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Surano A, del Grosso C, Musio B, Todisco S, Giampetruzzi A, Altamura G, Saponari M, Gallo V, Mastrorilli P, Boscia D, Saldarelli P. Exploring the xylem-sap to unravel biological features of Xylella fastidiosa subspecies pauca ST53 in immune, resistant and susceptible crop species through metabolomics and in vitro studies. Front Plant Sci 2024; 14:1343876. [PMID: 38312355 PMCID: PMC10834688 DOI: 10.3389/fpls.2023.1343876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 12/28/2023] [Indexed: 02/06/2024]
Abstract
Xylella fastidiosa subsp. pauca ST53 (Xfp) is a pathogenic bacterium causing one of the most severe plant diseases currently threatening the olive-growing areas of the Mediterranean, the Olive Quick Decline Syndrome (OQDS). The majority of the olive cultivars upon infections more or less rapidly develop severe desiccation phenomena, while few are resistant (e.g. Leccino and FS17), being less impacted by the infections. The present study contributes to elucidating the basis of the resistance phenomenon by investigating the influence of the composition of the xylem sap of plant species on the rate of bacterial multiplication. Xylem saps from Xfp host and non-host species were used for growing the bacterium in vitro, monitoring bacterial growth, biofilm formation, and the expression of specific genes. Moreover, species-specific metabolites, such as mannitol, quinic acid, tartaric acid, and choline were identified by non-targeted NMR-based metabolomic analysis in olive, grapevine, and citrus. In general, the xylem saps of immune species, including grapevine and citrus, were richer in amino acids, organic acids, and glucose. The results showed greater bacterial growth in the olive cultivar notoriously susceptible to Xfp (Cellina di Nardò), compared to that recorded in the resistant cultivar Leccino. Conversely, higher biofilm formation occurred in Leccino compared to Cellina di Nardò. Using the xylem saps of two Xfp-immune species (citrus and grapevine), a divergent bacterial behavior was recorded: low planktonic growth and biofilm production were detected in citrus compared to the grapevine. A parallel evaluation of the expression of 15 genes showed that Xfp directs its molecular functions mainly to virulence. Overall, the results gained through this multidisciplinary study contribute to extending the knowledge on the host-pathogen interaction, while confirming that the host response and resistance mechanism have a multifactorial basis, most likely with a cumulative effect on the phenotype.
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Affiliation(s)
- Antony Surano
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Carmine del Grosso
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Biagia Musio
- Department of Civil, Environmental, Land, Building Engineering and Chemistry (DICATECh), Polytechnic University of Bari, Bari, Italy
| | - Stefano Todisco
- Department of Civil, Environmental, Land, Building Engineering and Chemistry (DICATECh), Polytechnic University of Bari, Bari, Italy
| | - Annalisa Giampetruzzi
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Giuseppe Altamura
- CRSFA-Centro Ricerca, Sperimentazione e Formazione in Agricoltura Basile Caramia, Locorotondo, Italy
| | - Maria Saponari
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Vito Gallo
- Department of Civil, Environmental, Land, Building Engineering and Chemistry (DICATECh), Polytechnic University of Bari, Bari, Italy
- Innovative Solutions S.r.l.—Spin-Off Company of Polytechnic University of Bari, Noci, Italy
| | - Piero Mastrorilli
- Department of Civil, Environmental, Land, Building Engineering and Chemistry (DICATECh), Polytechnic University of Bari, Bari, Italy
- Innovative Solutions S.r.l.—Spin-Off Company of Polytechnic University of Bari, Noci, Italy
| | - Donato Boscia
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Pasquale Saldarelli
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
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Giampetruzzi A, Loconsole G, Zicca S, Boscia D, Balestra GM, Saponari M. Draft Genome Sequence Resource of Xylella fastidiosa Strain Alm_Lz_1 Associated with a New Outbreak in Lazio, Italy. Phytopathology 2023; 113:108-111. [PMID: 36515577 DOI: 10.1094/phyto-05-22-0185-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Affiliation(s)
| | - Giuliana Loconsole
- Istituto per la Protezione Sostenibile delle Piante, CNR, 70126 Bari, Italy
| | - Stefania Zicca
- Istituto per la Protezione Sostenibile delle Piante, CNR, 70126 Bari, Italy
| | - Donato Boscia
- Istituto per la Protezione Sostenibile delle Piante, CNR, 70126 Bari, Italy
| | - Giorgio Mariano Balestra
- Dipartimento di Scienze Agrarie e Forestali (DAFNE), Università degli Studi della Tuscia, 01100, Viterbo, Italy
| | - Maria Saponari
- Istituto per la Protezione Sostenibile delle Piante, CNR, 70126 Bari, Italy
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Landa BB, Saponari M, Feitosa-Junior OR, Giampetruzzi A, Vieira FJD, Mor E, Robatzek S. Xylella fastidiosa's relationships: the bacterium, the host plants, and the plant microbiome. New Phytol 2022; 234:1598-1605. [PMID: 35279849 DOI: 10.1111/nph.18089] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
Xylella fastidiosa is the causal agent of important crop diseases and is transmitted by xylem-sap-feeding insects. The bacterium colonizes xylem vessels and can persist with a commensal or pathogen lifestyle in more than 500 plant species. In the past decade, reports of X. fastidiosa across the globe have dramatically increased its known occurrence. This raises important questions: How does X. fastidiosa interact with the different host plants? How does the bacterium interact with the plant immune system? How does it influence the host's microbiome? We discuss recent strain genetic typing and plant transcriptome and microbiome analyses, which have advanced our understanding of factors that are important for X. fastidiosa plant infection.
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Affiliation(s)
- Blanca B Landa
- Institute for Sustainable Agriculture, CSIC, Alameda del Obispo S/N, Córdoba, 14004, Spain
| | - Maria Saponari
- CNR - Institute for Sustainable Plant Protection (IPSP), Via Amendola 165/A, Bari, 70126, Italy
| | | | - Annalisa Giampetruzzi
- CNR - Institute for Sustainable Plant Protection (IPSP), Via Amendola 165/A, Bari, 70126, Italy
| | - Filipe J D Vieira
- Genetics, LMU Biocentre, Grosshadener Strasse 4, Planegg, 82152, Germany
| | - Eliana Mor
- Genetics, LMU Biocentre, Grosshadener Strasse 4, Planegg, 82152, Germany
| | - Silke Robatzek
- Genetics, LMU Biocentre, Grosshadener Strasse 4, Planegg, 82152, Germany
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Sicard A, Saponari M, Vanhove M, Castillo AI, Giampetruzzi A, Loconsole G, Saldarelli P, Boscia D, Neema C, Almeida RPP. Introduction and adaptation of an emerging pathogen to olive trees in Italy. Microb Genom 2021; 7. [PMID: 34904938 PMCID: PMC8767334 DOI: 10.1099/mgen.0.000735] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The invasive plant pathogen Xylella fastidiosa currently threatens European flora through the loss of economically and culturally important host plants. This emerging vector-borne bacterium, native to the Americas, causes several important diseases in a wide range of plants including crops, ornamentals, and trees. Previously absent from Europe, and considered a quarantine pathogen, X. fastidiosa was first detected in Apulia, Italy in 2013 associated with a devastating disease of olive trees (Olive Quick Decline Syndrome, OQDS). OQDS has led to significant economic, environmental, cultural, as well as political crises. Although the biology of X. fastidiosa diseases have been studied for over a century, there is still no information on the determinants of specificity between bacterial genotypes and host plant species, which is particularly relevant today as X. fastidiosa is expanding in the naive European landscape. We analysed the genomes of 79 X. fastidiosa samples from diseased olive trees across the affected area in Italy as well as genomes of the most genetically closely related strains from Central America. We provided insights into the ecological and evolutionary emergence of this pathogen in Italy. We first showed that the outbreak in Apulia is due to a single introduction from Central America that we estimated to have occurred in 2008 [95 % HPD: 1930–2016]. By using a combination of population genomic approaches and evolutionary genomics methods, we further identified a short list of genes that could play a major role in the adaptation of X. fastidiosa to this new environment. We finally provided experimental evidence for the adaptation of the strain to this new environment.
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Affiliation(s)
- Anne Sicard
- UC Berkeley, Department of Environmental Science, Policy, and Management, Berkeley, CA 94720, U.S.A.,PHIM Plant Health Institute, Univ Montpellier, INRAE, Institut Agro, CIRAD, IRD, Montpellier, France
| | - Maria Saponari
- National Research Council (CNR), Institute for Sustainable Plant Protection, Via Amendola 122/D, 70126 Bari, Italy
| | - Mathieu Vanhove
- UC Berkeley, Department of Environmental Science, Policy, and Management, Berkeley, CA 94720, U.S.A
| | - Andreina I Castillo
- UC Berkeley, Department of Environmental Science, Policy, and Management, Berkeley, CA 94720, U.S.A
| | - Annalisa Giampetruzzi
- University of Bari Aldo Moro, Department of Soil, Plant and Food Sciences, Piazza Umberto I, 70121 Bari, Italy
| | - Giuliana Loconsole
- National Research Council (CNR), Institute for Sustainable Plant Protection, Via Amendola 122/D, 70126 Bari, Italy
| | - Pasquale Saldarelli
- National Research Council (CNR), Institute for Sustainable Plant Protection, Via Amendola 122/D, 70126 Bari, Italy
| | - Donato Boscia
- National Research Council (CNR), Institute for Sustainable Plant Protection, Via Amendola 122/D, 70126 Bari, Italy
| | - Claire Neema
- PHIM Plant Health Institute, Univ Montpellier, INRAE, Institut Agro, CIRAD, IRD, Montpellier, France
| | - Rodrigo P P Almeida
- UC Berkeley, Department of Environmental Science, Policy, and Management, Berkeley, CA 94720, U.S.A
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Giampetruzzi A, Baptista P, Morelli M, Cameirão C, Lino Neto T, Costa D, D’Attoma G, Abou Kubaa R, Altamura G, Saponari M, Pereira JA, Saldarelli P. Differences in the Endophytic Microbiome of Olive Cultivars Infected by Xylella fastidiosa across Seasons. Pathogens 2020; 9:pathogens9090723. [PMID: 32887278 PMCID: PMC7558191 DOI: 10.3390/pathogens9090723] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 12/26/2022] Open
Abstract
The dynamics of Xylella fastidiosa infections in the context of the endophytic microbiome was studied in field-grown plants of the susceptible and resistant olive cultivars Kalamata and FS17. Whole metagenome shotgun sequencing (WMSS) coupled with 16S/ITS rRNA gene sequencing was carried out on the same trees at two different stages of the infections: In Spring 2017 when plants were almost symptomless and in Autumn 2018 when the trees of the susceptible cultivar clearly showed desiccations. The progression of the infections detected in both cultivars clearly unraveled that Xylella tends to occupy the whole ecological niche and suppresses the diversity of the endophytic microbiome. However, this trend was mitigated in the resistant cultivar FS17, harboring lower population sizes and therefore lower Xylella average abundance ratio over total bacteria, and a higher α-diversity. Host cultivar had a negligible effect on the community composition and no clear associations of a single taxon or microbial consortia with the resistance cultivar were found with both sequencing approaches, suggesting that the mechanisms of resistance likely reside on factors that are independent of the microbiome structure. Overall, Proteobacteria, Actinobacteria, Firmicutes, and Bacteriodetes dominated the bacterial microbiome while Ascomycota and Basidiomycota those of Fungi.
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Affiliation(s)
- Annalisa Giampetruzzi
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari, 70126 Bari, Italy;
| | - Paula Baptista
- Centro de Investigação de Montanha (CIMO), Campus de Santa Apolónia, Instituto Politécnico de Bragança, 5300-253 Bragança, Portugal; (P.B.); (C.C.); (J.A.P.)
| | - Massimiliano Morelli
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Sede Secondaria di Bari, 70126 Bari, Italy; (M.M.); (G.D.); (R.A.K.); (G.A.); (M.S.)
| | - Cristina Cameirão
- Centro de Investigação de Montanha (CIMO), Campus de Santa Apolónia, Instituto Politécnico de Bragança, 5300-253 Bragança, Portugal; (P.B.); (C.C.); (J.A.P.)
| | - Teresa Lino Neto
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center (CBFP), Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal; (T.L.N.); (D.C.)
| | - Daniela Costa
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center (CBFP), Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal; (T.L.N.); (D.C.)
| | - Giusy D’Attoma
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Sede Secondaria di Bari, 70126 Bari, Italy; (M.M.); (G.D.); (R.A.K.); (G.A.); (M.S.)
| | - Raied Abou Kubaa
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Sede Secondaria di Bari, 70126 Bari, Italy; (M.M.); (G.D.); (R.A.K.); (G.A.); (M.S.)
| | - Giuseppe Altamura
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Sede Secondaria di Bari, 70126 Bari, Italy; (M.M.); (G.D.); (R.A.K.); (G.A.); (M.S.)
| | - Maria Saponari
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Sede Secondaria di Bari, 70126 Bari, Italy; (M.M.); (G.D.); (R.A.K.); (G.A.); (M.S.)
| | - José Alberto Pereira
- Centro de Investigação de Montanha (CIMO), Campus de Santa Apolónia, Instituto Politécnico de Bragança, 5300-253 Bragança, Portugal; (P.B.); (C.C.); (J.A.P.)
| | - Pasquale Saldarelli
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Sede Secondaria di Bari, 70126 Bari, Italy; (M.M.); (G.D.); (R.A.K.); (G.A.); (M.S.)
- Correspondence: ; Tel.: +39-0805443065
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6
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Arias-Giraldo LF, Giampetruzzi A, Metsis M, Marco-Noales E, Imperial J, Velasco-Amo MP, Román-Écija M, Landa BB. Complete Circularized Genome Data of Two Spanish strains of Xylella fastidiosa (IVIA5235 and IVIA5901) Using Hybrid Assembly Approaches. Phytopathology 2020; 110:969-972. [PMID: 32096699 DOI: 10.1094/phyto-01-20-0012-a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Xylella fastidiosa is an economically important plant pathogenic bacterium of global importance associated, since 2013, with a devastating epidemic in olive trees in Italy. Since then, several outbreaks of this pathogen have been reported in other European member countries including Spain, France, and Portugal. In Spain, the three major subspecies (subsp. fastidiosa, multiplex, and pauca) of the bacterium have been detected in the Balearic Islands, but only subspecies multiplex in the mainland (Alicante). We present the first complete genome sequences of two Spanish strains: X. fastidiosa subsp. fastidiosa IVIA5235 from Mallorca and X. fastidiosa subsp. multiplex IVIA5901 from Alicante, using Oxford Nanopore and Illumina sequence reads, and two hybrid approaches for genome assembly. These completed genomes will provide a resource to better understand the biology of these X. fastidiosa strains.
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Affiliation(s)
- Luis F Arias-Giraldo
- Institute for Sustainable Agriculture, Consejo superior de Investigaciones Científicas (CSIC), Córdoba, Spain
| | - Annalisa Giampetruzzi
- Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | | | - Ester Marco-Noales
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain
| | - Juan Imperial
- Institute of Agricultural Sciences, CSIC, Madrid, Spain
| | - María P Velasco-Amo
- Institute for Sustainable Agriculture, Consejo superior de Investigaciones Científicas (CSIC), Córdoba, Spain
| | - Miguel Román-Écija
- Institute for Sustainable Agriculture, Consejo superior de Investigaciones Científicas (CSIC), Córdoba, Spain
| | - Blanca B Landa
- Institute for Sustainable Agriculture, Consejo superior de Investigaciones Científicas (CSIC), Córdoba, Spain
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Saponari M, Giampetruzzi A, Selvaraj V, Maheshwari Y, Yokomi R. Identification and Characterization of Resistance-Breaking (RB) Isolates of Citrus tristeza virus. Methods Mol Biol 2020; 2015:105-126. [PMID: 31222699 DOI: 10.1007/978-1-4939-9558-5_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Resistance-breaking (RB) strains constitute a clade of biological and genetically distinct isolates of Citrus tristeza virus (CTV) that replicate and move systemically in Poncirus trifoliata (trifoliate orange), resistant to other known strains of CTV. Molecular markers have been developed by comparative genome analysis to allow quick identification of potential RB isolates. Here, methods are described to identify and characterize RB strains by reverse transcription-polymerase chain reaction (RT-PCR), quantitative real-time RT-PCR (RT-qPCR), full-length genome sequencing, and biological indexing.
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Affiliation(s)
- Maria Saponari
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy.
| | - Annalisa Giampetruzzi
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | | | - Yogita Maheshwari
- San Joaquin Valley Agricultural Sciences Center, USDA-ARS, Parlier, CA, USA
| | - Raymond Yokomi
- San Joaquin Valley Agricultural Sciences Center, USDA-ARS, Parlier, CA, USA
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Landa BB, Castillo AI, Giampetruzzi A, Kahn A, Román-Écija M, Velasco-Amo MP, Navas-Cortés JA, Marco-Noales E, Barbé S, Moralejo E, Coletta-Filho HD, Saldarelli P, Saponari M, Almeida RPP. Emergence of a Plant Pathogen in Europe Associated with Multiple Intercontinental Introductions. Appl Environ Microbiol 2020; 86:e01521-19. [PMID: 31704683 PMCID: PMC6974645 DOI: 10.1128/aem.01521-19] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/05/2019] [Indexed: 11/20/2022] Open
Abstract
Pathogen introductions have led to numerous disease outbreaks in naive regions of the globe. The plant pathogen Xylella fastidiosa has been associated with various recent epidemics in Europe affecting agricultural crops, such as almond, grapevine, and olive, but also endemic species occurring in natural forest landscapes and ornamental plants. We compared whole-genome sequences of X. fastidiosa subspecies multiplex from America and strains associated with recent outbreaks in southern Europe to infer their likely origins and paths of introduction within and between the two continents. Phylogenetic analyses indicated multiple introductions of X. fastidiosa subspecies multiplex into Italy, Spain, and France, most of which emerged from a clade with limited genetic diversity with a likely origin in California, USA. The limited genetic diversity observed in X. fastidiosa subspecies multiplex strains originating from California is likely due to the clade itself being an introduction from X. fastidiosa subspecies multiplex populations in the southeastern United States, where this subspecies is most likely endemic. Despite the genetic diversity found in some areas in Europe, there was no clear evidence of recombination occurring among introduced X. fastidiosa strains in Europe. Sequence type taxonomy, based on multilocus sequence typing (MLST), was shown, at least in one case, to not lead to monophyletic clades of this pathogen; whole-genome sequence data were more informative in resolving the history of introductions than MLST data. Although additional data are necessary to carefully tease out the paths of these recent dispersal events, our results indicate that whole-genome sequence data should be considered when developing management strategies for X. fastidiosa outbreaks.IMPORTANCEXylella fastidiosa is an economically important plant-pathogenic bacterium that has emerged as a pathogen of global importance associated with a devastating epidemic in olive trees in Italy associated with X. fastidiosa subspecies pauca and other outbreaks in Europe, such as X. fastidiosa subspecies fastidiosa and X. fastidiosa subspecies multiplex in Spain and X. fastidiosa subspecies multiplex in France. We present evidence of multiple introductions of X. fastidiosa subspecies multiplex, likely from the United States, into Spain, Italy, and France. These introductions illustrate the risks associated with the commercial trade of plant material at global scales and the need to develop effective policy to limit the likelihood of pathogen pollution into naive regions. Our study demonstrates the need to utilize whole-genome sequence data to study X. fastidiosa introductions at outbreak stages, since a limited number of genetic markers does not provide sufficient phylogenetic resolution to determine dispersal paths or relationships among strains that are of biological and quarantine relevance.
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Affiliation(s)
- Blanca B Landa
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Córdoba, Spain
| | - Andreina I Castillo
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA
| | - Annalisa Giampetruzzi
- Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Universit à degli Studi di Bari Aldo Moro, Bari, Italy
| | - Alexandra Kahn
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA
| | - Miguel Román-Écija
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Córdoba, Spain
| | - María Pilar Velasco-Amo
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Córdoba, Spain
| | - Juan A Navas-Cortés
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Córdoba, Spain
| | - Ester Marco-Noales
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain
| | - Silvia Barbé
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain
| | - Eduardo Moralejo
- Tragsa, Empresa de Transformación Agraria, Delegación de Baleares, Palma de Mallorca, Spain
| | | | | | - Maria Saponari
- Istituto per la Protezione Sostenibile delle Piante, CNR, Bari, Italy
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA
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D’Attoma G, Morelli M, Saldarelli P, Saponari M, Giampetruzzi A, Boscia D, Savino VN, De La Fuente L, Cobine PA. Ionomic Differences between Susceptible and Resistant Olive Cultivars Infected by Xylella fastidiosa in the Outbreak Area of Salento, Italy. Pathogens 2019; 8:pathogens8040272. [PMID: 31795218 PMCID: PMC6963573 DOI: 10.3390/pathogens8040272] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/22/2019] [Accepted: 11/26/2019] [Indexed: 12/29/2022] Open
Abstract
Olive quick decline syndrome (OQDS) is a devastating disease of olive trees in the Salento region, Italy. This disease is caused by the bacterium Xylella fastidiosa, which is widespread in the outbreak area; however, the “Leccino” variety of olives has proven to be resistant with fewer symptoms and lower bacterial populations than the “Ogliarola salentina” variety. We completed an empirical study to determine the mineral and trace element contents (viz; ionome) of leaves from infected trees comparing the two varieties, to develop hypotheses related to the resistance of Leccino trees to X. fastidiosa infection. All samples from both cultivars tested were infected by X. fastidiosa, even if leaves were asymptomatic at the time of collection, due to the high disease pressure in the outbreak area and the long incubation period of this disease. Leaves were binned for the analysis by variety, field location, and infected symptomatic and infected asymptomatic status by visual inspection. The ionome of leaf samples was determined using inductively coupled plasma optical emission spectroscopy (ICP-OES) and compared with each other. These analyses showed that Leccino variety consistently contained higher manganese (Mn) levels compared with Ogliarola salentina, and these levels were higher in both infected asymptomatic and infected symptomatic leaves. Infected asymptomatic and infected symptomatic leaves within a host genotype also showed differences in the ionome, particularly a higher concentration of calcium (Ca) and Mn levels in the Leccino cultivar, and sodium (Na) in both varieties. We hypothesize that the ionome differences in the two varieties contribute to protection against disease caused by X. fastidiosa infection.
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Affiliation(s)
- Giusy D’Attoma
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy; (G.D.); (A.G.); (V.N.S.)
- Italian National Research Council, Institute for Sustainable Plant Protection, 70126 Bari, Italy; (M.M.); (P.S.); (M.S.); (D.B.)
| | - Massimiliano Morelli
- Italian National Research Council, Institute for Sustainable Plant Protection, 70126 Bari, Italy; (M.M.); (P.S.); (M.S.); (D.B.)
| | - Pasquale Saldarelli
- Italian National Research Council, Institute for Sustainable Plant Protection, 70126 Bari, Italy; (M.M.); (P.S.); (M.S.); (D.B.)
| | - Maria Saponari
- Italian National Research Council, Institute for Sustainable Plant Protection, 70126 Bari, Italy; (M.M.); (P.S.); (M.S.); (D.B.)
| | - Annalisa Giampetruzzi
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy; (G.D.); (A.G.); (V.N.S.)
| | - Donato Boscia
- Italian National Research Council, Institute for Sustainable Plant Protection, 70126 Bari, Italy; (M.M.); (P.S.); (M.S.); (D.B.)
| | - Vito Nicola Savino
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy; (G.D.); (A.G.); (V.N.S.)
| | - Leonardo De La Fuente
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA;
| | - Paul A. Cobine
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
- Correspondence:
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10
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Giampetruzzi A, D'Attoma G, Zicca S, Abou Kubaa R, Rizzo D, Boscia D, Saldarelli P, Saponari M. Draft Genome Sequence Resources of Three Strains (TOS4, TOS5, and TOS14) of Xylella fastidiosa Infecting Different Host Plants in the Newly Discovered Outbreak in Tuscany, Italy. Phytopathology 2019; 109:1516-1518. [PMID: 31329051 DOI: 10.1094/phyto-04-19-0108-a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
An outbreak of Xylella fastidiosa was discovered in late 2018 in northern Italy affecting several plant species. Multilocus sequence typing analyses detected the presence of strains clustering in X. fastidiosa subsp. multiplex and harboring a hitherto uncharacterized sequence type, ST87. Three cultured strains (TOS4, TOS5, and TOS14) were subjected to high-throughput sequencing and the draft genomes assembled. Phylogenetic analysis conclusively indicated that they belong to the subspecies multiplex. The genetic information generated for these newly discovered strains further supports the evidence that sequence types are associated with the emergence of X. fastidiosa in Europe, posing major challenges for predicting the main threatened European and Mediterranean crops and plant species.
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Affiliation(s)
- Annalisa Giampetruzzi
- Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, 70126 Bari, Italy
| | - Giusy D'Attoma
- Istituto per la Protezione Sostenibile delle Piante, CNR, 70126 Bari, Italy
| | - Stefania Zicca
- Istituto per la Protezione Sostenibile delle Piante, CNR, 70126 Bari, Italy
| | - Raied Abou Kubaa
- Istituto per la Protezione Sostenibile delle Piante, CNR, 70126 Bari, Italy
| | - Domenico Rizzo
- Regione Toscana, Servizio Fitosanitario Regionale e di Vigilanza e Controllo Agroforestale, 50121 Firenze, Italy
| | - Donato Boscia
- Istituto per la Protezione Sostenibile delle Piante, CNR, 70126 Bari, Italy
| | | | - Maria Saponari
- Istituto per la Protezione Sostenibile delle Piante, CNR, 70126 Bari, Italy
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11
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Giampetruzzi A, Velasco-Amo MP, Marco-Noales E, Montes-Borrego M, Román-Écija M, Navarro I, Monterde A, Barbé S, Almeida RPP, Saldarelli P, Saponari M, Montilon V, Savino VN, Boscia D, Landa BB. Draft Genome Resources of Two Strains ("ESVL" and "IVIA5901") of Xylella fastidiosa Associated with Almond Leaf Scorch Disease in Alicante, Spain. Phytopathology 2019; 109:219-221. [PMID: 30592693 DOI: 10.1094/phyto-09-18-0328-a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
An outbreak of Xylella fastidiosa subsp. multiplex sequence type ST6 was discovered in 2017 in mainland Spain affecting almond trees. Two cultured almond strains, "ESVL" and "IVIA5901," were subjected to high throughput sequencing and the draft genomes assembled. Phylogenetic analysis conclusively indicated they belong to the subspecies multiplex, and pairwise comparisons of the chromosomal genomes showed an average nucleotide identity higher than 99%. Interestingly, the two strains differ for the presence of the plasmids pXF64-Hb_ESVL and pUCLA-ESVL detected only in the ESVL strain. The availability of these draft genomes contribute to extend the European genomic sequence dataset, a first step toward setting new research to elucidate the pathway of introduction and spread of the numerous strains of this subspecies so far detected in Europe.
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Affiliation(s)
- Annalisa Giampetruzzi
- 1 Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, 70126 Bari, Italy
| | - María Pilar Velasco-Amo
- 2 Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (IAS-CSIC), 14004 Córdoba, Spain
| | - Ester Marco-Noales
- 3 Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Spain
| | - Miguel Montes-Borrego
- 2 Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (IAS-CSIC), 14004 Córdoba, Spain
| | - Miguel Román-Écija
- 2 Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (IAS-CSIC), 14004 Córdoba, Spain
| | - Inmaculada Navarro
- 3 Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Spain
| | - Adela Monterde
- 3 Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Spain
| | - Silvia Barbé
- 3 Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Spain
| | - Rodrigo P P Almeida
- 4 Department of Environmental Science, Policy and Management, University of California, Berkeley 94720; and
| | - Pasquale Saldarelli
- 5 Istituto per la Protezione Sostenibile delle Piante, CNR, 70126 Bari, Italy
| | - Maria Saponari
- 5 Istituto per la Protezione Sostenibile delle Piante, CNR, 70126 Bari, Italy
| | - Vito Montilon
- 1 Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, 70126 Bari, Italy
| | - Vito Nicola Savino
- 1 Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, 70126 Bari, Italy
| | - Donato Boscia
- 5 Istituto per la Protezione Sostenibile delle Piante, CNR, 70126 Bari, Italy
| | - Blanca B Landa
- 2 Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (IAS-CSIC), 14004 Córdoba, Spain
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12
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Abstract
A dramatic outbreak of Xylella fastidiosa decimating olive was discovered in 2013 in Apulia, Southern Italy. This pathogen is a quarantine bacterium in the European Union (EU) and created unprecedented turmoil for the local economy and posed critical challenges for its management. With the new emerging threat to susceptible crops in the EU, efforts were devoted to gain basic knowledge on the pathogen biology, host, and environmental interactions (e.g., bacterial strain(s) and pathogenicity, hosts, vector(s), and fundamental drivers of its epidemics) in order to find means to control or mitigate the impacts of the infections. Field surveys, greenhouse tests, and laboratory analyses proved that a single bacterial introduction occurred in the area, with a single genotype, belonging to the subspecies pauca, associated with the epidemic. Infections caused by isolates of this genotype turned to be extremely aggressive on the local olive cultivars, causing a new disease termed olive quick decline syndrome. Due to the initial extension of the foci and the rapid spread of the infections, eradication measures (i.e., pathogen elimination from the area) were soon replaced by containment measures including intense border surveys of the contaminated area, removal of infected trees, and mandatory vector control. However, implementation of containment measures encountered serious difficulties, including public reluctance to accept control measures, poor stakeholder cooperation, misinformation from some media outlets, and lack of robust responses by some governmental authorities. This scenario delayed and limited containment efforts and allowed the bacterium to continue its rapid dissemination over more areas in the region, as shown by the continuous expansion of the official borders of the infected area. At the research level, the European Commission and regional authorities are now supporting several programs aimed to find effective methods to mitigate and contain the impact of X. fastidiosa on olives, the predominant host affected in this epidemic. Preliminary evidence of the presence of resistance in some olive cultivars represents a promising approach currently under investigation for long-term management strategies. The present review describes the current status of the epidemic and major research achievements since 2013.
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Affiliation(s)
- M Saponari
- First, fourth, and fifth author: Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, via Amendola 122/D, Bari, Italy; and second and third author: Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, via Amendola 165/A, Bari, Italy
| | - A Giampetruzzi
- First, fourth, and fifth author: Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, via Amendola 122/D, Bari, Italy; and second and third author: Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, via Amendola 165/A, Bari, Italy
| | - G Loconsole
- First, fourth, and fifth author: Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, via Amendola 122/D, Bari, Italy; and second and third author: Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, via Amendola 165/A, Bari, Italy
| | - D Boscia
- First, fourth, and fifth author: Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, via Amendola 122/D, Bari, Italy; and second and third author: Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, via Amendola 165/A, Bari, Italy
| | - P Saldarelli
- First, fourth, and fifth author: Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, via Amendola 122/D, Bari, Italy; and second and third author: Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, via Amendola 165/A, Bari, Italy
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13
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Yokomi R, Selvaraj V, Maheshwari Y, Chiumenti M, Saponari M, Giampetruzzi A, Weng Z, Xiong Z, Hajeri S. Molecular and biological characterization of a novel mild strain of citrus tristeza virus in California. Arch Virol 2018; 163:1795-1804. [PMID: 29550931 DOI: 10.1007/s00705-018-3799-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/28/2018] [Indexed: 10/17/2022]
Abstract
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 sequence comparisons differentiated these isolates into the genotypes VT (CA-VT-AT39), T30 (CA-T30-AT4), and a new strain called S1 (CA-S1-L and CA-S1-L65). S1 isolates had three common recombination events within portions of genes from VT, T36 and RB strains and were transmissible by Aphis gossypii. Virus indexing showed that CA-VT-AT39 could be classified as a severe strain, whereas CA-T30-AT4, CA-S1-L and CA-S1-L65 were mild. CA-VT-AT39, CA-S1-L, and CA-S1-L65 reacted with monoclonal antibody MCA13, whereas CA-T30-AT4 did not. RT-PCR and RT-qPCR detection assays for the S1 strain were developed and used to screen MCA13-reactive isolates in a CTV collection from central California collected from 1968 to 2011. Forty-two isolates were found to contain the S1 strain, alone or in combinations with other genotypes. BLAST and phylogenetic analysis of the S1 p25 gene region with other extant CTV sequences from the NCBI database suggested that putative S1-like isolates might occur elsewhere (e.g., China, South Korea, Turkey, Bosnia and Croatia). This information is important for CTV evolution, detection of specific strains, and cross-protection.
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Affiliation(s)
- Raymond Yokomi
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA, 93648-9757, USA.
| | - Vijayanandraj Selvaraj
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA, 93648-9757, USA
| | - Yogita Maheshwari
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA, 93648-9757, USA
| | - Michela Chiumenti
- Institute for Sustainable Plant Protection, Italian National Research Council, Sezione di Bari, Via Amendola 122/D, 70126, Bari, Italy
| | - Maria Saponari
- Institute for Sustainable Plant Protection, Italian National Research Council, Sezione di Bari, Via Amendola 122/D, 70126, Bari, Italy
| | - Annalisa Giampetruzzi
- Department of Soil Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | - Ziming Weng
- School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, AZ, 85721-7186, USA
| | - Zhongguo Xiong
- School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, AZ, 85721-7186, USA
| | - Subhas Hajeri
- Citrus Pest Detection Program, Central California Tristeza Eradication Agency, 22847 Road 140, Tulare, CA, 93274-9367, USA
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Giampetruzzi A, Chiumenti M, Minafra A, Saldarelli P. Small RNA Isolation from Tissues of Grapevine and Woody Plants. Methods Mol Biol 2018; 1746:27-36. [PMID: 29492883 DOI: 10.1007/978-1-4939-7683-6_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
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. The high quality of the sRNAs extracted from leaf or phloem tissues makes them suitable for all molecular biology reactions, in particular for next-generation sequencing library preparation.
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Affiliation(s)
- Annalisa Giampetruzzi
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Michela Chiumenti
- Istituto per la Protezione Sostenibile delle Piante del CNR, Bari, Italy
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Navarro B, Loconsole G, Giampetruzzi A, Aboughanem‐Sabanadzovic N, Ragozzino A, Ragozzino E, Di Serio F. Identification and characterization of privet leaf blotch-associated virus, a novel idaeovirus. Mol Plant Pathol 2017; 18:925-936. [PMID: 27349357 PMCID: PMC6638295 DOI: 10.1111/mpp.12450] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/29/2016] [Accepted: 06/22/2016] [Indexed: 05/23/2023]
Abstract
A novel virus has been identified by next-generation sequencing (NGS) in privet (Ligustrum japonicum L.) affected by a graft-transmissible disease characterized by leaf blotch symptoms resembling infectious variegation, a virus-like privet disease with an unclear aetiology. This virus, which has been tentatively named 'privet leaf blotch-associated virus' (PrLBaV), was absent in non-symptomatic privet plants, as revealed by NGS and reverse transcription-polymerase chain reaction (RT-PCR). Molecular characterization of PrLBaV showed that it has a segmented genome composed of two positive single-stranded RNAs, one of which (RNA1) is monocistronic and codes for the viral replicase, whereas the other (RNA2) contains two open reading frames (ORFs), ORF2a and ORF2b, coding for the putative movement (p38) and coat (p30) proteins, respectively. ORF2b is very probably expressed through a subgenomic RNA starting with six nucleotides (AUAUCU) that closely resemble those found in the 5'-terminal end of genomic RNA1 and RNA2 (AUAUUU and AUAUAU, respectively). The molecular signatures identified in the PrLBaV RNAs and proteins resemble those of Raspberry bushy dwarf virus (RBDV), currently the only member of the genus Idaeovirus. These data, together with phylogenetic analyses, are consistent with the proposal of considering PrLBaV as a representative of the second species in the genus Idaeovirus. Transient expression of a recombinant PrLBaV p38 fused to green fluorescent protein in leaves of Nicotiana benthamiana, coupled with confocal laser scanning microscopy assays, showed that it localizes at cell plasmodesmata, strongly supporting its involvement in viral movement/trafficking and providing the first functional characterization of an idaeovirus encoded protein.
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Affiliation(s)
- Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante CNR, UO BariVia Amendola 122/D, 70126 BariItaly
| | - Giuliana Loconsole
- Dipartimento di Scienze del Suolo, della Pianta e degli AlimentiUniversità degli Studi di Bari ‘Aldo Moro’Via Amendola 165/A, 70126 BariItaly
| | - Annalisa Giampetruzzi
- Dipartimento di Scienze del Suolo, della Pianta e degli AlimentiUniversità degli Studi di Bari ‘Aldo Moro’Via Amendola 165/A, 70126 BariItaly
| | | | - Antonio Ragozzino
- Dipartimento di AgrariaUniversità degli Studi di Napoli ‘Federico II’, Via Università100, 80055 PorticiItaly
| | - Ester Ragozzino
- Dipartimento di AgrariaUniversità degli Studi di Napoli ‘Federico II’, Via Università100, 80055 PorticiItaly
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante CNR, UO BariVia Amendola 122/D, 70126 BariItaly
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16
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Giampetruzzi A, Saponari M, Loconsole G, Boscia D, Savino VN, Almeida RPP, Zicca S, Landa BB, Chacón-Diaz C, Saldarelli P. Genome-Wide Analysis Provides Evidence on the Genetic Relatedness of the Emergent Xylella fastidiosa Genotype in Italy to Isolates from Central America. Phytopathology 2017; 107:816-827. [PMID: 28414633 DOI: 10.1094/phyto-12-16-0420-r] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Xylella fastidiosa is a plant-pathogenic bacterium recently introduced in Europe that is causing decline in olive trees in the South of Italy. Genetic studies have consistently shown that the bacterial genotype recovered from infected olive trees belongs to the sequence type ST53 within subspecies pauca. This genotype, ST53, has also been reported to occur in Costa Rica. The ancestry of ST53 was recently clarified, showing it contains alleles that are monophyletic with those of subsp. pauca in South America. To more robustly determine the phylogenetic placement of ST53 within X. fastidiosa, we performed a comparative analysis based on single nucleotide polymorphisms (SNPs) and the study of the pan-genome of the 27 currently public available whole genome sequences of X. fastidiosa. The resulting maximum-parsimony and maximum likelihood trees constructed using the SNPs and the pan-genome analysis are consistent with previously described X. fastidiosa taxonomy, distinguishing the subsp. fastidiosa, multiplex, pauca, sandyi, and morus. Within the subsp. pauca, the Italian and three Costa Rican isolates, all belonging to ST53, formed a compact phylotype in a clade divergent from the South American pauca isolates, also distinct from the recently described coffee isolate CFBP8072 imported into Europe from Ecuador. These findings were also supported by the gene characterization of a conjugative plasmid shared by all the four ST53 isolates. Furthermore, isolates of the ST53 clade possess an exclusive locus encoding a putative ATP-binding protein belonging to the family of histidine kinase-like ATPase gene, which is not present in isolates from the subspecies multiplex, sandyi, and pauca, but was detected in ST21 isolates of the subspecies fastidiosa from Costa Rica. The clustering and distinctiveness of the ST53 isolates supports the hypothesis of their common origin, and the limited genetic diversity among these isolates suggests this is an emerging clade within subsp. pauca.
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Affiliation(s)
- Annalisa Giampetruzzi
- First, third, and fifth authors: Università degli Studi di Bari Aldo Moro, Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, via Amendola 165/A, Bari, Italy; second, fourth, seventh, and tenth authors: Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, via Amendola 122/D, Bari, Italy; sixth author: Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720-3114; eighth author: Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas, 14004 Córdoba, Spain; and ninth author: Centro de Investigación en Enfermedades Tropicales (CIET), Facultad de Microbiología, Universidad de Costa Rica, 2060 San José, Costa Rica
| | - Maria Saponari
- First, third, and fifth authors: Università degli Studi di Bari Aldo Moro, Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, via Amendola 165/A, Bari, Italy; second, fourth, seventh, and tenth authors: Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, via Amendola 122/D, Bari, Italy; sixth author: Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720-3114; eighth author: Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas, 14004 Córdoba, Spain; and ninth author: Centro de Investigación en Enfermedades Tropicales (CIET), Facultad de Microbiología, Universidad de Costa Rica, 2060 San José, Costa Rica
| | - Giuliana Loconsole
- First, third, and fifth authors: Università degli Studi di Bari Aldo Moro, Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, via Amendola 165/A, Bari, Italy; second, fourth, seventh, and tenth authors: Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, via Amendola 122/D, Bari, Italy; sixth author: Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720-3114; eighth author: Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas, 14004 Córdoba, Spain; and ninth author: Centro de Investigación en Enfermedades Tropicales (CIET), Facultad de Microbiología, Universidad de Costa Rica, 2060 San José, Costa Rica
| | - Donato Boscia
- First, third, and fifth authors: Università degli Studi di Bari Aldo Moro, Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, via Amendola 165/A, Bari, Italy; second, fourth, seventh, and tenth authors: Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, via Amendola 122/D, Bari, Italy; sixth author: Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720-3114; eighth author: Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas, 14004 Córdoba, Spain; and ninth author: Centro de Investigación en Enfermedades Tropicales (CIET), Facultad de Microbiología, Universidad de Costa Rica, 2060 San José, Costa Rica
| | - Vito Nicola Savino
- First, third, and fifth authors: Università degli Studi di Bari Aldo Moro, Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, via Amendola 165/A, Bari, Italy; second, fourth, seventh, and tenth authors: Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, via Amendola 122/D, Bari, Italy; sixth author: Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720-3114; eighth author: Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas, 14004 Córdoba, Spain; and ninth author: Centro de Investigación en Enfermedades Tropicales (CIET), Facultad de Microbiología, Universidad de Costa Rica, 2060 San José, Costa Rica
| | - Rodrigo P P Almeida
- First, third, and fifth authors: Università degli Studi di Bari Aldo Moro, Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, via Amendola 165/A, Bari, Italy; second, fourth, seventh, and tenth authors: Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, via Amendola 122/D, Bari, Italy; sixth author: Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720-3114; eighth author: Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas, 14004 Córdoba, Spain; and ninth author: Centro de Investigación en Enfermedades Tropicales (CIET), Facultad de Microbiología, Universidad de Costa Rica, 2060 San José, Costa Rica
| | - Stefania Zicca
- First, third, and fifth authors: Università degli Studi di Bari Aldo Moro, Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, via Amendola 165/A, Bari, Italy; second, fourth, seventh, and tenth authors: Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, via Amendola 122/D, Bari, Italy; sixth author: Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720-3114; eighth author: Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas, 14004 Córdoba, Spain; and ninth author: Centro de Investigación en Enfermedades Tropicales (CIET), Facultad de Microbiología, Universidad de Costa Rica, 2060 San José, Costa Rica
| | - Blanca B Landa
- First, third, and fifth authors: Università degli Studi di Bari Aldo Moro, Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, via Amendola 165/A, Bari, Italy; second, fourth, seventh, and tenth authors: Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, via Amendola 122/D, Bari, Italy; sixth author: Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720-3114; eighth author: Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas, 14004 Córdoba, Spain; and ninth author: Centro de Investigación en Enfermedades Tropicales (CIET), Facultad de Microbiología, Universidad de Costa Rica, 2060 San José, Costa Rica
| | - Carlos Chacón-Diaz
- First, third, and fifth authors: Università degli Studi di Bari Aldo Moro, Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, via Amendola 165/A, Bari, Italy; second, fourth, seventh, and tenth authors: Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, via Amendola 122/D, Bari, Italy; sixth author: Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720-3114; eighth author: Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas, 14004 Córdoba, Spain; and ninth author: Centro de Investigación en Enfermedades Tropicales (CIET), Facultad de Microbiología, Universidad de Costa Rica, 2060 San José, Costa Rica
| | - Pasquale Saldarelli
- First, third, and fifth authors: Università degli Studi di Bari Aldo Moro, Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, via Amendola 165/A, Bari, Italy; second, fourth, seventh, and tenth authors: Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, via Amendola 122/D, Bari, Italy; sixth author: Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720-3114; eighth author: Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas, 14004 Córdoba, Spain; and ninth author: Centro de Investigación en Enfermedades Tropicales (CIET), Facultad de Microbiología, Universidad de Costa Rica, 2060 San José, Costa Rica
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Yokomi RK, Selvaraj V, Maheshwari Y, Saponari M, Giampetruzzi A, Chiumenti M, Hajeri S. Identification and Characterization of Citrus tristeza virus Isolates Breaking Resistance in Trifoliate Orange in California. Phytopathology 2017; 107:901-908. [PMID: 28453412 DOI: 10.1094/phyto-01-17-0007-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
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 assembled, annotated and trifoliate orange resistance-breaking (RB) isolates of CTV were identified. Phylogenetic relationships based on their full genomes placed three isolates in the RB clade: CA-RB-115, CA-RB-AT25, and CA-RB-AT35. The latter two isolates were obtained by aphid transmission from Murcott and Dekopon trees, respectively, containing CTV mixtures. The California RB isolates were further distinguished into two subclades. Group I included CA-RB-115 and CA-RB-AT25 with 99% nucleotide sequence identity with RB type strain NZRB-G90; and group II included CA-RB-AT35 with 99 and 96% sequence identity with Taiwan Pumelo/SP/T1 and HA18-9, respectively. The RB phenotype was confirmed by detecting CTV replication in graft-inoculated Poncirus trifoliata and transmission from P. trifoliata to sweet orange. The California RB isolates induced mild symptoms compared with severe isolates in greenhouse indexing tests. Further examination of 570 CTV accessions, acquired from approximately 1960 and maintained in planta at the Central California Tristeza Eradication Agency, revealed 16 RB positive isolates based on partial p65 sequences. Six isolates collected from 1992 to 2011 from Tulare and Kern counties were CA-RB-115-like; and 10 isolates collected from 1968 to 2010 from Riverside, Fresno, and Kern counties were CA-RB-AT35-like. The presence of the RB genotype is relevant because P. trifoliata and its hybrids are the most popular rootstocks in California.
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Affiliation(s)
- Raymond K Yokomi
- First, second, and third authors: U.S. Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA 93648-9757; fourth and sixth authors: Institute for Sustainable Plant Protection, National Research Council, Sezione di Bari, Via Amendola 165/A, 70126 Bari, Italy; fifth author: Department of Soil Plant and Food Science, University of Bari, Via Amendola 165/A, 70126 Bari, Italy; and seventh author: Citrus Pest Detection Program, Central California Tristeza Eradication Agency, 22847 Road 140, Tulare, CA 93274-9367
| | - Vijayanandraj Selvaraj
- First, second, and third authors: U.S. Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA 93648-9757; fourth and sixth authors: Institute for Sustainable Plant Protection, National Research Council, Sezione di Bari, Via Amendola 165/A, 70126 Bari, Italy; fifth author: Department of Soil Plant and Food Science, University of Bari, Via Amendola 165/A, 70126 Bari, Italy; and seventh author: Citrus Pest Detection Program, Central California Tristeza Eradication Agency, 22847 Road 140, Tulare, CA 93274-9367
| | - Yogita Maheshwari
- First, second, and third authors: U.S. Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA 93648-9757; fourth and sixth authors: Institute for Sustainable Plant Protection, National Research Council, Sezione di Bari, Via Amendola 165/A, 70126 Bari, Italy; fifth author: Department of Soil Plant and Food Science, University of Bari, Via Amendola 165/A, 70126 Bari, Italy; and seventh author: Citrus Pest Detection Program, Central California Tristeza Eradication Agency, 22847 Road 140, Tulare, CA 93274-9367
| | - Maria Saponari
- First, second, and third authors: U.S. Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA 93648-9757; fourth and sixth authors: Institute for Sustainable Plant Protection, National Research Council, Sezione di Bari, Via Amendola 165/A, 70126 Bari, Italy; fifth author: Department of Soil Plant and Food Science, University of Bari, Via Amendola 165/A, 70126 Bari, Italy; and seventh author: Citrus Pest Detection Program, Central California Tristeza Eradication Agency, 22847 Road 140, Tulare, CA 93274-9367
| | - Annalisa Giampetruzzi
- First, second, and third authors: U.S. Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA 93648-9757; fourth and sixth authors: Institute for Sustainable Plant Protection, National Research Council, Sezione di Bari, Via Amendola 165/A, 70126 Bari, Italy; fifth author: Department of Soil Plant and Food Science, University of Bari, Via Amendola 165/A, 70126 Bari, Italy; and seventh author: Citrus Pest Detection Program, Central California Tristeza Eradication Agency, 22847 Road 140, Tulare, CA 93274-9367
| | - Michela Chiumenti
- First, second, and third authors: U.S. Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA 93648-9757; fourth and sixth authors: Institute for Sustainable Plant Protection, National Research Council, Sezione di Bari, Via Amendola 165/A, 70126 Bari, Italy; fifth author: Department of Soil Plant and Food Science, University of Bari, Via Amendola 165/A, 70126 Bari, Italy; and seventh author: Citrus Pest Detection Program, Central California Tristeza Eradication Agency, 22847 Road 140, Tulare, CA 93274-9367
| | - Subhas Hajeri
- First, second, and third authors: U.S. Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA 93648-9757; fourth and sixth authors: Institute for Sustainable Plant Protection, National Research Council, Sezione di Bari, Via Amendola 165/A, 70126 Bari, Italy; fifth author: Department of Soil Plant and Food Science, University of Bari, Via Amendola 165/A, 70126 Bari, Italy; and seventh author: Citrus Pest Detection Program, Central California Tristeza Eradication Agency, 22847 Road 140, Tulare, CA 93274-9367
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18
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Cox SN, Pesce F, El-Sayed Moustafa JS, Sallustio F, Serino G, Kkoufou C, Giampetruzzi A, Ancona N, Falchi M, Schena FP. Multiple rare genetic variants co-segregating with familial IgA nephropathy all act within a single immune-related network. J Intern Med 2017; 281:189-205. [PMID: 27730700 PMCID: PMC5297991 DOI: 10.1111/joim.12565] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND IgA nephropathy (IgAN) is a common complex disease with a strong genetic involvement. We aimed to identify novel, rare, highly penetrant risk variants combining family-based linkage analysis with whole-exome sequencing (WES). METHODS Linkage analysis of 16 kindreds of South Italian ancestry was performed using an 'affected-only' strategy. Eight most informative trios composed of two familial cases and an intrafamilial control were selected for WES. High-priority variants in linked regions were identified and validated using Sanger sequencing. Custom TaqMan assays were designed and carried out in the 16 kindreds and an independent cohort of 240 IgAN patients and 113 control subjects. RESULTS We found suggestive linkage signals in 12 loci. After sequential filtering and validation of WES data, we identified 24 private or extremely rare (MAF <0.0003) linked variants segregating with IgAN status. These were present within coding or regulatory regions of 23 genes that merged into a common functional network. The genes were interconnected by AKT, CTNNB1, NFKB, MYC and UBC, key modulators of WNT/β-catenin and PI3K/Akt pathways, which are implicated in IgAN pathogenesis. Overlaying publicly available expression data, genes/proteins with expression notably altered in IgAN were included in this immune-related network. In particular, the network included the glucocorticoid receptor gene, NR3C1, which is the target of corticosteroid therapy routinely used in the treatment of IgAN. CONCLUSION Our findings suggest that disease susceptibility could be influenced by multiple rare variants acting in a common network that could provide the starting point for the identification of potential drug targets for personalized therapy.
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Affiliation(s)
- S N Cox
- Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy.,C.A.R.S.O. Consortium, University of Bari, Bari, Italy
| | - F Pesce
- Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy.,Department of Genomics of Common Disease, Imperial College London, London, UK
| | - J S El-Sayed Moustafa
- Department of Genomics of Common Disease, Imperial College London, London, UK.,Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - F Sallustio
- Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy
| | - G Serino
- Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy.,IRCCS 'de Bellis', Laboratory of Experimental Immunopathology, Bari, Italy
| | - C Kkoufou
- Department of Genomics of Common Disease, Imperial College London, London, UK
| | - A Giampetruzzi
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | | | - M Falchi
- Department of Genomics of Common Disease, Imperial College London, London, UK.,Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - F P Schena
- Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy.,C.A.R.S.O. Consortium, University of Bari, Bari, Italy
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Morelli M, Giampetruzzi A, Laghezza L, Catalano L, Savino VN, Saldarelli P. Identification and characterization of an isolate of apple green crinkle associated virus involved in a severe disease of quince (Cydonia oblonga, Mill.). Arch Virol 2016; 162:299-306. [PMID: 27709400 DOI: 10.1007/s00705-016-3074-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 09/17/2016] [Indexed: 12/01/2022]
Abstract
A quince tree showing severe symptoms of a previously undescribed viral disease occurring in northern Apulia (Italy) was analysed using high-throughput sequencing of small RNA libraries, leading to the identification of a new strain of apple green crinkle associated virus (isolate AGCaV-CYD) showing peculiar traits. RT-PCR with specific primers detected AGCaV-CYD in consistent association with symptoms in the surveyed orchards. Molecular characterization of the reconstructed genome, together with phylogenetic analysis, showed it to be closely related to an AGCaV strain causing green crinkle disease in apple (AGCaV-AUR) and divergent from the type strain of apple stem pitting virus (ASPV-PA66).
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Affiliation(s)
- Massimiliano Morelli
- CNR-Istituto per la Protezione Sostenibile delle Piante (IPSP), Via Amendola 122/D, 70126, Bari, Italy.
| | - Annalisa Giampetruzzi
- CNR-Istituto per la Protezione Sostenibile delle Piante (IPSP), Via Amendola 122/D, 70126, Bari, Italy
| | - Lorenzo Laghezza
- Agrimeca Grape and Fruit Consulting S.r.l., Via Elefante 17, 70010, Turi, Bari, Italy
| | - Luigi Catalano
- Agrimeca Grape and Fruit Consulting S.r.l., Via Elefante 17, 70010, Turi, Bari, Italy
| | - Vito Nicola Savino
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi Aldo Moro, Bari, Italy
| | - Pasquale Saldarelli
- CNR-Istituto per la Protezione Sostenibile delle Piante (IPSP), Via Amendola 122/D, 70126, Bari, Italy
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20
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Giampetruzzi A, Morelli M, Saponari M, Loconsole G, Chiumenti M, Boscia D, Savino VN, Martelli GP, Saldarelli P. Transcriptome profiling of two olive cultivars in response to infection by the CoDiRO strain of Xylella fastidiosa subsp. pauca. BMC Genomics 2016; 17:475. [PMID: 27350531 PMCID: PMC4924284 DOI: 10.1186/s12864-016-2833-9] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/13/2016] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The recent Xylella fastidiosa subsp. pauca (Xfp) outbreak in olive (Olea europaea) groves in southern Italy is causing a destructive disease denoted Olive Quick Decline Syndrome (OQDS). Field observations disclosed that Xfp-infected plants of cv. Leccino show much milder symptoms, than the more widely grown and highly susceptible cv. Ogliarola salentina. To determine whether these field observations underlie a tolerant condition of cv. Leccino, which could be exploited for lessening the economic impact of the disease on the local olive industry, transcriptional changes occurring in plants of the two cultivars affected by Xfp were investigated. RESULTS A global quantitative transcriptome profiling comparing susceptible (Ogliarola salentina) and tolerant (Leccino) olive cultivars, infected or not by Xfp, was done on messenger RNA (mRNAs) extracted from xylem tissues. The study revealed that 659 and 447 genes were differentially regulated in cvs Leccino and Ogliarola upon Xfp infection, respectively, whereas 512 genes were altered when the transcriptome of both infected cultivars was compared. Analysis of these differentially expressed genes (DEGs) shows that the presence of Xfp is perceived by the plants of both cultivars, in which it triggers a differential response strongly involving the cell wall. Up-regulation of genes encoding receptor-like kinases (RLK) and receptor-like proteins (RLP) is the predominant response of cv. Leccino, which is missing in cv. Ogliarola salentina. Moreover, both cultivars react with a strong re-modelling of cell wall proteins. These data suggest that Xfp elicits a different transcriptome response in the two cultivars, which determines a lower pathogen concentration in cv. Leccino and indicates that this cultivar may harbor genetic constituents and/or regulatory elements which counteract Xfp infection. CONCLUSIONS Collectively these findings suggest that cv. Leccino is endowed with an intrinsic tolerance to Xfp, which makes it eligible for further studies aiming at investigating molecular basis and pathways modulating its different defense response.
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Affiliation(s)
- Annalisa Giampetruzzi
- />Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, via Amendola 165/A, Bari, Italy
| | - Massimiliano Morelli
- />Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, SS Bari, via Amendola 122/D, Bari, Italy
| | - Maria Saponari
- />Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, SS Bari, via Amendola 122/D, Bari, Italy
| | - Giuliana Loconsole
- />Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, via Amendola 165/A, Bari, Italy
| | - Michela Chiumenti
- />Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, SS Bari, via Amendola 122/D, Bari, Italy
| | - Donato Boscia
- />Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, SS Bari, via Amendola 122/D, Bari, Italy
| | - Vito N. Savino
- />Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, via Amendola 165/A, Bari, Italy
| | - Giovanni P. Martelli
- />Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, via Amendola 165/A, Bari, Italy
| | - Pasquale Saldarelli
- />Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, SS Bari, via Amendola 122/D, Bari, Italy
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21
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Cox SN, Pesce F, El-Sayed Moustafa JS, Sallustio F, Serino G, Giampetruzzi A, Ancona N, Falchi M, Schena FP. MO062RARE GENETIC VARIANTS IMPLICATED IN INNATE AND ADAPTIVE IMMUNITY CO-SEGREGATE WITH FAMILIAL IGA NEPHROPATHY. Nephrol Dial Transplant 2016. [DOI: 10.1093/ndt/gfw141.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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22
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Chiumenti M, Giampetruzzi A, Morelli M, Savino VN, Martelli GP, La Notte P, Palmisano F, Saldarelli P. Detection and molecular characterization of a Grapevine Roditis leaf discoloration-associated virus (GRLDaV) variant in an autochthonous grape from Apulia (Italy). Virus Genes 2016; 52:428-31. [PMID: 26924587 DOI: 10.1007/s11262-016-1305-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/16/2016] [Indexed: 11/26/2022]
Abstract
The complete nucleotide sequence and genome organization of a new Badnavirus isolated from the autochthonous grapevine variety "Bombino nero" from Apulia (Italy) was determined. The genome of this virus consists of 7097 nt and has four open reading frames (ORFs). Analysis of putative proteins encoded by each ORF revealed greatest sequence similarity to Grapevine Roditis leaf discoloration-associated virus w4 (GRLDaV; NC_027131). In a pairwise alignment with GLRDaV w4 genome sequence, the "Bombino Nero" sequence was 109 nt longer with a major 57 nt insertion between positions 2405 and 2413. Furthermore, its putative ORF4 is located after the ORF3, while in the GLRDaV w4 sequence, the putative ORF4 completely overlapped ORF3. Nucleotide analysis classifies this new Badnavirus as a GLRDaV strain, which was named GRLDaV-BN. Multi-year field observations showed that the GLRDaV-BN-infected vine was symptomless.
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Affiliation(s)
- Michela Chiumenti
- CNR-Istituto per la Protezione Sostenibile delle Piante (IPSP), UOS Bari, Via Amendola 122/D, 70126, Bari, Italy.
| | - Annalisa Giampetruzzi
- CNR-Istituto per la Protezione Sostenibile delle Piante (IPSP), UOS Bari, Via Amendola 122/D, 70126, Bari, Italy
| | - Massimiliano Morelli
- CNR-Istituto per la Protezione Sostenibile delle Piante (IPSP), UOS Bari, Via Amendola 122/D, 70126, Bari, Italy
| | - Vito Nicola Savino
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti (DiSSPA), Università degli Studi di Bari Aldo Moro, 70126, Bari, Italy
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura (CRSFA) "Basile Caramia", Locorotondo, 70010, Bari, Italy
| | - Giovanni Paolo Martelli
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti (DiSSPA), Università degli Studi di Bari Aldo Moro, 70126, Bari, Italy
| | - Pierfederico La Notte
- CNR-Istituto per la Protezione Sostenibile delle Piante (IPSP), UOS Bari, Via Amendola 122/D, 70126, Bari, Italy
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura (CRSFA) "Basile Caramia", Locorotondo, 70010, Bari, Italy
| | - Francesco Palmisano
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura (CRSFA) "Basile Caramia", Locorotondo, 70010, Bari, Italy
| | - Pasquale Saldarelli
- CNR-Istituto per la Protezione Sostenibile delle Piante (IPSP), UOS Bari, Via Amendola 122/D, 70126, Bari, Italy
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23
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Giampetruzzi A, Loconsole G, Boscia D, Calzolari A, Chiumenti M, Martelli GP, Saldarelli P, Almeida RPP, Saponari M. Draft Genome Sequence of CO33, a Coffee-Infecting Isolate of Xylella fastidiosa. Genome Announc 2015; 3:e01472-15. [PMID: 26679584 PMCID: PMC4683229 DOI: 10.1128/genomea.01472-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 10/30/2015] [Indexed: 11/20/2022]
Abstract
The draft genome sequence of Xylella fastidiosa CO33 isolate, retrieved from symptomatic leaves of coffee plant intercepted in northern Italy, is reported. The CO33 genome size is 2,681,926 bp with a GC content of 51.7%.
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Affiliation(s)
- Annalisa Giampetruzzi
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Giuliana Loconsole
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Donato Boscia
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | | | - Michela Chiumenti
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Giovanni P Martelli
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Pasquale Saldarelli
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
| | - Maria Saponari
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
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24
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Licciardello G, Scuderi G, Ferraro R, Giampetruzzi A, Russo M, Lombardo A, Raspagliesi D, Bar-Joseph M, Catara A. Deep sequencing and analysis of small RNAs in sweet orange grafted on sour orange infected with two citrus tristeza virus isolates prevalent in Sicily. Arch Virol 2015; 160:2583-9. [PMID: 26175068 DOI: 10.1007/s00705-015-2516-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 06/29/2015] [Indexed: 01/30/2023]
Abstract
Two representative isolates of a citrus tristeza virus population in Sicily, SG29 (aggressive) and Bau282 (mild), were sequenced via viral small RNAs (vsRNA) produced in budlings of sweet orange grafted on sour orange. Phylogenetic relationships with Mediterranean and exotic isolates revealed that SG29 clustered within the "VT-Asian" subtype, whereas Bau282 belonged to the cluster T30. The study confirms that molecular data need to be integrated with bio-indexing in order to obtain adequate information for risk assessment.
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Affiliation(s)
- Grazia Licciardello
- Parco Scientifico e Tecnologico della Sicilia, z.i. Blocco Palma I, Str. le Lancia 57, 95121, Catania, Italy.
| | - Giuseppe Scuderi
- Parco Scientifico e Tecnologico della Sicilia, z.i. Blocco Palma I, Str. le Lancia 57, 95121, Catania, Italy
| | - Rosario Ferraro
- Parco Scientifico e Tecnologico della Sicilia, z.i. Blocco Palma I, Str. le Lancia 57, 95121, Catania, Italy
| | - Annalisa Giampetruzzi
- CNR, Institute for Sustainable Plant Protection, Via Amendola 165/A, 70126, Bari, Italy
| | - Marcella Russo
- Parco Scientifico e Tecnologico della Sicilia, z.i. Blocco Palma I, Str. le Lancia 57, 95121, Catania, Italy
| | - Alessandro Lombardo
- Parco Scientifico e Tecnologico della Sicilia, z.i. Blocco Palma I, Str. le Lancia 57, 95121, Catania, Italy
| | - Domenico Raspagliesi
- Parco Scientifico e Tecnologico della Sicilia, z.i. Blocco Palma I, Str. le Lancia 57, 95121, Catania, Italy
| | | | - Antonino Catara
- Parco Scientifico e Tecnologico della Sicilia, z.i. Blocco Palma I, Str. le Lancia 57, 95121, Catania, Italy
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Cox SN, Pesce F, Moustafa JSE, Sallustio F, Serino G, Giampetruzzi A, Ancona N, Falchi M, Schena FP. SP006FAMILY-BASED LINKAGE ANALYSIS AND FULL EXOME SEQUENCING FOR THE IDENTIFICATION OF POTENTIAL RISK VARIANTS IN IGA NEPHROPATHY. Nephrol Dial Transplant 2015. [DOI: 10.1093/ndt/gfv187.06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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26
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Saldarelli P, Giampetruzzi A, Morelli M, Malossini U, Pirolo C, Bianchedi P, Gualandri V. Genetic Variability of Grapevine Pinot gris virus and Its Association with Grapevine Leaf Mottling and Deformation. Phytopathology 2015; 105:555-563. [PMID: 25423070 DOI: 10.1094/phyto-09-14-0241-r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The role of Grapevine Pinot gris virus (GPGV) in the etiology of grapevine leaf mottling and deformation was investigated by biological and molecular assays. A survey on different cultivars from the Trentino Region in Italy showed a widespread distribution of GPGV, which was associated with symptomatic (79%) but also with symptomless (21%) vines. Symptomatic and GPGV-infected 'Pinot gris' vines induced symptoms on grafted vines of healthy Pinot gris or 'Traminer', whereas GPGV-infected but symptomless vines did not. High-throughput sequencing of small RNA (sRNA) populations of two infected Pinot gris accessions confirmed the existence of nearly overlapping viromes in vines with or without symptoms but phylogenetic analyses of the genomes of seven GPGV isolates from Italy and the Czech and Slovak Republics clearly differentiated those infecting symptomatic vines. The involvement of Grapevine rupestris vein feathering virus (GRVFV) in the disease, which was only infecting the symptomatic vine, was ruled out by reverse-transcription polymerase chain reaction studies. Maximum likelihood and Bayesian phylogenetic analysis of two GPGV genomic regions, encompassing part of the movement protein (MP) and coat protein gene sequences and the RNA-dependent RNA polymerase domain of the replicase gene, showed that isolates from symptomatic vines form a lineage distinct from that of symptomless vines. Moreover, the presence or lack of the MP stop codon identified in viral isolates from symptomatic or symptomless vines, respectively, is likely responsible for an MP six amino acids longer in symptomless isolates.
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Affiliation(s)
- P Saldarelli
- First, second, third, and fifth authors: CNR Istituto per la Protezione Sostenibile delle Piante, UOS-Bari, and Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari via Amendola 165/A, 70126, Bari, Italy; and fourth, sixth, and seventh authors: FEM-IASMA, Centre for Technology Transfer, via E. Mach 1, 38010, San Michele all'Adige (Trento), Italy
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27
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Garcia-Ruiz H, Carbonell A, Hoyer JS, Fahlgren N, Gilbert KB, Takeda A, Giampetruzzi A, Garcia Ruiz MT, McGinn MG, Lowery N, Martinez Baladejo MT, Carrington JC. Roles and programming of Arabidopsis ARGONAUTE proteins during Turnip mosaic virus infection. PLoS Pathog 2015; 11:e1004755. [PMID: 25806948 PMCID: PMC4373807 DOI: 10.1371/journal.ppat.1004755] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/19/2015] [Indexed: 11/24/2022] Open
Abstract
In eukaryotes, ARGONAUTE proteins (AGOs) associate with microRNAs (miRNAs), short interfering RNAs (siRNAs), and other classes of small RNAs to regulate target RNA or target loci. Viral infection in plants induces a potent and highly specific antiviral RNA silencing response characterized by the formation of virus-derived siRNAs. Arabidopsis thaliana has ten AGO genes of which AGO1, AGO2, and AGO7 have been shown to play roles in antiviral defense. A genetic analysis was used to identify and characterize the roles of AGO proteins in antiviral defense against Turnip mosaic virus (TuMV) in Arabidopsis. AGO1, AGO2 and AGO10 promoted anti-TuMV defense in a modular way in various organs, with AGO2 providing a prominent antiviral role in leaves. AGO5, AGO7 and AGO10 had minor effects in leaves. AGO1 and AGO10 had overlapping antiviral functions in inflorescence tissues after systemic movement of the virus, although the roles of AGO1 and AGO10 accounted for only a minor amount of the overall antiviral activity. By combining AGO protein immunoprecipitation with high-throughput sequencing of associated small RNAs, AGO2, AGO10, and to a lesser extent AGO1 were shown to associate with siRNAs derived from silencing suppressor (HC-Pro)-deficient TuMV-AS9, but not with siRNAs derived from wild-type TuMV. Co-immunoprecipitation and small RNA sequencing revealed that viral siRNAs broadly associated with wild-type HC-Pro during TuMV infection. These results support the hypothesis that suppression of antiviral silencing during TuMV infection, at least in part, occurs through sequestration of virus-derived siRNAs away from antiviral AGO proteins by HC-Pro. These findings indicate that distinct AGO proteins function as antiviral modules, and provide a molecular explanation for the silencing suppressor activity of HC-Pro. RNA silencing is a primary, adaptive defense system against viruses in plants. Viruses have evolved counter-defensive mechanisms that inhibit RNA silencing through the activity of silencing suppressor proteins. Understanding how antiviral silencing is controlled, and how suppressor proteins function, is essential for understanding how plants normally resist viruses, why some viruses are highly virulent in different hosts, and how sustainable antiviral resistance strategies can be deployed in agricultural settings. We used a mutant version of Turnip mosaic virus lacking a functional silencing suppressor (HC-Pro) to understand the genetic requirements for resistance in the model plant Arabidopsis thaliana. We focused on ARGONAUTE proteins, which have long been hypothesized to bind short interfering RNAs (siRNAs) derived from virus genomes for use as sequence-specific guides to recognize and target viral RNA for degradation or repression. We demonstrated specialized antiviral roles for specific ARGONAUTES and showed that several can bind viral siRNAs from across the entire viral genome. However, ARGONAUTE proteins are only loaded with virus-derived siRNAs in the absence of HC-Pro, which we showed binds siRNAs from the viral genome. This indicates that several AGO proteins, which collectively are necessary for full anti-TuMV defense, need to properly load virus-derived siRNAs to execute their antiviral roles.
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Affiliation(s)
- Hernan Garcia-Ruiz
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Alberto Carbonell
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - J. Steen Hoyer
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Computational and Systems Biology Program, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Noah Fahlgren
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Kerrigan B. Gilbert
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Atsushi Takeda
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Annalisa Giampetruzzi
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Mayra T. Garcia Ruiz
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Michaela G. McGinn
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Nicholas Lowery
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | | | - James C. Carrington
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
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Giampetruzzi A, Chiumenti M, Saponari M, Donvito G, Italiano A, Loconsole G, Boscia D, Cariddi C, Martelli GP, Saldarelli P. Draft Genome Sequence of the Xylella fastidiosa CoDiRO Strain. Genome Announc 2015; 3:e01538-14. [PMID: 25676759 PMCID: PMC4333659 DOI: 10.1128/genomea.01538-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 01/05/2015] [Indexed: 11/22/2022]
Abstract
We determined the draft genome sequence of the Xylella fastidiosa CoDiRO strain, which has been isolated from olive plants in southern Italy (Apulia). It is associated with olive quick decline syndrome (OQDS) and characterized by extensive scorching and desiccation of leaves and twigs.
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Affiliation(s)
- Annalisa Giampetruzzi
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Michela Chiumenti
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Maria Saponari
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Giacinto Donvito
- Department of Physics, University of Bari Aldo Moro, Bari, Italy
| | | | - Giuliana Loconsole
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Donato Boscia
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Corrado Cariddi
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | | | - Pasquale Saldarelli
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
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29
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Loconsole G, Onelge N, Potere O, Giampetruzzi A, Bozan O, Satar S, De Stradis A, Savino V, Yokomi RK, Saponari M. Identification and characterization of citrus yellow vein clearing virus, a putative new member of the genus Mandarivirus. Phytopathology 2012; 102:1168-75. [PMID: 22913410 DOI: 10.1094/phyto-06-12-0140-r] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Molecular features and genomic organization were determined for Citrus yellow vein clearing virus (CYVCV), the putative viral causal agent of yellow vein clearing disease of lemon trees, reported in Pakistan, India, and more recently in Turkey and China. CYVCV isolate Y1 from Adana, Turkey, was used for deep sequencing analysis of the virus-induced small RNA fractions and for mechanical and graft inoculation of herbaceous and citrus indicator plants. A polyclonal antiserum was developed from CYVCV-Y1 purified from Phaseolus vulgaris and used in western blot assays to characterize the coat protein of CYVCV-Y1 and determine its serological relationship with related viruses. Contigs assembled from the Illumina sequenced short reads were used to construct the whole genome of Citrus yellow vein clearing virus (CYVCV), consisting in a positive-sense RNA of 7,529 nucleotides and containing six predicted open reading frames. The CYVCV genome organization and size resembled that of flexiviruses, and search for sequence homologies revealed that Indian citrus ringspot virus (ICRSV) (Mandarivirus, Alphaflexiviridae) is the most closely related virus. However, CYVCV had an overall nucleotide sequence identity of ≈74% with ICRSV. Although the two viruses were similar with regard to genome organization, viral particles, and herbaceous host range, CYVCV caused different symptoms in citrus and was serologically distinct from ICRSV. Primer pairs were designed and used to detect the virus by conventional and quantitative reverse transcription-polymerase chain reaction on yellow vein clearing symptomatic field trees as well as graft- and mechanically inoculated host plants. Collectively, these data suggest that CYVCV is the causal agent of yellow vein clearing disease and represents a new species in the genus Mandarivirus.
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Affiliation(s)
- G Loconsole
- Dipartimento di Scienze del Suolo, Della Pianta e Alimenti, Università di Bari "Aldo Moro", Italy
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30
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Giampetruzzi A, Roumi V, Roberto R, Malossini U, Yoshikawa N, La Notte P, Terlizzi F, Credi R, Saldarelli P. A new grapevine virus discovered by deep sequencing of virus- and viroid-derived small RNAs in Cv Pinot gris. Virus Res 2012; 163:262-8. [DOI: 10.1016/j.virusres.2011.10.010] [Citation(s) in RCA: 189] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 10/12/2011] [Accepted: 10/15/2011] [Indexed: 12/13/2022]
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31
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Pantaleo V, Saldarelli P, Miozzi L, Giampetruzzi A, Gisel A, Moxon S, Dalmay T, Bisztray G, Burgyan J. Deep sequencing analysis of viral short RNAs from an infected Pinot Noir grapevine. Virology 2010; 408:49-56. [PMID: 20875658 DOI: 10.1016/j.virol.2010.09.001] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 07/16/2010] [Accepted: 09/01/2010] [Indexed: 01/20/2023]
Abstract
Virus-derived short interfering RNAs (vsiRNAs) isolated from grapevine V. vinifera Pinot Noir clone ENTAV 115 were analyzed by high-throughput sequencing using the Illumina Solexa platform. We identified and characterized vsiRNAs derived from grapevine field plants naturally infected with different viruses belonging to the genera Foveavirus, Maculavirus, Marafivirus and Nepovirus. These vsiRNAs were mainly of 21 and 22 nucleotides (nt) in size and were discontinuously distributed throughout Grapevine rupestris stem-pitting associated virus (GRSPaV) and Grapevine fleck virus (GFkV) genomic RNAs. Among the studied viruses, GRSPaV and GFkV vsiRNAs had a 5' terminal nucleotide bias, which differed from that described for experimental viral infections in Arabidopsis thaliana. VsiRNAs were found to originate from both genomic and antigenomic GRSPaV RNA strands, whereas with the grapevine tymoviruses GFkV and Grapevine Red Globe associated virus (GRGV), the large majority derived from the antigenomic viral strand, a feature never observed in other plant-virus interactions.
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Affiliation(s)
- Vitantonio Pantaleo
- Istituto di Virologia Vegetale del C.N.R., Strada delle Cacce 73, Turin, Italy.
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