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21دورية أكاديمية
المؤلفون: Rott, Philippe, Chatenet, Michèle, Mazarin, Candy, Fernandez, Emmanuel, Gargani, Daniel, Royer, Monique, Rao, Govind P., Lockhart, Ben E. L., Girard, Jean-Claude
المصدر: Sugar Tech; Oct2023, Vol. 25 Issue 5, p1134-1143, 10p
مستخلص: Five sugarcane leaf samples exhibiting mosaic symptoms and collected in 1999–2003 in Bangladesh, India, Sri Lanka, Thailand, and Vietnam tested negative in serological assays (ELISA and TBIA) using antiserum to sugarcane mosaic virus (SCMV) and a potyvirus specific monoclonal antibody. In addition, these samples reacted negative in RT-PCR assays with SCMV, sorghum mosaic virus (SrMV), and potyvirus specific primers. Mosaic symptoms were reproduced after mechanical inoculation of sugarcane, maize, and sorghum plants with diseased leaf extracts, but symptoms were less severe than those of SCMV and SrMV. Electron microscopy of partially purified virions from inoculated plants showed flexuous filaments characteristic of the Potyviridae family. The five sugarcane leaf samples tested positive in RT-PCR assays with two primer pairs designed to detect sugarcane streak mosaic virus (SCSMV), and in immunological assays with SCSMV antisera. SCSMV was detected by ELISA with three different antisera and by RT-PCR in 34 leaf samples from 30 cultivars exhibiting mosaic symptoms and originating from six Asian countries (the five mentioned above and Pakistan). The sequences of the RT-PCR amplicons (376 nucleotides) showed 98.5–100% identity with SCSMV isolates from GenBank. The immunological, molecular, and pathogenic characteristics of SCSMV were different from those of SCMV and SrMV. Our results suggested that SCSMV was already widespread in Asia more than two decades ago. Furthermore, immunological variation occurs among SCSMV isolates, which needs to be considered for serological diagnosis of the virus. RT-PCR primers developed in this study proved to be very efficient for detection of SCSMV from different countries. [ABSTRACT FROM AUTHOR]
: Copyright of Sugar Tech is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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22مؤتمر
المؤلفون: Bernardo, Pauline, Charles-Dominique, Tristan, Barakat, Mohamed, Ortet, Philippe, Fernandez, Emmanuel, Filloux, Denis, Hartnady, Penelope, Rebelo, Tony A., Cousins, Stephen, Mesleard, François, Cohez, Damien, Yaverkovski, Nicole, Varsani, Arvind, Harkins, Gordon William, Peterschmitt, Michel, Malmstrom, Carolyn, Martin, Darren Patrick, Roumagnac, Philippe
المصدر: Book of abstract Pathobiome 2018
الوصف: Disease emergence events regularly result from human activities such as agriculture, which frequently brings large populations of genetically uniform hosts into contact with potential pathogens. Although viruses cause nearly 50% of emerging plant diseases, there is little systematic information about virus distribution across agro‐ecological interfaces and large gaps in understanding of virus diversity in nature. Here we applied a novel landscape‐scale geometagenomics approach to examine relationships between agricultural land use and distributions of plant‐associated viruses in two Mediterranean‐climate biodiversity hotspots (Western Cape region of South Africa and Rhône river delta region of France). In total, we analysed 1725 geo‐referenced plant samples collected over two years from 4.5 km x 4.5 km grids spanning farmlands and adjacent uncultivated vegetation. We found substantial virus prevalence (25.8–35.9%) in all ecosystems, but prevalence and identified family‐level virus diversity were greatest in cultivated areas, with some virus families displaying strong agricultural associations. Our survey revealed 94 previously unknown virus species, primarily from uncultivated plants. This is the first effort to systematically evaluate plant‐associated viromes across broad agro‐ecological interfaces. Our findings indicate that agriculture substantially influences plant virus distributions and highlight the extent of current ignorance about the diversity and roles of viruses in nature.
وصف الملف: text
العلاقة: http://agritrop.cirad.fr/587557Test/; Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale. O13. Bernardo Pauline, Charles-Dominique Tristan, Barakat Mohamed, Ortet Philippe, Fernandez Emmanuel, Filloux Denis, Hartnady Penelope, Rebelo Tony A., Cousins Stephen, Mesleard François, Cohez Damien, Yaverkovski Nicole, Varsani Arvind, Harkins Gordon William, Peterschmitt Michel, Malmstrom Carolyn, Martin Darren Patrick, Roumagnac Philippe. 2018. In : Book of abstract Pathobiome 2018. INRA. Ajaccio : INRA, Résumé, 25-26. Pathobiome, Ajaccio, France, 18 Mars 2018/20 Mars 2018.https://colloque.inra.fr/pathobiome-2018/Abstract-book/Abstract-bookTest; http://agritrop.cirad.fr/587557/1/ID587557.pdfTest
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23مؤتمر
المؤلفون: Poulicard, Nils, Dereeper, Alexis, Pinel-Galzi, Agnès, Fernandez, Emmanuel, Julian, Charlotte, Hubert, Judith, Filloux, Denis, Fargette, Denis, Roumagnac, Philippe, Hebrard, Eugénie
المصدر: Book of abstract of the International Phytobiomes Conference 2018
الوصف: The virome is an essential component of the phytobiome as viruses correspond to the most abundant and diverse biological entity in Nature and interact with all living organisms. The recent advances in high-throughput sequencing (HTS) has proven efficient for characterizing within-host diversity of several viruses, which has shed light on the influence of this diversity on the global fitness and virulence of viruses. We here aimed at evaluating the impact of rice management on the within-host diversity of Rice yellow mottle virus (RYMV) in order to optimize the cultural practices and to limit the burden of Rice yellow mottle disease in Africa. We worked on rice plants collected from traditional and intensive rice fields in East Africa, which is the center of origin of Rice yellow mottle virus. Interestingly, several strains with contrasted pathogenic and epidemiological parameters co -exist in this region and recombination between strains were identified recently. We selected twelve RYMV sympto-matic samples from fields managed under different types of practices that were analyzed using two HTS strategies: a metagenomics-based approach and a RYMV specific sequencing approach. Combining both strategies, we tested if the RYMV was associated with other viral species in rice, and if some cases of co-infections between RYMV strains occurred. Both approaches indicate a significant within-host RYMV diversity, which allows us to perceive the diversification processes of RYMV strains at the field scale. The detection of recombinants and the comparison of the within-host genetic diversity depending on the cultivation practices are underway.
وصف الملف: text
العلاقة: http://agritrop.cirad.fr/591982Test/; Exploring within-host diversity of plant viruses in rice agrosystems using two high-throughput sequencing strategies. Poulicard Nils, Dereeper Alexis, Pinel-Galzi Agnès, Fernandez Emmanuel, Julian Charlotte, Hubert Judith, Filloux Denis, Fargette Denis, Roumagnac Philippe, Hebrard Eugénie. 2018. In : Book of abstract of the International Phytobiomes Conference 2018. International Phytobiomes Alliance, INRA, IRD. Montpellier : International Phytobiomes Alliance-INRA, 68. International phytobiomes conference. 2, Montpellier, France, 4 Décembre 2018/6 Décembre 2018.http://phytobiomesconference.org/wp-content/uploads/2018/12/Phytobiomes-Conference-2018_Abstract-book-FINAL.pdfTest; http://agritrop.cirad.fr/591982/1/ID591982.pdfTest
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24مؤتمر
المؤلفون: Alonso, Pascal, Filloux, Denis, Blondin, Laurence, Mahé, Frédéric, Fournier, Elisabeth, Gladieux, Pierre, Ducasse, Aurélie, Morel, Jean-Benoit, Mournet, Pierre, Huang, Huichuan, Jin, Baihui, He, Xiahong, Ferdinand, Romain, Fernandez, Emmanuel, Vernière, Christian, Roumagnac, Philippe
المصدر: Book of abstract of the International Phytobiomes Conference 2018
الوصف: Plant microbial communities may moderate the plant responses to different abiotic or biotic stresses like pathogens. On the other hand, plant genotypes may influence the composition and structure of the plant microbiota. In the Chinese Yuanyang terraces (YYT), a sustainable rice disease control has been achieved for centuries using mixtures of traditional genetically diverse rice varieties harboring a wide panel of resistance genes. However, this centuries-old agrosystem is currently challenged by the introduction of several “modern” rice varieties. The potential simplification of the rice varietal landscape is likely to drive a modification of the rice microbiota, which may have an impact on the plant-pathogen dynamics, and further on the frequency, extent and impact of disease emergence events. We here investigated the microbial communities (bacteria, fungi and viruses) associated with roots and aerial organs from eleven and eight YYT fields cultivated with traditional and “modern” rice varieties, respectively. Besides using a genotyping-by-sequencing approach (GBS) to decipher the rice genetic diversity, microbial communities were characterized by metagenomics approaches. The GBS approach confirms a shift of the rice genetic diversity and split the varieties into three lineages (traditional varieties, “modern” introduced varieties and one Japonica traditional variety). Metagenomics approaches show that microbial communities from aerial organs are lineage-dependent and that microbial communities from the roots are more homogeneous and not different among rice lineages. Interestingly, our study reveals a high prevalence (15%) of Southern rice black-streaked dwarf virus in Yuanyang terraces, and that this virus is significantly more prevalent in traditional local varieties.
وصف الملف: text
العلاقة: http://agritrop.cirad.fr/591698Test/; Rice genetic diversity and microbiome characterization of a centuries-old Chinese rice agro-system. Alonso Pascal, Filloux Denis, Blondin Laurence, Mahé Frédéric, Fournier Elisabeth, Gladieux Pierre, Ducasse Aurélie, Morel Jean-Benoit, Mournet Pierre, Huang Huichuan, Jin Baihui, He Xiahong, Ferdinand Romain, Fernandez Emmanuel, Vernière Christian, Roumagnac Philippe. 2018. In : Book of abstract of the International Phytobiomes Conference 2018. International Phytobiomes Alliance, INRA, IRD. Montpellier : International Phytobiomes Alliance-INRA, 48. International phytobiomes conference. 2, Montpellier, France, 4 Décembre 2018/6 Décembre 2018.http://phytobiomesconference.org/wp-content/uploads/2018/12/Phytobiomes-Conference-2018_Abstract-book-FINAL.pdfTest; http://agritrop.cirad.fr/591698/4/ID591698.pdfTest
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25مؤتمر
المؤلفون: Filloux, Denis, Fernandez, Emmanuel, Mollov, Dimitre S., Julian, Charlotte, Rott, Philippe, Roumagnac, Philippe, Daugrois, Jean-Heinrich
المصدر: Book of Abstracts XII ISSCT Pathology Workshop
وصف الملف: text
العلاقة: http://agritrop.cirad.fr/590125Test/; Genomic characterization of sugarcane mild mosaic virus. Filloux Denis, Fernandez Emmanuel, Mollov Dimitre S., Julian Charlotte, Rott Philippe, Roumagnac Philippe, Daugrois Jean-Heinrich. 2018. In : Book of Abstracts XII ISSCT Pathology Workshop. Coimbatore : ISSCT, 26-27. ISSCT Pathology Workshop. 12, Coimbatore, Inde, 3 Septembre 2018/7 Septembre 2018.; http://agritrop.cirad.fr/590125/6/ID590125.pdfTest
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26مؤتمر
المصدر: Actes de conférences : Le printemps de Baillarguet
الوصف: Depuis 1960, les émergences des maladies de plantes ont drastiquement augmenté avec l'intensification de l'agriculture, du transport des humains et des plantes et les changements environnementaux. Dans ce nouveau contexte géo-économique et avec l'augmentation des populations mondiales, l'étude et la modélisation des paramètres d'émergence des maladies permettent de mieux comprendre les émergences contemporaines mais aussi d'anticiper de nouvelles émergences. Des études récentes ont montré que des acides nucléiques viraux plus ou moins intacts pouvaient être présents dans des échantillons issus de collections d'herbiers. L'identification de virus conservés dans ces collections d'herbiers apparaît donc primordiale afin d'estimer l'origine des virus contemporains en nous renseignant sur la diversité virale passée et en datant les événements de divergence des principaux groupes viraux isolés de nos jours. Notre travail de recherche s'appuiera sur des techniques moléculaire et bio-informatiques de métagénomique afin d'identifier sans a priori des acides nucléiques viraux " fossiles " à partir d'échantillons végétaux anciens conservés dans des herbiers, de reconstituer leur phylogénie et si possible, de reconstituer leurs génomes et de les corréler avec les lignées virales actuelles.
وصف الملف: text
العلاقة: http://agritrop.cirad.fr/593165Test/; Étude de la diversité des virus des plantes conservés dans les herbiers. Delattre R., Julian Charlotte, Fernandez Emmanuel, Filloux Denis, Roumagnac Philippe. 2018. In : Actes de conférences : Le printemps de Baillarguet. CIRAD. Montpellier : CIRAD, Résumé, 12. Le printemps de Baillarguet 2018. 10, Montpellier, 28 Mai 2018/29 Mai 2018.http://printemps-baillarguet.e-monsite.com/pages/acte-de-conference-2018.htmlTest; http://agritrop.cirad.fr/593165/1/ID593165.pdfTest
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27مؤتمر
المؤلفون: Filloux, Denis, Ferdinand, Romain, Fernandez, Emmanuel, Huang, Huichuan, Jin, Baihui, He, Xiahong, Ali, S., Vernière, Christian, Roumagnac, Philippe
المصدر: Book of abstract Pathobiome 2018
الوصف: Rice has been annually cultivated for more than 1400 years in the Yuanyang terraces (YYT) of Yunnan, China. Interestingly, the level of diseases observed in this region has always remained low and, consequently, the YYT rice production has never been constrained by a heavy disease burden. A recent study has shown that the arsenal of resistance genes overall born by the rice traditional varieties that are grown in YYT prevents the dissemination of the highly virulent fungal pathogen Magnaporthe oryzae (Liao et al 2016). While the use of more than 40 traditional rice varieties has been maintained for centuries in YYT, but the use of a few modern improved varieties has been drastically increased the last few years. This significant change in the overall level of diversity of the rice varieties growing in YYT may affect the long‐term sustainable rice protection of this region. Our overarching hypothesis is that the simplification of the varietal landscape is driving a modification of the YYT rice microbiota, which may by extension have an impact on the YYT plant pathogen dynamics, and further on the pathogen emergence or non‐emergence. In this study, we have focused our sampling design on a YYT village where both traditional and modern varieties have been equally cultivated for 3‐4 years. We have sampled 9 fields cultivated with traditional rice varieties and 9 fields cultivated with improved rice varieties. The 180 collected plants (10 plants X 18 fields) were genotyped after partial genome sequencing (genotyping‐by‐sequencing approach, GBS). The GBS library was established using the ApekI restriction enzyme, we genotyped the panel of samples with up to 5000 informative SNP markers. This GBS study has confirmed the high degree of diversity of YYT traditional rice varieties in comparison to the low level of diversity of the modern improved varieties that are increasingly introduced in the YYT region. We have further characterized the roots and the stem microbiota using the virion‐associated nucleic acid ...
وصف الملف: text
العلاقة: http://agritrop.cirad.fr/587558Test/; Relationship between rice genetic diversity and microbiota composition in traditional Yuanyang rice terraces of China. P1. Filloux Denis, Ferdinand Romain, Fernandez Emmanuel, Huang Huichuan, Jin Baihui, He Xiahong, Ali S., Vernière Christian, Roumagnac Philippe. 2018. In : Book of abstract Pathobiome 2018. INRA. Ajaccio : INRA, Résumé, 32. Pathobiome, Ajaccio, France, 18 Mars 2018/20 Mars 2018.https://colloque.inra.fr/pathobiome-2018/Abstract-book/Abstract-bookTest; http://agritrop.cirad.fr/587558/1/ID587558.pdfTest
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28دورية أكاديمية
المؤلفون: Rott, Philippe, Grinstead, Samuel, Dallot, Sylvie, Foster, Zachary, Daugrois, Jean Heinrich, Fernandez, Emmanuel, Kaye, Claudia Jill, Hendrickson, Leticia, Hu, Xiaojun, Adhikari, Bishwo, Malapi-Wight, Martha, Grünwald, Niklaus, Roumagnac, Philippe, Mollov, Dimitre
المساهمون: Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), USDA Agricultural Research Service Beltsville, Maryland, USDA-ARS : Agricultural Research Service, US Sugar Corp, USDA Animal and Plant Health Inspection Service (USDA-APHIS), United States Department of Agriculture (USDA), USDA-ARS project 8042-22000-280-00, Cirad’s project “Quarantaine canne à sucre”
المصدر: ISSN: 0191-2917 ; Plant Disease ; https://hal.inrae.fr/hal-04082214Test ; Plant Disease, 2023, 107 (11), pp.3437-3447. ⟨10.1094/PDIS-10-22-2405-RE⟩.
مصطلحات موضوعية: detection, evolution, recombination, RT-PCR, sugarcane, sugarcane yellow leaf virus, SCYLV, virus diversity, [MATH]Mathematics [math]
الوصف: International audience ; Sugarcane yellow leaf virus (SCYLV), the causal agent of yellow leaf, has been reported in an increasing number of sugarcane growing locations since its first report in the 1990s in Brazil, Florida, and Hawaii. In this study, the genetic diversity of SCYLV was investigated using the genome coding sequence (5561-5612 nt) of 109 virus isolates from 19 geographical locations, including 65 new isolates from 16 geographical regions worldwide. These isolates were distributed in three major phylogenetic lineages (BRA, CUB, and REU), with the exception of one isolate from Guatemala. Twenty-two recombination events were identified among the 109 isolates of SCYLV, thus confirming that recombination was a significant driving force in the genetic diversity and evolution of this virus. No temporal signal was found in the genomic sequence data set, most likely because of the short temporal window of the 109 SCYLV isolates (1998-2020). Among 27 primers reported in the literature for the detection of the virus by RT-PCR, none matched 100% with all the 109 SCYLV sequences, suggesting that the use of some primer pairs may not result in the detection of all virus isolates. Primers YLS111/YLS462, which were the first primer pair used by numerous research organizations to detect the virus by RT-PCR, failed to detect isolates belonging to the CUB lineage. In contrast, primer pair ScYLVf1/ScYLVr1 efficiently detected isolates of all three lineages. Continuous pursuit of knowledge of SCYLV genetic variability is therefore critical for effective diagnosis of yellow leaf, especially in virus-infected and mainly asymptomatic sugarcane plants.
العلاقة: hal-04082214; https://hal.inrae.fr/hal-04082214Test; WOS: 001097311400001
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29دورية أكاديمية
المؤلفون: Mollov, Dimitre S., Filloux, Denis, Grinstead, Samuel, Bolus, Stephen, Claude, Lisa, Fernandez, Emmanuel, Julian, Charlotte, Candresse, Thierry, Lockhart, Benham E.L., Roumagnac, Philippe, Rott, Philippe, Daugrois, Jean-Heinrich
المصدر: Plant Pathology
مصطلحات موضوعية: H20 - Maladies des plantes, F30 - Génétique et amélioration des plantes, Virus des végétaux, Virus mosaïque canne à sucre, Génome, Contrôle de maladies, Pathologie végétale, http://aims.fao.org/aos/agrovoc/c_5985Test, http://aims.fao.org/aos/agrovoc/c_35631Test, http://aims.fao.org/aos/agrovoc/c_3224Test, http://aims.fao.org/aos/agrovoc/c_2327Test, http://aims.fao.org/aos/agrovoc/c_5974Test
الوصف: The complete genome sequence of a previously uncharacterized sugarcane-infecting virus of the genus Ampelovirus was obtained by high-throughput sequencing (HTS) and rapid amplification of cDNA ends. This genome consists of 13,114 nucleotides (nt) and harbours seven open reading frames. Phylogenetic and pairwise identity analyses with the complete or near-complete genome sequences of 16 isolates revealed that they all belong to a new Ampelovirus species, family Closteroviridae. These 16 isolates were distributed in three phylogenetic groups and potential recombinant events were identified for only one of these isolates. An immunocapture-reverse transcription-PCR (IC-RT-PCR) assay was developed with antibodies previously produced against a clostero-like virus that had not yet been recognized by the International Committee on Taxonomy of Viruses but for which the name sugarcane mild mosaic virus (SCMMV) had been proposed. The new ampelovirus was detected by IC-RT-PCR, and Sanger-sequenced amplicons confirmed the identity of the virus based on HTS data. SCMMV was detected in 65 of 350 samples of quarantined sugarcane germplasm using RT-PCR targeting the hsp70 gene. These samples originated from Africa, the Caribbean, North America, South America and South-east Asia, thus revealing that SCMMV is present in many sugarcane-growing regions of the world. The complete or near-complete sequences reported here represent the first genomic sequences for SCMMV. Furthermore, the newly developed RT-PCR diagnostic assay will facilitate the understanding of SCMMV epidemiology and will help improve management practices.
وصف الملف: text
العلاقة: http://agritrop.cirad.fr/602507Test/; Sugarcane mild mosaic virus: The rediscovery of an identified but unrecognized virus. Mollov Dimitre S., Filloux Denis, Grinstead Samuel, Bolus Stephen, Claude Lisa, Fernandez Emmanuel, Julian Charlotte, Candresse Thierry, Lockhart Benham E.L., Roumagnac Philippe, Rott Philippe, Daugrois Jean-Heinrich. 2023. Plant Pathology, 72 (2) : 312-321.https://doi.org/10.1111/ppa.13654Test; http://agritrop.cirad.fr/602507/7/602507.pdfTest
الإتاحة: https://doi.org/10.1111/ppa.13654Test
http://agritrop.cirad.fr/602507Test/
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30دورية أكاديمية
المساهمون: Durham University, Consejo Nacional de Ciencia y Tecnologia, Santander Universities, Quaternary Research Association, NERC
المصدر: Marine Geology ; volume 463, page 107100 ; ISSN 0025-3227
مصطلحات موضوعية: Geochemistry and Petrology, Geology, Oceanography
الإتاحة: https://doi.org/10.1016/j.margeo.2023.107100Test
https://api.elsevier.com/content/article/PII:S0025322723001123?httpAccept=text/xmlTest
https://api.elsevier.com/content/article/PII:S0025322723001123?httpAccept=text/plainTest
