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1. COVID-19-Associated Pulmonary Aspergillosis Isolates Are Genomically Diverse but Similar to Each Other in Their Responses to Infection-Relevant Stresses

Author

Mead, Matthew E., de Castro, Patricia Alves L., Steenwyk, Jacob L., Gangneux, Jean-Pierre, Hoenigl, Martin, Prattes, Juergen, Rautemaa‐richardson, Riina, Guegan, H, Moore, C, Lass-Floerl, Cornelia, Reizine, Florian, Valero, Clara, van Rhijn, Norman J., Bromley, Michael J, Rokas, Antonis H., Goldman, Gustavo H., Gago, Sara, Vanderbilt University [Nashville], Universidade de São Paulo = University of São Paulo (USP), Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), École des Hautes Études en Santé Publique [EHESP] (EHESP), Hôpital Sud [CHU Rennes], CHU Pontchaillou [Rennes], Medical University Graz, University of Manchester [Manchester], Leopold Franzens Universität Innsbruck - University of Innsbruck, Howard Hughes Medical Institute through the James H. Gilliam Fellowships for Advanced Study program, National Science Foundation [DEB-2110404], National Institutes of Health/National Institute of Allergy and Infectious Diseases [R56 AI146096, R01 AI153356], Burroughs Wellcome Fund, NIHR Manchester Biomedical Research Centre, Fungal Infection Trust, Manchester Academy of Health Sciences, Dowager Countess Eleanor Peel Trust, Wellcome Trust [219551/Z/19/], Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) from Brazil [2021/04977-5, BEPE 2020/01131-5], Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) from Brazil [301058/2019-9, 404735/2018-5, 163550/2020-4], and National Institutes of Health/National Institute of Allergy and Infectious Diseases grant [R01AI153356]

Subjects
strain heterogeneity, SARS-CoV-2, Aspergillus fumigatus, [SDV]Life Sciences [q-bio], fungal pathogen, coinfection
Abstract

International audience; Secondary infections caused by the pulmonary fungal pathogen Aspergillus fumigatus are a significant cause of mortality in patients with severe coronavirus disease 19 (COVID-19). Even though epithelial cell damage and aberrant cytokine responses have been linked to susceptibility to COVID-19-associated pulmonary aspergillosis (CAPA), little is known about the mechanisms underpinning copathogenicity. Here, we analyzed the genomes of 11 A. fumigatus isolates from patients with CAPA in three centers from different European countries. CAPA isolates did not cluster based on geographic origin in a genome-scale phylogeny of representative A. fumigatus isolates. Phenotypically, CAPA isolates were more similar to the A. fumigatus A1160 reference strain than to the Af293 strain when grown in infection-relevant stresses, except for interactions with human immune cells wherein macrophage responses were similar to those induced by the Af293 reference strain. Collectively, our data indicate that CAPA isolates are genomically diverse but are more similar to each other in their responses to infection-relevant stresses. A larger number of isolates from CAPA patients should be studied to better understand the molecular epidemiology of CAPA and to identify genetic drivers of copathogenicity and antifungal resistance in patients with COVID-19. IMPORTANCE Coronavirus disease 2019 (COVID-19)-associated pulmonary aspergillosis (CAPA) has been globally reported as a life-threatening complication in some patients with severe COVID-19. Most of these infections are caused by the environmental mold Aspergillus fumigatus, which ranks third in the fungal pathogen priority list of the WHO. However, little is known about the molecular epidemiology of Aspergillus fumigatus CAPA strains. Here, we analyzed the genomes of 11 A. fumigatus isolates from patients with CAPA in three centers from different European countries, and carried out phenotypic analyses with a view to understanding the pathophysiology of the disease. Our data indicate that A. fumigatus CAPA isolates are genomically diverse but are more similar to each other in their responses to infection-relevant stresses.

Published
2023

2. A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny

Author

Azani, Nasim, Babineau, Marielle, Bailey, C. Donovan, Banks, Hannah, Barbosa, Ariane R., Pinto, Rafael Barbosa, Boatwright, James S., Borges, Leonardo M., Brown, Gillian K., Bruneau, Anne, Candido, Elisa, Cardoso, Domingos, Chung, Kuo-Fang, Clark, Ruth P., Conceicao, Adilva S., Crisp, Michael, Cubas, Paloma, Delgado-Salinas, Alfonso, Dexter, Kyle G., Doyle, Jeff J., Duminil, Jerome, Egan, Ashley N., La Estrella, Manuel, Falcao, Marcus J., Filatov, Dmitry A., Fortuna-Perez, Ana Paula, Fortunato, Renee H., Gagnon, Edeline, Gasson, Peter, Rando, Juliana Gastaldello, Goulart Azevedo Tozzi, Ana Maria, Gunn, Bee, Harris, David, Haston, Elspeth, Hawkins, Julie A., Herendeen, Patrick S., Hughes, Colin E., Iganci, Joao R. V., Javadi, Firouzeh, Kanu, Sheku Alfred, Kazempour-Osaloo, Shahrokh, Kite, Geoffrey C., Klitgaard, Bente B., Kochanovski, Fabio J., Koenen, Erik J. M., Kovar, Lynsey, Lavin, Matt, Le Roux, Marianne, Lewis, Gwilym P., Lima, Haroldo C., Lopez-Roberts, Maria Cristina, Mackinder, Barbara, Maia, Vitor Hugo, Malecot, Valery, Mansano, Vidal F., Marazzi, Brigitte, Mattapha, Sawai, Miller, Joseph T., Mitsuyuki, Chika, Moura, Tania, Murphy, Daniel J., Nageswara-Rao, Madhugiri, Nevado, Bruno, Neves, Danilo, Ojeda, Dario I., Pennington, R. Toby, Prado, Darirn E., Prenner, Gerhard, Queiroz, Luciano Paganucci, Ramos, Gustavo, Ranzato Filardi, Fabiana L., Ribeiro, Petala G., Rico-Arce, Maria Lourdes, Sanderson, Michael J., Santos-Silva, Juliana, Sao-Mateus, Wallace M. B., Silva, Marcos J. S., Simon, Marcelo F., Sinou, Carole, Snak, Cristiane, Souza, Elvia R., Sprent, Janet, Steele, Kelly P., Steier, Julia E., Steeves, Royce, Charles Stirton, Tagane, Shuichiro, Torke, Benjamin M., Toyama, Hironori, Cruz, Daiane Trabuco Da, Vatanparast, Mohammad, Wieringa, Jan J., Wink, Michael, Wojciechowski, Martin F., Yahara, Tetsukazu, Yi, Tingshuang, Zimmerman, Erin, Department of Plant Science, University of Oxford [Oxford], Institut de Recherche en Biologie Végétale, Université de Montréal (UdeM), Département de Sciences Biologiques, University of Montreal, Department of Biology, Northern Arizona University [Flagstaff], Royal Botanic Gardens, Kew, Departamento Ciências Biológicas, Universidade Estadual de Feira de Santana, Departamento de Biologia Vegetal, Universidad de Barcelona, Department of Biodiversity and Conservation Biology, University of Western Cape, Departamento de Botânica, Universidade Federal da Bahia (UFBA), School of BioSciences, Australia and Queensland Herbarium, University of Melbourne, Instituto de Biologia, Universidade Federal de Pelotas = Federal University of Pelotas (UFPel), School of Forestry and Resource Conservation, National Taiwan University, Departamento de Educação, Campus VIII, Universidade do Estado da Bahia, Research School of Biology, Australian National University (ANU), Departamento de Biología Vegetal II, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Instituto de Biología – Botánica, Universidad Nacional Autónoma de México (UNAM), School of GeoSciences, University of Edinburgh, Plant Biology Department, Cornell University [New York], Service Évolution Biologique et Écologie, Université libre de Bruxelles (ULB), Department of Botany, Smithsonian Institution, National Museum of Natural History, Jardim Botânico do Rio de Janeiro, Instituto de Pesquisas, Department of Plant Sciences, University of California, Instituto de Recursos Biologicos, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Instituto Nacional de Tecnología Agropecuaria (INTA), University of Morón, Ciências Ambientais, Universidade Federal do Oeste da Bahia (UFOB), Royal Botanic Gardens, School of Biological Sciences [Reading], University of Reading (UOR), Chicago Botanic Garden, Department of Systematic and Evolutionary Botany, University of Vienna [Vienna], Institute of Decision Science for a Sustainable Society, Kyushu University, Department of Agriculture and Animal Health, University of South Africa (UNISA), Department of Plant Biology, Royal Veterinary and Agricultural University = Kongelige Veterinær- og Landbohøjskole (KVL ), Department Plant Sciences and Plant Pathology [Bozeman], Montana State University (MSU), South African National Biodiversity Institute, Department of Botany and Plant Biotechnology (DBPB), Department of Botany and Plant Biotechnology-Universite of Johannesburg, Departamento de Biologia, Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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), Museo Cantonale di Storia Naturale, Office of International Science and Engineering, National Science Foundation, Missouri Botanical Garden, Plant Sciences and Biodiversity, Royal Botanic Gardens Victoria, Instituto de Investigaciones en Ciencias Agrarias de Rosario [Zavalla] (IICAR), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Ciencias Agrarias [Zavalla] (FCAGR), Universidad Nacional de Rosario [Santa Fe]-Universidad Nacional de Rosario [Santa Fe], Department of Ecology and Evolutionary Biology (Faculty of Biology), University of Science-Vietnam National Universities, Sistemática e Evolução, Universidade Federal do Rio Grande do Norte [Natal] (UFRN), Departamento de Botânica, Instituto de Ciências Biológicas, Federal University of Goiás (UFG), Embrapa Recursos Genéticos e Biotecnologia (CENARGEN), Department of Biological Sciences, Bolus Herbarium, University of Cape Town, Institute of Systematic Botany, New York Botanical Garden (NYBG), Naturalis Biodiversity Center, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Kunming Institute of Botany [CAS] (KIB), Chinese Academy of Sciences [Beijing] (CAS), Natural Sciences and Engineering Research Council of Canada, U.K. Natural Environment Research Council [NE/I028122/1], Swiss National Science Foundation [31003A_13552], Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES/Program POS CSF) [1951/13-0], Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (Project Sisbiota) [563084/2010-3], Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (Project Casadinho/Procad) [5525892011-0], Fundacao de Amparo a Pesquisa do Estado da Bahia (FAPESB PES) [0053/2011], Fundacao de Amparo a Pesquisa do Estado de Sao Paulo FAPESP, Conselho Nacional de Desenvolvimento Cientifico e Tecnologico CNPq of Brazil, Smithsonian Institution, U.S. National Science Foundation [DEB-1352217], Environment Research and Technology Development Fund (S9) of the Ministry of the Environment of Japan, Arizona State University, Université de Montréal [Montréal], Royal Botanic Gardens Kew, Universidad Complutense de Madrid [Madrid] (UCM), Cornell University, Université Libre de Bruxelles [Bruxelles] (ULB), Universidade Federal do Oeste da Bahia, The Royal Veterinary and Agricultural University, Pontificia Universidade Católica do Rio de Janeiro, Missouri Botanical Garden (USA), Kunming Institute of Botany, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), AGROCAMPUS OUEST, 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)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), and Naturalis Biodiversity Center [Leiden]

Subjects
plastid matK phylogeny, Caesalpinioideae, [SDV]Life Sciences [q-bio], Cercidoideae, mimosoid clade, Papilionoideae, Detarioideae, Duparquetioideae, Dialioideae
Abstract

The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well-supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community-endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircumscribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or clade-based classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use.

Published
2017

3. First report of, and additional information on, Meloidogyne konaensis (Nematoda: Meloidogyninae) parasitising various crops in Brazil

Author

Valdir R. Correa, Jessica M.S. Monteiro, Maria Ritta A. Almeida, Philippe Castagnone-Sereno, Marcilene F.A. Santos, Regina M. D. G. Carneiro, Juvenil Enrique Cares, Vanessa S. Mattos, Ana Cristina M. M. Gomes, Carmem Dolores Gonzaga Santos, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Ministério da Agricultura, Pecuária e Abastecimento [Brasil] (MAPA), Governo do Brasil-Governo do Brasil, Universidade de Brasília (UnB), Instituto Federal de Educaçao, Cienciae Tecnologia de Alagoas, Universidade Federal do Ceará = Federal University of Ceará (UFC), Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Consorcio Brasileiro do Cafe e Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) of Brazil, CAPES, and CNPq

Subjects
0106 biological sciences, Veterinary medicine, root-knot nematode, [SDV]Life Sciences [q-bio], species identification, 010607 zoology, host range, 01 natural sciences, Esterase, Morinda citrifolia, taxonomy, Meloidogyne paranaensis, Botany, morphology, diagnostics, Root-knot nematode, molecular, Ecology, Evolution, Behavior and Systematics, Morphometrics, Nematology, biology, morphometrics, Host (biology), Carica papaya, biology.organism_classification, [SDE]Environmental Sciences, Taxonomy (biology), Agronomy and Crop Science, Terra incognita, Physalis angulata, 010606 plant biology & botany, Specific identification, Brassica capitata
Abstract

In a survey for Meloidogyne spp. in different crops from 11 regions in Ceará State, Brazil, using esterase isozyme electrophoresis as a specific identification method, four atypical populations were characterised from cabbage, papaya, noni and canapum plants, all of which showed an esterase profile different from those previously detected in Brazil. Morphological studies showed typical characteristics of Meloidogyne konaensis. Perineal patterns of females were variable, similar to M. arenaria and M. incognita, stylet length 14-20 μm. In females, the knobs gradually merged with the shaft and the dorsal pharyngeal gland orifice (DGO) ranged from 4 to 7 μm. Although males are not frequently found, the stylet morphology provides the most useful source of diagnostic character for the species, having 6-12 large projections protruding from the shaft. The esterase pattern K3 is unique and species-specific with three major bands Rm 1.0, 1.17, 1.27 and a secondary band Rm 1.10. Some confusion about the true identity of this species was clarified in this study, including differentiation from M. paranaensis. A species-specific SCAR marker developed for M. paranaensis was tested and no amplification products were observed. In Neighbour-Joining analyses of ITS and D2-D3 rRNA sequences, M. konaensis from Brazil appeared clearly separated from M. paranaensis. Pathological tests indicated that coffee is not a host of M. konaensis as previously reported in the original description of this species.

Published
2016

4. Meloidogyne luci n. sp (Nematoda: Meloidogynidae), a root-knot nematode parasitising different crops in Brazil, Chile and Iran

Author

Regina M.D.G. Carneiro, Valdir R. Correa, Maria Ritta A. Almeida, Ana Cristina M.M. Gomes, Abbas Mohammad Deimi, Philippe Castagnone-Sereno, Gerrit Karssen, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Ministério da Agricultura, Pecuária e Abastecimento [Brasil] (MAPA), Governo do Brasil-Governo do Brasil, Universidade de Brasília (UnB), Islamic Azad University, Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Wageningen University and Research Centre (WUR), Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) of Brazil, and Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior-CAPES

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Population, 010607 zoology, 01 natural sciences, Tylenchida, Botany, Root-knot nematode, esterase phenotype, molecular, education, Laboratorium voor Nematologie, Ecology, Evolution, Behavior and Systematics, Morphometrics, education.field_of_study, Nematology, biology, morphometrics, PE&RC, ethiopica, populations, biology.organism_classification, Stylet, Horticulture, tylenchida, Nematode, enzyme phenotypes, [SDE]Environmental Sciences, identification, Laboratory of Nematology, kiwi, Agronomy and Crop Science, Ethiopica, additional information, 010606 plant biology & botany
Abstract

A new root-knot nematode parasitising vegetables, flowers and fruits in Brazil, Iran and Chile, is described as Meloidogyne luci n. sp. The female has an oval to squarish perineal pattern with a low to moderately high dorsal arc and without shoulders, similar to M. ethiopica. The female stylet is robust and 15-16 μm long; the distance from the dorsal pharyngeal gland orifice to the stylet base (DGO) is 3-4 μm. Males have a high, rounded head cap continuous with the body contour. The labial disc is fused with the medial lips to form an elongated lip structure. The head region is not marked by incomplete annulations. Male stylet robust, 20.8-23.0 μm long with rounded knobs; the DGO is 2.5-4.5 μm. The stylet of second-stage juveniles (J2) is 12.0-13.5 μm long and the DGO to the stylet base is 2.3-3.3 μm. The J2 tail is conoid with finely rounded terminus and is 40.0-48.5 μm long. Biochemically, the esterase phenotype L3 (: 1.05, 1.10, 1.25) is unique and is the most useful character to differentiate M. luci n. sp. from all other Meloidogyne species. Reproduction is by mitotic parthenogenesis (2n = 42-46 chromosomes). In a differential host test, the population from Lavandula spica, Caxias do Sul, RS State, Brazil, reproduced on tomato cv. Rutgers, tobacco cv. NC95 and pepper cv. California Wonder. No reproduction occurred on watermelon cv. Charleston Gray, cotton cv. Deltapine 61 or peanut cv. Florunner. In Neighbour-Joining analyses of ITS and D2-D3 rRNA sequences, populations of M. luci n. sp. from Brazil, Chile and Iran clustered together and were clearly separated from other Meloidogyne spp., thus confirming that all three populations are very similar and conspecific.

Published
2014

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