” represent two of the smallest known bacterial genomes at 190 kb and 112 kb, respectively. Genome sequences are nearly identical to strains reporte...
Poster
Full-text available
Scientists often see the potential offered by Open Research Data, but most are still unready to engage in data archive and curation. One of the main issues that hinders data sharing is related to the lack of incentive mechanisms, both in terms of dedicated budgets and in terms of ready-to-use technical support tools to store, manage and make access...
Article
Full-text available
Arbuscular mycorrhiza (AM) is one of the most spread symbiosis established between 80% of land plants and soil fungi belonging to the Glomeromycota. Molecular determinants involved in the formation of arbuscular mycorrhizas are still poorly understood. It has been demonstrated that in both Legumes and rice plants, several GRAS transcription factors...
Article
Full-text available
The N-terminal region of the Ourmia melon virus (OuMV) coat protein (CP) contains a short lysine/arginine-rich (KR) region. By alanine scanning mutagenesis, we showed that the KR region influences pathogenicity and virulence of OuMV without altering viral particle assembly. A mutant, called OuMV6710, with three basic residue substitutions in the KR...
Article
Full-text available
Many initiatives actively encourage investigators to make their research data available, but the process of sharing data is perceived by most researchers more as a burden than as a chance to increase the visibility of their results and improve the value of their research. One of the main barriers to open research data (ORD) is the need for interope...
Article
Full-text available
To highlight different transcriptional behaviors of the phytoplasma in the plant and animal host, expression of 14 genes of 'Candidatus Phytoplasma asteris', chrysanthemum yellows strain, was investigated at different times following the infection of a plant host (Arabidopsis thaliana) and two insect vector species (Macrosteles quadripunctulatus an...
Article
Full-text available
The phytoplasma-borne disease flavescence doree is still a threat to European viticulture, despite mandatory control measures and prophylaxis against the leafhopper vector. Given the economic importance of grapevine, it is essential to find alternative strategies to contain the spread, in order to possibly reduce the current use of harmful insectic...
Article
Fungi living in heavy metal polluted soils have evolved different cellular and molecular systems to adapt and survive in these harsh environments. Oidiodendron maius Zn is an ericoid mycorrhizal fungus previously shown to be highly tolerant to zinc thanks to antioxidative enzymes and membrane transporters. A novel gene, OmFCR1, was recently identif...
Technical Report
Full-text available
CNR IVV and CNR IPP Institutes have been dealing with NGS DATA (Next-gen sequencing) for years, but, until 2012, no CNR-based high-performance server was available in Turin. Powerful multi-core servers, clusters and virtual cloud-based machines are essential to address the computational demands of NGS. CNR CERIS Institute built up a server for such...
Article
Full-text available
Background: Translational and post-translational protein modifications play a key role in the response of plants to pathogen infection. Among the latter, phosphorylation is critical in modulating protein structure, localization and interaction with other partners. In this work, we used a multiplex staining approach with 2D gels to study quantitati...
Data
Detailed list of the differentially expressed proteins. The following parameters are reported for each spot: sequence of the matched peptides, normalized volume values (PPM) and coefficient of variation, statistical significance. Sheet 1: healthy/infected Sypro® Ruby staining (total proteins); sheet 2: healthy/recovered Sypro® Ruby staining; sheet...
Data
GO classification and KEGG map assignments of the identified V. vinifera proteins. GOslim term assignment was performed by Blast2GO. GO classification is expressed by GO Names (third column) preceded by “P” for “biological process”, “C” for cellular component and “F” for “molecular function”. The forth column of the table reports the names of the K...
Data
List of the over-represented GO categories in infected and recovered plants following Singular Enrichment Analysis. Proteins are grouped according to the GO categories to which they belong. Only the statistically significant (False discovery rate: FDR ≤0.05) GO terms are shown. “Category” indicates the main GO categories: “B”, biological process; “...
Chapter
Full-text available
Ericoid mycorrhizal (ERM) fungi are a diverse assemblage of symbiotic fungi that features culturable ascomycetes in the Helotiales and Onygenales, but also so far unculturable basidiomycetes in the Sebacinales. They form a distinct endomycorrhizal association with some plant genera in the Ericaceae. ERM plants dominate in heathlands characterised b...
Data
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
Data
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
Article
Full-text available
Cadmium is a genotoxic pollutant known to target proteins that are involved in DNA repair and in antioxidant defence, altering their functions and ultimately causing mutagenic and carcinogenic effects. We have identified a PLAC8 domain-containing protein, named OmFCR, by a yeast functional screen aimed at identifying genes involved in cadmium resis...
Article
Full-text available
admium is a genotoxic pollutant known to target proteins that are involved in DNA repair and in antioxidant defence, altering their functions and ultimately causing mutagenic and carcinogenic effects. We have identified a PLAC8 domain-containing protein, named OmFCR, by a yeast functional screen aimed at identifying genes involved in cadmium resis...
Article
The Tuber melanosporum genome has been analysed with the aim of identifying and characterizing the genes involved in the environmental stress response. A whole genome array (7496 genes/probe) was used to verify the fungal transcriptional profiling upon a cold temperature period (7 days at 4 °C). A total of 423 genes resulted to be differentially ex...
Article
Full-text available
The genome sequences of mycorrhizal fungi will provide new opportunities for studying the biology and the evolution underlying this symbiotic lifestyle. The generation of null mutants at the wild-type loci is one of the best methods for gene-function assignment in the post-genomic era. To our knowledge, the generation of superoxide dismutase 1 (SOD...
Chapter
In mid-2005, 6.5 billion people shared the planet and, according to 2004 estimates by the population division of the UN Secretariat, world population is expected to rise in the next 45 years by 2.6 billion, to reach a total of 9.1 billion in 2050 (www.unfpa.org). Consequently, one of the main challenges of the twenty-first century will be to produc...
Article
Full-text available
Expression profiles of isocitrate lyase (TbICL), malate synthase (TbMLS) and fructose-1,6-bisphosphatase (TbFBP) from the mycorrhizal ascomycete Tuber borchii were investigated by real-time RT-PCR in fruiting bodies at different stages of maturation. In addition, a time course experiment was set up to determine how the transcription profile of TbIC...
Article
The focus of this work is on the nitrogen starvation stress responses operating in a plant symbiotic fungus. A cDNA array profiling analysis was conducted on N-limited mycelia of the mycorrhizal ascomycete Tuber borchii. Fifty-one unique transcripts, out of 2062 redundant arrayed cDNAs, were differentially expressed by at least 1.5-fold in response...
Article
Full-text available
The expressed sequence tag M6G10 was originally isolated from a screening for differentially expressed transcripts during the reproductive stage of the white truffle Tuber borchii. mRNA levels for M6G10 increased dramatically during fruiting body maturation compared to the vegetative mycelial stage. Bioinformatics tools, phylogenetic analysis and e...
Article
Full-text available
cDNA arrays were used to explore mechanisms controlling fruiting body development in the truffle Tuber borchii. Differences in gene expression were higher between reproductive and vegetative stage than between two stages of fruiting body maturation. We suggest hypotheses about the importance of various physiological processes during the development...
Article
Full-text available
A heavy metal tolerant strain of the ericoid mycorrhizal species Oidiodendron maius, isolated from roots of Vaccinium myrtillus growing in soil heavily contaminated with zinc, was previously shown to tolerate high concentrations of zinc and cadmium ions in the growth medium. We have investigated the genetic basis of this fungal strain tolerance to...