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2. Complete Genome Sequence of the Plant-Pathogenic Fungus Colletotrichum lupini

Author

Baroncelli R., Pensec F., Lio D. D., Boufleur T., Vicente I., Sarrocco S., Picot A., Baraldi E., Sukno S., Thon M., Le Floch G., Baroncelli R., Pensec F., Lio D.D., Boufleur T., Vicente I., Sarrocco S., Picot A., Baraldi E., Sukno S., Thon M., and Le Floch G.

Subjects
Lupinus sp, fungi, Plant Disease, food and beverages, SMRT sequencing, Complete genome, Ascomycota, Fungus-plant interaction, Comparative genomic, Genome, Mitochondrial, Genomic, Colletotrichum, Anthracnose, Genome, Fungal
Abstract

Colletotrichum is a fungal genus (Ascomycota, Sordariomycetes, Glomerellaceae) that includes many economically important plant pathogens that cause devastating diseases of a wide range of plants. In this work, using a combination of long- and short-read sequencing technologies, we sequenced the genome of Colletotrichum lupini RB221, isolated from white lupin (Lupinus albus) in France during a survey in 2014. The genome was assembled into 11 nuclear chromosomes and a mitochondrial genome with a total assembly size of 63.41 Mb and 36.55 kb, respectively. In total, 18,324 protein-encoding genes have been predicted, of which only 39 are specific to C. lupini. This resource will provide insight into pathogenicity factors and will help provide a better understanding of the evolution and genome structure of this important plant pathogen.

Published
2021

4. Deciphering the infectious process of Colletotrichum lupini in lupin through transcriptomic and proteomic analysis

Author

Dubrulle G., Picot A., Madec S., Corre E., Pawtowski A., Baroncelli R., Zivy M., Balliau T., Le Floch G., Pensec F., Dubrulle G., Picot A., Madec S., Corre E., Pawtowski A., Baroncelli R., Zivy M., Balliau T., Le Floch G., and Pensec F.

Subjects
Anthracnose disease, Pathogenicity factor, Proteome, Transcriptome
Abstract

The fungal phytopathogen Colletotrichum lupini is responsible for lupin anthracnose, resulting in significant yield losses worldwide. The molecular mechanisms underlying this infectious process are yet to be elucidated. This study proposes to evaluate C. lupini gene expression and protein synthesis during lupin infection, using, respectively, an RNAseq-based transcriptomic approach and a mass spectrometry-based proteomic approach. Patterns of differentially-expressed genes in planta were evaluated from 24 to 84 hours post-inoculation, and compared to in vitro cultures. A total of 897 differentially-expressed genes were identified from C. lupini during interaction with white lupin, of which 520 genes were predicted to have a putative function, including carbohydrate active enzyme, effector, protease or transporter-encoding genes, commonly described as pathogenicity factors for other Colletotrichum species during plant infection, and 377 hypothetical proteins. Simultaneously, a total of 304 proteins produced during the interaction were identified and quantified by mass spectrometry. Taken together, the results highlight that the dynamics of symptoms, gene expression and protein synthesis shared similarities to those of hemibiotrophic pathogens. In addition, a few genes with unknown or poorly-described functions were found to be specifically associated with the early or late stages of infection, suggesting that they may be of importance for pathogenicity. This study, conducted for the first time on a species belonging to the Colletotrichum acutatum species complex, presents an opportunity to deepen functional analyses of the genes involved in the pathogenicity of Colletotrichum spp. during the onset of plant infection.

Published
2020

6. Fungal Planet description sheets: 1182–1283

Author

Crous, P.W., Cowan, D.A., Maggs-Kölling, G., Yilmaz, N., Thangavel, R., Wingfield, M.J., Noordeloos, M.E., Dima, B., Brandrud, T.E., Jansen, G.M., Morozova, O.V., Vila, J., Shivas, R.G., Tan, Y.P., Bishop-Hurley, S., Lacey, E., Marney, T.S., Larsson, E., Le Floch, G., Lombard, L., Nodet, P., Hubka, V., Alvarado, P., Berraf-Tebbal, A., Reyes, J.D., Delgado, G., Eichmeier, A., Jordal, J.B., Kachalkin, A.V., Kubátová, A., Maciá-Vicente, J.G., Malysheva, E.F., Papp, V., Rajeshkumar, K.C., Sharma, A., Spetik, M., Szabóová, D., Tomashevskaya, M.A., Abad, J.A., Abad, Z.G., Alexandrova, A.V., Anand, G., Arenas, F., Ashtekar, N., Balashov, S., Bañares, Á., Baroncelli, R., Bera, I., Biketova, A.Yu., Blomquist, C.L., Boekhout, T., Boertmann, D., Bulyonkova, T.M., Burgess, T.I., Carnegie, A.J., Cobo-Diaz, J.F., Corriol, G., Cunnington, J.H., da Cruz, M.O., Damm, U., Davoodian, N., de A. Santiago, A.L.C.M., Dearnaley, J., de Freitas, L.W.S., Dhileepan, K., Dimitrov, R., Di Piazza, S., Fatima, S., Fuljer, F., Galera, H., Ghosh, A., Giraldo, A., Glushakova, A.M., Gorczak, M., Gouliamova, D.E., Gramaje, D., Groenewald, M., Gunsch, C.K., Gutiérrez, A., Holdom, D., Houbraken, J., Ismailov, A.B., Istel, Ł., Iturriaga, T., Jeppson, M., Jurjević, Ž., Kalinina, L.B., Kapitonov, V.I., Kautmanova, I., Khalid, A.N., Kiran, M., Kiss, L., Kovács, Á., Kurose, D., Kusan, I., Lad, S., Læssøe, T., Lee, H.B., Luangsa-ard, J.J., Lynch, M., Mahamedi, A.E., Malysheva, V.F., Mateos, A., Matočec, N., Mešić, A., Miller, A.N., Mongkolsamrit, S., Moreno, G., Morte, A., Mostowfizadeh-Ghalamfarsa, R., Naseer, A., Navarro-Ródenas, A., Nguyen, T.T.T., Noisripoom, W., Ntandu, J.E., Nuytinck, J., Ostrý, V., Pankratov, T.A., Pawłowska, J., Pecenka, J., Pham, T.H.G., Polhorský, A., Posta, A., Raudabaugh, D.B., Reschke, K., Rodríguez, A., Romero, M., Rooney-Latham, S., Roux, J., Sandoval-Denis, M., Smith, M.Th., Steinrucken, T.V., Svetasheva, T.Y., Tkalčec, Z., van der Linde, E.J., v.d. Vegte, M., Vauras, J., Verbeken, A., Visagie, C.M., Vitelli, J.S., Volobuev, S.V., Weill, A., Wrzosek, M., Zmitrovich, I.V., Zvyagina, E.A., Groenewald, J.Z., Crous, P.W., Cowan, D.A., Maggs-Kölling, G., Yilmaz, N., Thangavel, R., Wingfield, M.J., Noordeloos, M.E., Dima, B., Brandrud, T.E., Jansen, G.M., Morozova, O.V., Vila, J., Shivas, R.G., Tan, Y.P., Bishop-Hurley, S., Lacey, E., Marney, T.S., Larsson, E., Le Floch, G., Lombard, L., Nodet, P., Hubka, V., Alvarado, P., Berraf-Tebbal, A., Reyes, J.D., Delgado, G., Eichmeier, A., Jordal, J.B., Kachalkin, A.V., Kubátová, A., Maciá-Vicente, J.G., Malysheva, E.F., Papp, V., Rajeshkumar, K.C., Sharma, A., Spetik, M., Szabóová, D., Tomashevskaya, M.A., Abad, J.A., Abad, Z.G., Alexandrova, A.V., Anand, G., Arenas, F., Ashtekar, N., Balashov, S., Bañares, Á., Baroncelli, R., Bera, I., Biketova, A.Yu., Blomquist, C.L., Boekhout, T., Boertmann, D., Bulyonkova, T.M., Burgess, T.I., Carnegie, A.J., Cobo-Diaz, J.F., Corriol, G., Cunnington, J.H., da Cruz, M.O., Damm, U., Davoodian, N., de A. Santiago, A.L.C.M., Dearnaley, J., de Freitas, L.W.S., Dhileepan, K., Dimitrov, R., Di Piazza, S., Fatima, S., Fuljer, F., Galera, H., Ghosh, A., Giraldo, A., Glushakova, A.M., Gorczak, M., Gouliamova, D.E., Gramaje, D., Groenewald, M., Gunsch, C.K., Gutiérrez, A., Holdom, D., Houbraken, J., Ismailov, A.B., Istel, Ł., Iturriaga, T., Jeppson, M., Jurjević, Ž., Kalinina, L.B., Kapitonov, V.I., Kautmanova, I., Khalid, A.N., Kiran, M., Kiss, L., Kovács, Á., Kurose, D., Kusan, I., Lad, S., Læssøe, T., Lee, H.B., Luangsa-ard, J.J., Lynch, M., Mahamedi, A.E., Malysheva, V.F., Mateos, A., Matočec, N., Mešić, A., Miller, A.N., Mongkolsamrit, S., Moreno, G., Morte, A., Mostowfizadeh-Ghalamfarsa, R., Naseer, A., Navarro-Ródenas, A., Nguyen, T.T.T., Noisripoom, W., Ntandu, J.E., Nuytinck, J., Ostrý, V., Pankratov, T.A., Pawłowska, J., Pecenka, J., Pham, T.H.G., Polhorský, A., Posta, A., Raudabaugh, D.B., Reschke, K., Rodríguez, A., Romero, M., Rooney-Latham, S., Roux, J., Sandoval-Denis, M., Smith, M.Th., Steinrucken, T.V., Svetasheva, T.Y., Tkalčec, Z., van der Linde, E.J., v.d. Vegte, M., Vauras, J., Verbeken, A., Visagie, C.M., Vitelli, J.S., Volobuev, S.V., Weill, A., Wrzosek, M., Zmitrovich, I.V., Zvyagina, E.A., and Groenewald, J.Z.

Abstract

Novel species of fungi described in this study include those from various countries as follows: Algeria, Phaeoacremonium adelophialidum from Vitis vinifera. Antarctica, Comoclathris antarctica from soil. Australia, Coniochaeta salicifolia as endophyte from healthy leaves of Geijera salicifolia, Eremothecium peggii in fruit of Citrus australis, Microdochium ratticaudae from stem of Sporobolus natalensis, Neocelosporium corymbiae on stems of Corymbia variegata, Phytophthora kelmanii from rhizosphere soil of Ptilotus pyramidatus, Pseudosydowia backhousiae on living leaves of Backhousia citriodora, Pseudosydowia indoor oopillyensis, Pseudosydowia louisecottisiae and Pseudosydowia queenslandica on living leaves of Eucalyptus sp. Brazil, Absidia montepascoalis from soil. Chile, Ilyonectria zarorii from soil under Maytenus boaria. Costa Rica, Colletotrichum filicis from an unidentified fern. Croatia, Mollisia endogranulata on deteriorated hardwood. Czech Republic, Arcopilus navicularis from tea bag with fruit tea, Neosetophoma buxi as endophyte from Buxus sempervirens, Xerochrysium bohemicum on surface of biscuits with chocolate glaze and filled with jam. France, Entoloma cyaneobasale on basic to calcareous soil, Fusarium aconidiale from Triticum aestivum, Fusarium juglandicola from buds of Juglans regia. Germany, Tetraploa endophytica as endophyte from Microthlaspi perfoliatum roots. India, Castanediella ambae on leaves of Mangifera indica, Lactifluus kanadii on soil under Castanopsis sp., Penicillium uttarakhandense from soil. Italy, Penicillium ferraniaense from compost. Namibia, Bezerromyces gobabebensis on leaves of unidentified succulent, Cladosporium stipagrostidicola on leaves of Stipagrostis sp., Cymostachys euphorbiae on leaves of Euphorbia sp., Deniquelata hypolithi from hypolith under a rock, Hysterobrevium walvisbayicola on leaves of unidentified tree, Knufia hypolithi and Knufia walvisbayicola from hypolith under a rock, Lapidomyces stipagrostidicola on leave

Published
2021

7. Fungal Planet description sheets: 1182–1283

Author

Crous, P.W. (Pedro Willem), Cowan, D.A., Maggs-Kölling, G., Yilmaz, N., Thangavel, R., Wingfield, M.J., Noordeloos, M.E., Dima, B., Brandrud, (Tor Erik), Jansen, G.M., Morozova, O.V., Vila, J., Shivas, R.G., Tan, Y.P., Bishop-Hurley, S., Lacey, E., Marney, T.S., Larsson, E., Le Floch, G., Lombard, L., Nodet, P., Hubka, V., Alvarado, P., Berraf-Tebbal, A., Reyes, J.D., Delgado, G., Eichmeier, A., Jordal, J.B., Kachalkin, A.V., Kubátová, A., Maciá-Vicente, J.G., Malysheva, E.F., Papp, V., Rajeshkumar, K.C., Sharma, A., Spetik, M., Szabóová, D., Tomashevskaya, M.A., Abad, J.A., Gloria Abad, Z., Alexandrova, A.V., Anand, G., Arenas, F., Ashtekar, N., Balashov, S., Banares, Á., Baroncelli, R., Bera, I., Biketova, A.Yu., Blomquist, C.L., Boekhout, T., Boertmann, D., Bulyonkova, T.M., Burgess, T.I., Carnegie, A.J., Cobo-Diaz, J.F., Corriol, G., Cunnington, J.H., da Cruz, M.O., Damm, U., Davoodian, N., de A. Santiago, A.L.C.M., Dearnaley, J., de Freitas, L.W.S., Dhileepan, K., Dimitrov, R., Di Piazza, S., Fatima, S., Fuljer, F., Galera, H., Ghosh, A., Giraldo, A., Glushakova, A.M., Gorczak, M., Gouliamova, D.E., Gramaje, D., Groenewald, M., Gunsch, C.K., Gutiérrez, A., Holdom, D., Houbraken, J., Ismailov, A.B., Istel, Ł., Iturriaga, T., Jeppson, M., Jurjević, Ž., Kalinina, L.B., Kapitonov, V.I., Kautmanova, I., Khalid, A.N., Kiran, M., Kiss, L., Kovács, Á., Kurose, D., Kusan, I., Lad, S., Læssøe, T., Lee, H.B., Luangsa-ard, J.J., Lynch, M., Mahamedi, A.E., Malysheva, V.F., Mateos, A., Matočec, N., Mešić, A., Miller, A.N., Mongkolsamrit, S., Moreno, G., Morte, A., Mostowfizadeh-Ghalamfarsa, R., Naseer, A., Navarro-Ródenas, A., Nguyen, T.T.T., Noisripoom, W., Ntandu, J.E., Nuytinck, J., Ostrý, V., Pankratov, T.A., Pawłowska, J., Pecenka, J., Pham, T.H.G., Polhorský, A., Posta, A., Raudabaugh, D.B., Reschke, K., Rodríguez, A., Romero, M., Rooney-Latham, S., Roux, J., Sandoval-Denis, M., Smith, M.Th., Steinrucken, T.V., Svetasheva, T.Y., Tkalčec, Z., van der Linde, E.J., v.d. Vegte, M., Vauras, J., Verbeken, A., Visagie, C.M., Vitelli, J.S., Volobuev, S.V., Weill, A., Wrzosek, M., Zmitrovich, I.V., Zvyagina, E.A., Groenewald, J.Z., Crous, P.W. (Pedro Willem), Cowan, D.A., Maggs-Kölling, G., Yilmaz, N., Thangavel, R., Wingfield, M.J., Noordeloos, M.E., Dima, B., Brandrud, (Tor Erik), Jansen, G.M., Morozova, O.V., Vila, J., Shivas, R.G., Tan, Y.P., Bishop-Hurley, S., Lacey, E., Marney, T.S., Larsson, E., Le Floch, G., Lombard, L., Nodet, P., Hubka, V., Alvarado, P., Berraf-Tebbal, A., Reyes, J.D., Delgado, G., Eichmeier, A., Jordal, J.B., Kachalkin, A.V., Kubátová, A., Maciá-Vicente, J.G., Malysheva, E.F., Papp, V., Rajeshkumar, K.C., Sharma, A., Spetik, M., Szabóová, D., Tomashevskaya, M.A., Abad, J.A., Gloria Abad, Z., Alexandrova, A.V., Anand, G., Arenas, F., Ashtekar, N., Balashov, S., Banares, Á., Baroncelli, R., Bera, I., Biketova, A.Yu., Blomquist, C.L., Boekhout, T., Boertmann, D., Bulyonkova, T.M., Burgess, T.I., Carnegie, A.J., Cobo-Diaz, J.F., Corriol, G., Cunnington, J.H., da Cruz, M.O., Damm, U., Davoodian, N., de A. Santiago, A.L.C.M., Dearnaley, J., de Freitas, L.W.S., Dhileepan, K., Dimitrov, R., Di Piazza, S., Fatima, S., Fuljer, F., Galera, H., Ghosh, A., Giraldo, A., Glushakova, A.M., Gorczak, M., Gouliamova, D.E., Gramaje, D., Groenewald, M., Gunsch, C.K., Gutiérrez, A., Holdom, D., Houbraken, J., Ismailov, A.B., Istel, Ł., Iturriaga, T., Jeppson, M., Jurjević, Ž., Kalinina, L.B., Kapitonov, V.I., Kautmanova, I., Khalid, A.N., Kiran, M., Kiss, L., Kovács, Á., Kurose, D., Kusan, I., Lad, S., Læssøe, T., Lee, H.B., Luangsa-ard, J.J., Lynch, M., Mahamedi, A.E., Malysheva, V.F., Mateos, A., Matočec, N., Mešić, A., Miller, A.N., Mongkolsamrit, S., Moreno, G., Morte, A., Mostowfizadeh-Ghalamfarsa, R., Naseer, A., Navarro-Ródenas, A., Nguyen, T.T.T., Noisripoom, W., Ntandu, J.E., Nuytinck, J., Ostrý, V., Pankratov, T.A., Pawłowska, J., Pecenka, J., Pham, T.H.G., Polhorský, A., Posta, A., Raudabaugh, D.B., Reschke, K., Rodríguez, A., Romero, M., Rooney-Latham, S., Roux, J., Sandoval-Denis, M., Smith, M.Th., Steinrucken, T.V., Svetasheva, T.Y., Tkalčec, Z., van der Linde, E.J., v.d. Vegte, M., Vauras, J., Verbeken, A., Visagie, C.M., Vitelli, J.S., Volobuev, S.V., Weill, A., Wrzosek, M., Zmitrovich, I.V., Zvyagina, E.A., and Groenewald, J.Z.

Abstract

Novel species of fungi described in this study include those from various countries as follows: Algeria, Phaeoacremonium adelophialidum from Vitis vinifera. Antarctica, Comoclathris antarctica from soil. Australia, Coniochaeta salicifolia as endophyte from healthy leaves of Geijera salicifolia, Eremothecium peggii in fruit of Citrus australis, Microdochium ratticaudae from stem of Sporobolus natalensis, Neocelosporium corymbiae on stems of Corymbia variegata, Phytophthora kelmanii from rhizosphere soil of Ptilotus pyramidatus, Pseudosydowia backhousiae on living leaves of Backhousia citriodora, Pseudosydowia indooroopillyensis, Pseudosydowia louisecottisiae and Pseudosydowia queenslandica on living leaves of Eucalyptus sp. Brazil, Absidia montepascoalis from soil. Chile, Ilyonectria zarorii from soil under Maytenus boaria. Costa Rica, Colletotrichum filicis from an unidentified fern. Croatia, Mollisia endogranulata on deteriorated hardwood. Czech Republic, Arcopilus navicularis from tea bag with fruit tea, Neosetophoma buxi as endophyte from Buxus sempervirens, Xerochrysium bohemicum on surface of biscuits with chocolate glaze and filled with jam. France, Entoloma cyaneobasale on basic to calcareous soil, Fusarium aconidiale from Triticum aestivum, Fusarium juglandicola from buds of Juglans regia. Germany, Tetraploa endophytica as endophyte from Microthlaspi perfoliatum roots. India, Castanediella ambae on leaves of Mangifera indica, Lactifluus kanadii on soil under Castanopsis sp., Penicillium uttarakhandense from soil. Italy, Penicillium ferraniaense from compost. Namibia, Bezerromyces gobabebensis on leaves of unidentified succulent, Cladosporium stipagrostidicola on leaves of Stipagrostis sp., Cymostachys euphorbiae on leaves of Euphorbia sp., Deniquelata hypolithi from hypolith under a rock, Hysterobrevium walvisbayicola on leaves of unidentified tree, Knufia hypolithi and Knufia walvisbayicola from hypolith under a rock, Lapidomyces stipagrostidicola on leaves

Published
2021
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8. Fungal Planet description sheets:1182-1283

Author

Crous, P. W., Cowan, D. A., Maggs-Kölling, G., Yilmaz, N., Thangavel, R., Wingfield, M. J., Noordeloos, M. E., Dima, B., Brandrud, T. E., Jansen, G. M., Morozova, O. V., Vila, J., Shivas, R. G., Tan, Y. P., Bishop-Hurley, S., Lacey, E., Marney, T. S., Larsson, E., Le Floch, G., Lombard, L., Nodet, P., Hubka, V., Alvarado, P., Berraf-Tebbal, A., Reyes, J. D., Delgado, G., Eichmeier, A., Jordal, J. B., Kachalkin, A. V., Kubatova, A., Maciá-Vicente, J. G., Malysheva, E. F., Papp, V., Rajeshkumar, K. C., Sharma, A., Spetik, M., Szabóová, D., Tomashevskaya, M. A., Abad, J. A., Abad, Z. G., Alexandrova, A. V., Anand, G., Arenas, F., Ashtekar, N., Balashov, S., Bañares, Á., Baroncelli, R., Bera, I, Biketova, A. Yu., Blomquist, C. L., Boekhout, T., Boertmann, D., Bulyonkova, T. M., Burgess, T. I., Carnegie, A. J., Cobo-Diaz, J. F., Corriol, G., Cunnington, J. H., da Cruz, M. O., Damm, U., Davoodian, N., Santiago, A. L. C. M. de A., Dearnaley, J., de Freitas, L. W. S., Dhileepan, K., Dimitrov, R., Di Piazza, S., Fatima, S., Fuljer, F., Galera, H., Ghosh, A., Giraldo, A., Glushakova, A. M., Gorczak, M., Gouliamova, D. E., Gramaje, D., Groenewald, M., Gunsch, C. K., Gutiérrez, A., Holdom, D., Houbraken, J., Ismailov, A. B., Istel, L., Iturriaga, T., Jeppson, M., Jurjevic, Z., Kalinina, L. B., Kapitonov, V. I., Kautmanová, I., Khalid, A. N., Kiran, M., Kiss, L., Kovács, Á., Kurose, D., Kusan, I., Lad, S., Læssøe, T., Lee, H. B., Luangsa-ard, J. J., Lynch, M., Mahamedi, A. E., Malysheva, V. F., Mateos, A., Matocec, N., Mesic, A., Miller, A. N., Mongkolsamrit, S., Moreno, G., Morte, A., Mostowfizadeh-Ghalamfarsa, R., Naseer, A., Navarro-Rodenas, A., Nguyen, T. T. T., Noisripoom, W., Ntandu, J. E., Nuytinck, J., Ostrý, V., Pankratov, T. A., Pawlowska, J., Pecenka, J., Pham, T. H. G., Polhorsky, A., Posta, A., Raudabaugh, D. B., Reschke, K., Rodriguez, A., Romero, M., Rooney-Latham, S., Roux, J., Sandoval-Denis, M., Smith, M. Th., Steinrucken, T. V., Svetasheva, T. Y., van der Linde, E. J., Vegte, M. v.d., Vauras, J., Verbeken, A., Visagie, C. M., Vitelli, J. S., Volobuev, S. V., Weill, A., Wrzosek, M., Zmitrovich, I. V., Zvyagina, E. A., Groenewald, J. Z., Crous, P. W., Cowan, D. A., Maggs-Kölling, G., Yilmaz, N., Thangavel, R., Wingfield, M. J., Noordeloos, M. E., Dima, B., Brandrud, T. E., Jansen, G. M., Morozova, O. V., Vila, J., Shivas, R. G., Tan, Y. P., Bishop-Hurley, S., Lacey, E., Marney, T. S., Larsson, E., Le Floch, G., Lombard, L., Nodet, P., Hubka, V., Alvarado, P., Berraf-Tebbal, A., Reyes, J. D., Delgado, G., Eichmeier, A., Jordal, J. B., Kachalkin, A. V., Kubatova, A., Maciá-Vicente, J. G., Malysheva, E. F., Papp, V., Rajeshkumar, K. C., Sharma, A., Spetik, M., Szabóová, D., Tomashevskaya, M. A., Abad, J. A., Abad, Z. G., Alexandrova, A. V., Anand, G., Arenas, F., Ashtekar, N., Balashov, S., Bañares, Á., Baroncelli, R., Bera, I, Biketova, A. Yu., Blomquist, C. L., Boekhout, T., Boertmann, D., Bulyonkova, T. M., Burgess, T. I., Carnegie, A. J., Cobo-Diaz, J. F., Corriol, G., Cunnington, J. H., da Cruz, M. O., Damm, U., Davoodian, N., Santiago, A. L. C. M. de A., Dearnaley, J., de Freitas, L. W. S., Dhileepan, K., Dimitrov, R., Di Piazza, S., Fatima, S., Fuljer, F., Galera, H., Ghosh, A., Giraldo, A., Glushakova, A. M., Gorczak, M., Gouliamova, D. E., Gramaje, D., Groenewald, M., Gunsch, C. K., Gutiérrez, A., Holdom, D., Houbraken, J., Ismailov, A. B., Istel, L., Iturriaga, T., Jeppson, M., Jurjevic, Z., Kalinina, L. B., Kapitonov, V. I., Kautmanová, I., Khalid, A. N., Kiran, M., Kiss, L., Kovács, Á., Kurose, D., Kusan, I., Lad, S., Læssøe, T., Lee, H. B., Luangsa-ard, J. J., Lynch, M., Mahamedi, A. E., Malysheva, V. F., Mateos, A., Matocec, N., Mesic, A., Miller, A. N., Mongkolsamrit, S., Moreno, G., Morte, A., Mostowfizadeh-Ghalamfarsa, R., Naseer, A., Navarro-Rodenas, A., Nguyen, T. T. T., Noisripoom, W., Ntandu, J. E., Nuytinck, J., Ostrý, V., Pankratov, T. A., Pawlowska, J., Pecenka, J., Pham, T. H. G., Polhorsky, A., Posta, A., Raudabaugh, D. B., Reschke, K., Rodriguez, A., Romero, M., Rooney-Latham, S., Roux, J., Sandoval-Denis, M., Smith, M. Th., Steinrucken, T. V., Svetasheva, T. Y., van der Linde, E. J., Vegte, M. v.d., Vauras, J., Verbeken, A., Visagie, C. M., Vitelli, J. S., Volobuev, S. V., Weill, A., Wrzosek, M., Zmitrovich, I. V., Zvyagina, E. A., and Groenewald, J. Z.

Abstract

Novel species of fungi described in this study include those from various countries as follows: Algeria, Phaeoacremonium adelophialidum from Vitis vinifera. Antarctica, Comoclathris antarctica from soil. Australia, Coniochaeta salicifolia as endophyte from healthy leaves of Geijera salicifolia, Eremothecium peggii in fruit of Citrus australis, Microdochium ratticaudae from stem of Sporobolus natalensis, Neocelosporium corymbiae on stems of Corymbia variegata, Phytophthora kelmanii from rhizosphere soil of Ptilotus pyramidatus, Pseudosydowia backhousiae on living leaves of Backhousia citriodora, Pseudosydowia indooroopillyensis, Pseudosydowia louisecottisiae and Pseudosydowia queenslandica on living leaves of Eucalyptus sp. Brazil, Absidia montepascoalis from soil. Chile, Ilyonectria zarorii from soil under Maytenus boaria. Costa Rica, Colletotrichum filicis from an unidentified fern. Croatia, Mollisia endogranulata on deteriorated hardwood. Czech Republic, Arcopilus navicularis from tea bag with fruit tea, Neosetophoma buxi as endophyte from Buxus sempervirens, Xerochrysium bohemicum on surface of biscuits with chocolate glaze and filled with jam. France, Entoloma cyaneobasale on basic to calcareous soil, Fusarium aconidiale from Triticum aestivum, Fusarium juglandicola from buds of Juglans regia. Germany, Tetraploa endophytica as endophyte from Microthlaspi perfoliatum roots. India, Castanediella ambae on leaves of Mangifera indica, Lactifluus kanadii on soil under Castanopsis sp., Penicillium uttarakhandense from soil. Italy, Penicillium ferraniaense from compost. Namibia, Bezerromyces gobabebensis on leaves of unidentified succulent, Cladosporium stipagrostidicola on leaves of Stipagrostis sp., Cymostachys euphorbiae on leaves of Euphorbia sp., Deniquelata hypolithi from hypolith under a rock, Hysterobrevium walvisbayicola on leaves of unidentified tree, Knufia hypolithi and Knufia walvisbayicola from hypolith under a rock, Lapidomyces stipagrostidicola on lea

Published
2021

9. Fungal Planet description sheets: 1182-1283

Author

Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco, Russian Foundation for Basic Research, Russian Academy of Sciences, Swedish Taxonomy Initiative, German Research Foundation, LOEWE Center for Insect Biotechnology & Bioresources, Russian Government, Lomonosov Moscow State University, Ministry of Science and Higher Education of the Russian Federation, University of Warsaw, European Commission, Hemvati Nandan Bahuguna Garhwal University, Russian Science Foundation, Rural Industries Research and Development Corporation (Australia), Department of Agriculture and Water Resources (Australia), Croatian Science Foundation, Department of Science and Technology (India), International Centre for Genetic Engineering and Biotechnology, Bulgarian National Science Fund, Universidad de Alcalá, Charles University (Czech Republic), Ministry of Agriculture of the Czech Republic, Ministry of Innovation and Technology (Hungary), National Research, Development and Innovation Office (Hungary), Norwegian Biodiversity Information Centre, University of Oslo, Ministerio de Economía y Competitividad (España), Fundación Séneca, Ministry of Health of the Czech Republic, Crous, P. W., Cowan, D. A., Maggs-Kölling, G., Yilmaz, N., Thangavel, R., Wingfield, M. J., Noordeloos, M. E., Dima, B., Brandrud, T. E., Jansen, G. M., Morozova, O. V., Cunnington, J. H., Biketova, A. Yu., Blomquist, C. L., Boekhout, T., Boertmann, D., Bulyonkova, T. M., Burgess, T. I., Cruz, M. O. da, Damm, U., Davoodian, N., Matočec, N., Santiago, A. L. C. M. de A., Dearnaley, J., Freitas, L. W. S., Mahamedi, A. E., Dhileepan, K., Dimitrov, R., Di Piazza, S., Fatima, S., Fuljer, F., Galera, H., Kušan, I., Ghosh, A., Giraldo, A., Glushakova, A. M., Gorczak, M., Malysheva, V. F, Gouliamova, D. E., Gramaje, David, Groenewald, M., Gunsch, C. K., Gutierrez-Aguirregabiria, A., Lad, S., Holdom, D., Houbraken, J., Ismailov, A. B., Istel, Ł., Iturriaga, T., Mateos, A., Jeppson, M., Jurjević, Željko, Kalinina, L. B., Kapitonov, V. I., Læssøe, T., Kautmanová, I., Khalid, Abdul Nasir, Kiran, M., Kiss, L., Kovács, A., Kurose, D., Lee, H. B., Luangsa-Ard, J. J., Lynch, M., Mešić, A., Miller, A. N., Mongkolsamrit, S., Bishop-Hurley, S., Moreno, G., Morte, A., Mostowfizadeh-Ghalamfarsa, R., Vila, J., Naseer, Arooj, Navarro-Ródenas, A., Nguyen, T. T. T., Noisripoom, W., Ntandu, J. E., Nuytinck, J., Volobuev, S. V., Ostrý, V., Pankratov, T. A., Pawłowska, J., Pečenka, Jakub, Shivas, R. G., Pham, T. H. G., Polhorský, A., Pošta, A., Raudabaugh, D. B., Reschke, K., Weill, A., Rodríguez, A., Romero, M., Rooney-Latham, S., Roux, J., Sandoval-Denis, M., Tan, Y. P., Smith, M. Th., Steinrucken, T. V., Svetasheva, T. Y., Tkalčec, Z., Wrzosek, M., Linde, E. J. van der, Vegte, M., Vauras, J., Verbeken, A., Visagie, C. M., Vitelli, J. S., Zmitrovich, I. V., Zvyagina, E. A., Groenewald, J. Z., Lacey, E., Marney, T. S., Larsson, K.-H., Carnegie, A. J., Le Floch, G, Lombard, L., Nodet, P., Hubka, V., Alvarado, P., Berraf-Tebbal, Akila, Reyes, J. D., Delgado, Gregorio, Eichmeier, Ales, Jordal, J. B., Cobo-Díaz, José F., Kachalkin, A.V., Kubátová, A., Maciá-Vicente, José G., Malysheva, E. F., Papp, V., Rajeshkumar, Kunhiraman C., Sharma, A., Spetik, M., Szabóová, D., Tomashevskaya, M. A., Corriol, G., Abad, J. A., Abad, Z. G., Alexandrova, A. V., Anand, G., Arenas, F., Ashtekar, N., Balashov, S., Bañares, Ángel, Baroncelli, R., Bera, I., Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco, Russian Foundation for Basic Research, Russian Academy of Sciences, Swedish Taxonomy Initiative, German Research Foundation, LOEWE Center for Insect Biotechnology & Bioresources, Russian Government, Lomonosov Moscow State University, Ministry of Science and Higher Education of the Russian Federation, University of Warsaw, European Commission, Hemvati Nandan Bahuguna Garhwal University, Russian Science Foundation, Rural Industries Research and Development Corporation (Australia), Department of Agriculture and Water Resources (Australia), Croatian Science Foundation, Department of Science and Technology (India), International Centre for Genetic Engineering and Biotechnology, Bulgarian National Science Fund, Universidad de Alcalá, Charles University (Czech Republic), Ministry of Agriculture of the Czech Republic, Ministry of Innovation and Technology (Hungary), National Research, Development and Innovation Office (Hungary), Norwegian Biodiversity Information Centre, University of Oslo, Ministerio de Economía y Competitividad (España), Fundación Séneca, Ministry of Health of the Czech Republic, Crous, P. W., Cowan, D. A., Maggs-Kölling, G., Yilmaz, N., Thangavel, R., Wingfield, M. J., Noordeloos, M. E., Dima, B., Brandrud, T. E., Jansen, G. M., Morozova, O. V., Cunnington, J. H., Biketova, A. Yu., Blomquist, C. L., Boekhout, T., Boertmann, D., Bulyonkova, T. M., Burgess, T. I., Cruz, M. O. da, Damm, U., Davoodian, N., Matočec, N., Santiago, A. L. C. M. de A., Dearnaley, J., Freitas, L. W. S., Mahamedi, A. E., Dhileepan, K., Dimitrov, R., Di Piazza, S., Fatima, S., Fuljer, F., Galera, H., Kušan, I., Ghosh, A., Giraldo, A., Glushakova, A. M., Gorczak, M., Malysheva, V. F, Gouliamova, D. E., Gramaje, David, Groenewald, M., Gunsch, C. K., Gutierrez-Aguirregabiria, A., Lad, S., Holdom, D., Houbraken, J., Ismailov, A. B., Istel, Ł., Iturriaga, T., Mateos, A., Jeppson, M., Jurjević, Željko, Kalinina, L. B., Kapitonov, V. I., Læssøe, T., Kautmanová, I., Khalid, Abdul Nasir, Kiran, M., Kiss, L., Kovács, A., Kurose, D., Lee, H. B., Luangsa-Ard, J. J., Lynch, M., Mešić, A., Miller, A. N., Mongkolsamrit, S., Bishop-Hurley, S., Moreno, G., Morte, A., Mostowfizadeh-Ghalamfarsa, R., Vila, J., Naseer, Arooj, Navarro-Ródenas, A., Nguyen, T. T. T., Noisripoom, W., Ntandu, J. E., Nuytinck, J., Volobuev, S. V., Ostrý, V., Pankratov, T. A., Pawłowska, J., Pečenka, Jakub, Shivas, R. G., Pham, T. H. G., Polhorský, A., Pošta, A., Raudabaugh, D. B., Reschke, K., Weill, A., Rodríguez, A., Romero, M., Rooney-Latham, S., Roux, J., Sandoval-Denis, M., Tan, Y. P., Smith, M. Th., Steinrucken, T. V., Svetasheva, T. Y., Tkalčec, Z., Wrzosek, M., Linde, E. J. van der, Vegte, M., Vauras, J., Verbeken, A., Visagie, C. M., Vitelli, J. S., Zmitrovich, I. V., Zvyagina, E. A., Groenewald, J. Z., Lacey, E., Marney, T. S., Larsson, K.-H., Carnegie, A. J., Le Floch, G, Lombard, L., Nodet, P., Hubka, V., Alvarado, P., Berraf-Tebbal, Akila, Reyes, J. D., Delgado, Gregorio, Eichmeier, Ales, Jordal, J. B., Cobo-Díaz, José F., Kachalkin, A.V., Kubátová, A., Maciá-Vicente, José G., Malysheva, E. F., Papp, V., Rajeshkumar, Kunhiraman C., Sharma, A., Spetik, M., Szabóová, D., Tomashevskaya, M. A., Corriol, G., Abad, J. A., Abad, Z. G., Alexandrova, A. V., Anand, G., Arenas, F., Ashtekar, N., Balashov, S., Bañares, Ángel, Baroncelli, R., and Bera, I.

Abstract

Novel species of fungi described in this study include those from various countries as follows: Algeria, Phaeoacremonium adelophialidum from Vitis vinifera. Antarctica, Comoclathris antarctica from soil. Australia, Coniochaeta salicifolia as endophyte from healthy leaves of Geijera salicifolia, Eremothecium peggii in fruit of Citrus australis, Microdochium ratticaudae from stem of Sporobolus natalensis, Neocelosporium corymbiae on stems of Corymbia variegata, Phytophthora kelmanii from rhizosphere soil of Ptilotus pyramidatus, Pseudosydowia backhousiae on living leaves of Backhousia citriodora, Pseudosydowia indoor oopillyensis, Pseudosydowia louisecottisiae and Pseudosydowia queenslandica on living leaves of Eucalyptus sp. Brazil, Absidia montepascoalis from soil. Chile, Ilyonectria zarorii from soil under Maytenus boaria. Costa Rica, Colletotrichum filicis from an unidentified fern. Croatia, Mollisia endogranulata on deteriorated hardwood. Czech Republic, Arcopilus navicularis from tea bag with fruit tea, Neosetophoma buxi as endophyte from Buxus sempervirens, Xerochrysium bohemicum on surface of biscuits with chocolate glaze and filled with jam. France, Entoloma cyaneobasale on basic to calcareous soil, Fusarium aconidiale from Triticum aestivum, Fusarium juglandicola from buds of Juglans regia. Germany, Tetraploa endophytica as endophyte from Microthlaspi perfoliatum roots. India, Castanediella ambae on leaves of Mangifera indica, Lactifluus kanadii on soil under Castanopsis sp., Penicillium uttarakhandense from soil. Italy, Penicillium ferraniaense from compost. Namibia, Bezerromyces gobabebensis on leaves of unidentified succulent, Cladosporium stipagrostidicola on leaves of Stipagrostis sp., Cymostachys euphorbiae on leaves of Euphorbia sp., Deniquelata hypolithi from hypolith under a rock, Hysterobrevium walvisbayicola on leaves of unidentified tree, Knufia hypolithi and Knufia walvisbayicola from hypolith under a rock, Lapidomyces stipagrostidicola on leave

Published
2021

11. Combined metabarcoding and co-occurrence network analysis to profile the bacterial, fungal and fusarium communities and their interactions in maize stalks

Author

Cobo-Diaz J. F., Baroncelli R., Le Floch G., Picot A., Cobo-Diaz J.F., Baroncelli R., Le Floch G., and Picot A.

Subjects
biocontrol agent, bacterial communitie, co-occurrence network, maize residues, Fusarium communitie, food and beverages, fungal communitie
Abstract

Fusarium Head Blight (FHB) is one of the most devastating diseases of cereals worldwide, threatening both crop production by affecting cereal grain development, and human and animal health by contaminating grains with mycotoxins. Despite that maize residues constitute the primary source of inoculum for Fusarium pathogenic species, the structure and diversity of Fusarium spp. and microbial communities in maize residues have received much less attention than in grains. In this study, a metabarcoding approach was used to study the bacterial, fungal and Fusarium communities encountered in maize stalks collected from 8 fields in Brittany, France, after maize harvest during fall 2015. Some predominant genera found in maize residues were cereal or maize pathogens, such as the fungal Fusarium, Acremonium, and Phoma genera, and the bacterial Pseudomonas and Erwinia genera. Furthermore, a high predominance of genera with previously reported biocontrol activity was found, including the bacterial Sphingomonas, Pedobacter, Flavobacterium, Pseudomonas, and Janthinobacterium genera; and the fungal Epicoccum, Articulospora, Exophiala, and Sarocladium genera. Among Fusarium spp., F. graminearum and F. avenaceum were dominant. We also found that the maize cultivar and previous crop could influence the structure of microbial communities. Using SparCC co-occurrence network analysis, significant negative correlations were obtained between Fusarium spp. responsible for FHB (including F. graminearum and F. avenaceum) and bacterial OTUs classified as Sphingomonas and fungal OTUs classified as Sarocladium and Epicoccum. Considering that isolates belonging to these taxa have already been associated with antagonist effect against different Fusarium spp. and/or other pathogenic microorganisms and due to their predominance and negative associations with Fusarium spp., they may be good candidates as biocontrol agents. Combining the use of Fusarium-specific primers with universal primers for bacteria and fungi allowed us to study the microbial communities, but also to track correlations between Fusarium spp. and other bacterial and fungal genera, using co-occurrence network analysis. Such approach could be a useful tool as part of a screening strategy for novel antagonist candidates against toxigenic Fusarium spp., allowing the selection of taxa of interest.

Published
2019

12. Fungal Planet description sheets: 1182–1283

Author

Crous, P.W., primary, Cowan, D.A., additional, Maggs-Kölling, G., additional, Yilmaz, N., additional, Thangavel, R., additional, Wingfield, M.J., additional, Noordeloos, M.E., additional, Dima, B., additional, Brandrud, T.E., additional, Jansen, G.M., additional, Morozova, O.V., additional, Vila, J., additional, Shivas, R.G., additional, Tan, Y.P., additional, Bishop-Hurley, S., additional, Lacey, E., additional, Marney, T.S., additional, Larsson, E., additional, Le Floch, G., additional, Lombard, L., additional, Nodet, P., additional, Hubka, V., additional, Alvarado, P., additional, Berraf-Tebbal, A., additional, Reyes, J.D., additional, Delgado, G., additional, Eichmeier, A., additional, Jordal, J.B., additional, Kachalkin, A.V., additional, Kubátová, A., additional, Maciá-Vicente, J.G., additional, Malysheva, E.F., additional, Papp, V., additional, Rajeshkumar, K.C., additional, Sharma, A., additional, Spetik, M., additional, Szabóová, D., additional, Tomashevskaya, M.A., additional, Abad, J.A., additional, Abad, Z.G., additional, Alexandrova, A.V., additional, Anand, G., additional, Arenas, F., additional, Ashtekar, N., additional, Balashov, S., additional, Bañares, Á., additional, Baroncelli, R., additional, Bera, I., additional, Biketova, A.Yu., additional, Blomquist, C.L., additional, Boekhout, T., additional, Boertmann, D., additional, Bulyonkova, T.M., additional, Burgess, T.I., additional, Carnegie, A.J., additional, Cobo-Diaz, J.F., additional, Corriol, G., additional, Cunnington, J.H., additional, da Cruz, M.O., additional, Damm, U., additional, Davoodian, N., additional, de A. Santiago, A.L.C.M., additional, Dearnaley, J., additional, de Freitas, L.W.S., additional, Dhileepan, K., additional, Dimitrov, R., additional, Di Piazza, S., additional, Fatima, S., additional, Fuljer, F., additional, Galera, H., additional, Ghosh, A., additional, Giraldo, A., additional, Glushakova, A.M., additional, Gorczak, M., additional, Gouliamova, D.E., additional, Gramaje, D., additional, Groenewald, M., additional, Gunsch, C.K., additional, Gutiérrez, A., additional, Holdom, D., additional, Houbraken, J., additional, Ismailov, A.B., additional, Istel, Ł., additional, Iturriaga, T., additional, Jeppson, M., additional, Jurjević, Ž., additional, Kalinina, L.B., additional, Kapitonov, V.I., additional, Kautmanova, I., additional, Khalid, A.N., additional, Kiran, M., additional, Kiss, L., additional, Kovács, Á., additional, Kurose, D., additional, Kusan, I., additional, Lad, S., additional, Læssøe, T., additional, Lee, H.B., additional, Luangsa-ard, J.J., additional, Lynch, M., additional, Mahamedi, A.E., additional, Malysheva, V.F., additional, Mateos, A., additional, Matočec, N., additional, Mešić, A., additional, Miller, A.N., additional, Mongkolsamrit, S., additional, Moreno, G., additional, Morte, A., additional, Mostowfizadeh-Ghalamfarsa, R., additional, Naseer, A., additional, Navarro-Ródenas, A., additional, Nguyen, T.T.T., additional, Noisripoom, W., additional, Ntandu, J.E., additional, Nuytinck, J., additional, Ostrý, V., additional, Pankratov, T.A., additional, Pawłowska, J., additional, Pecenka, J., additional, Pham, T.H.G., additional, Polhorský, A., additional, Posta, A., additional, Raudabaugh, D.B., additional, Reschke, K., additional, Rodríguez, A., additional, Romero, M., additional, Rooney-Latham, S., additional, Roux, J., additional, Sandoval-Denis, M., additional, Smith, M.Th., additional, Steinrucken, T.V., additional, Svetasheva, T.Y., additional, Tkalčec, Z., additional, van der Linde, E.J., additional, v.d. Vegte, M., additional, Vauras, J., additional, Verbeken, A., additional, Visagie, C.M., additional, Vitelli, J.S., additional, Volobuev, S.V., additional, Weill, A., additional, Wrzosek, M., additional, Zmitrovich, I.V., additional, Zvyagina, E.A., additional, and Groenewald, J.Z., additional

Published
2021
Full Text
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16. Anthracnose of lupins caused by Colletotrichum lupini: A recent disease and a successful worldwide pathogen

Author

Talhinhas P., Baroncelli R., Le Floch G., Talhinhas P., Baroncelli R., and Le Floch G.

Subjects
Colletotrichum lupini, Lupinus spp, Lupin, food and beverages, Colletotrichum acutatum sensu lato, Anthracnose
Abstract

Lupins are grain legume crops cultivated in several parts of the world, with important roles in the agricultural and natural ecosystems. Recently lupin breeding faced a new and important challenge, a destructive seed- and airborne disease affecting stems and pods, named anthracnose. The current disease outbreak began in the 1980s and rapidly spread worldwide, affecting apparently all lupin species. The pathogen belongs to Colletotrichum lupini, a member of the acutatum species complex, and contrasts with other members of the latter by its host specificity and by its apparent clonality. However, in a matter of a few decades this pathogen managed to cause severe epidemics in lupin crops from diverse species (both of Mediterranean and North and South American origins) throughout the world, whether in humid or in dry climates, frequently causing high yield losses and in many cases leading farmers to replace lupin with other crops. Although several lupin crops rely on rich genetic resources, it proved very difficult to find effective resistance sources. Recent successes in this matter (backed by advances in genome sequencing of some lupin species) are still conditioned by the very narrow range of resistance genes available for breeders, risking a possible overcoming of such resistances if the pathogen finds itself means to create diversity that enables it to overcome resistance. To this end, advances in Colletotrichum genomics, with the forthcoming sequencing of the genome of C. lupini, are of great importance to understand the genetic nature of C. lupini host specificity and reproduction strategies.

Published
2016

19. A new methodology for assessing root amino acid exudation in soil and interactions with the rhizosphere

Author

Bobille, Helene, Limami, Anis M., Robins, Richard J., Le Floch, G., Fustec, Joëlle, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, and 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2015

29. Genome sequence of Colletotrichum abscissum the causal agent of citrus Post-Bloom Fruit Drop and the closely related species C. filicis

Author

Eduardo Goulin, Thais Regina Boufleur, Francesca Negrini, Greice Amaral Carneiro, Elena Baraldi, Marcos Antonio Machado, Gaetan Le Floch, Riccardo Baroncelli, and Goulin E, Boufleur T, Negrini F, Carneiro G, Baraldi E, Machado M, Le Floch G, Baroncelli R.

Subjects
colletotrichum, fungal genome, plant pathogens, Plant Science, Agronomy and Crop Science
Abstract

Colletotrichum is one of the most diverse and destructive plant pathogenic fungi containing genus, responsible for significant losses in agriculture and forest plants. In the present study, we present the draft whole-genome sequence of two closely related species belonging to the Colletotrichum acutatum species complex: C. abscissum, the causal agent of citrus post-bloom fruit drop and C. filicis, a rare species described to accommodate an isolate obtained from an identified fern in Costa Rica. The data resources presented here will provide insights into genetic elements associated with citrus post-bloom fruit drop and into the evolution of Colletotrichum.

Published
2023

30. Phylogenetic Diversity and Effect of Temperature on Pathogenicity of Colletotrichum lupini

Author

Guillaume Dubrulle, Flora Pensec, Sophie Nicolleau, Riccardo Baroncelli, Patrice Nodet, Nathalie Harzic, Adeline Picot, Karim Rigalma, Audrey Pawtowski, Gaétan Le Floch, Dubrulle G., Pensec F., Picot A., Rigalma K., Pawtowski A., Nicolleau S., Harzic N., Nodet P., Baroncelli R., Le Floch G., Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), Universidad de Salamanca, Salamanca, Spain, and Universidad de Salamanca

Subjects
0106 biological sciences, Species complex, Colletotrichum acutatum species complex, Microsclerotia, DNA quantification, Plant Science, Lupin anthracnose, 01 natural sciences, 03 medical and health sciences, Aggressivene, Colletotrichum acutatum, Colletotrichum lupini, Botany, Pathogen, ComputingMilieux_MISCELLANEOUS, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Genetic diversity, biology, Phylogenetic tree, food and beverages, biology.organism_classification, Pathogenicity, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Phylogenetic diversity, Agronomy and Crop Science, 010606 plant biology & botany
Abstract

Although lupin anthracnose caused by Colletotrichum lupini is a significant threat for spring and winter lupin crops, it has been poorly studied so far. This study aimed at characterizing the (i) phylogenetic, (ii) morphological, and (iii) physiological diversity of collected isolates from anthracnose-affected lupins. The genetic identification of representative isolates (n = 71) revealed that they were all C. lupini species, further confirming that lupin anthracnose is caused by this species. However, multilocus sequencing on these isolates and 16 additional reference strains of C. lupini revealed a separation into two distinct genetic groups, both of them characterized by a very low genetic diversity. The diversity of morphological characteristics of a selected subset of C. lupini isolates was further evaluated. To the best of our knowledge, microsclerotia production observed for some isolates has never been reported so far within the Colletotrichum acutatum species complex. Finally, the modeling of growth responses of a subset of C. lupini strains revealed the capacity of some strains to grow in vitro at 5°C. This ability was also evidenced in planta, because C. lupini DNA was detectable in plants from 14 days postinoculation at 5°C onward, whereas symptoms began to appear a week later, although at a very low level. Since lupin crops are planted during winter or early spring, growth studies in vitro and in planta demonstrated the capability of the species to grow at temperatures ranging from 5 to 30°C, with an optimum close to 25°C. In this study, C. lupini-specific primers were also designed for real-time quantitative PCR on fungal DNA and allowed the detection of C. lupini in asymptomatic field samples. These results open perspectives to detect earlier and limit the development of this pathogen in lupin crops.

Published
2020

31. Fungal Planet description sheets: 1182–1283

Author

Akila Berraf-Tebbal, Johannes Z. Groenewald, Neriman Yilmaz, J. Vauras, J. Vila, P. Nodet, S. Balashov, S. Di Piazza, Teun Boekhout, J. D. Reyes, D. Kurose, Jose G. Maciá-Vicente, Thomas S. Marney, A. E. Mahamedi, Milan Špetík, Suzanne Rooney-Latham, J. Jennifer Luangsa-ard, Francisco Arenas, G. Le Floch, Yu Pei Tan, T. T. T. Nguyen, W. Noisripoom, Ivan V. Zmitrovich, Ellen Larsson, Teresa Iturriaga, Jorinde Nuytinck, A. Rodríguez, C. L. Blomquist, A. Yu. Biketova, Z. G. Abad, Gabriel Moreno, M.Th. Smith, S. Lad, Abdul Nasir Khalid, G. Delgado, Halina Galera, A. Naseer, N. Ashtekar, Asunción Morte, Thomas Læssøe, James H. Cunnington, A. Polhorský, Mikael Jeppson, I. Bera, Cobus M. Visagie, A. Mateos, Lorenzo Lombard, Michael J. Wingfield, V. Ostrý, D. A. Cowan, A. V. Alexandrova, J. Pecenka, A. Ghosh, T. H. G. Pham, M. V. D. Vegte, Á Bañares, Armin Mešić, John Dearnaley, M. A. Tomashevskaya, Łukasz Istel, D. Szabóová, Ivona Kautmanová, A. Desantiago, Annemieke Verbeken, Jos Houbraken, Bálint Dima, J. A. Abad, J. S. Vitelli, L. W. S. De Freitas, Claudia K. Gunsch, N. Davoodian, Ulrike Damm, H. B. Lee, D.E. Gouliamova, Alena Kubátová, Treena I. Burgess, Andrew N. Miller, D. G. Holdom, E. F. Malysheva, J. B. Jordal, David Gramaje, Angus J. Carnegie, Aleš Eichmeier, Alfonso Navarro-Ródenas, A. Giraldo, F. Fuljer, T. V. Steinrucken, K. Reschke, S. Bishop-Hurley, G. Anand, A. M. Glushakova, Levente Kiss, J. E. Ntandu, M. Lynch, Kunjithapatham Dhileepan, Suchada Mongkolsamrit, E. J. Van Der Linde, V. I. Kapitonov, Machiel E. Noordeloos, L. B. Kalinina, A. Pošta, G. Corriol, Reza Mostowfizadeh-Ghalamfarsa, Roger G. Shivas, T. M. Bulyonkova, Ernest Lacey, A. Sharma, Tor Erik Brandrud, Marta Wrzosek, Julia Pawłowska, Zdenko Tkalčec, Marcelo Sandoval-Denis, E. A. Zvyagina, J. F. Cobo-Diaz, Aleksey V. Kachalkin, T. A. Pankratov, Raja Thangavel, M. O. Da Cruz, S. V. Volobuev, I. Kusan, Jolanda Roux, Kunhiraman C. Rajeshkumar, O.V. Morozova, A. Weill, Viktor Papp, Marizeth Groenewald, Roumen Dimitrov, Željko Jurjević, G. M. Jansen, S. Fatima, Munazza Kiran, M. Romero, Michał Gorczak, D. Boertmann, Pedro W. Crous, Tatyana Yu. Svetasheva, Vit Hubka, Neven Matočec, A. Gutiérrez, D. B. Raudabaugh, A. B. Ismailov, Riccardo Baroncelli, Pablo Alvarado, V. F. Malysheva, Á Kovács, G. Maggs-Kölling, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco, Russian Foundation for Basic Research, Russian Academy of Sciences, Swedish Taxonomy Initiative, German Research Foundation, LOEWE Center for Insect Biotechnology & Bioresources, Russian Government, Lomonosov Moscow State University, Ministry of Science and Higher Education of the Russian Federation, University of Warsaw, European Commission, Hemvati Nandan Bahuguna Garhwal University, Russian Science Foundation, Rural Industries Research and Development Corporation (Australia), Department of Agriculture and Water Resources (Australia), Croatian Science Foundation, Department of Science and Technology (India), International Centre for Genetic Engineering and Biotechnology, Bulgarian National Science Fund, Universidad de Alcalá, Charles University (Czech Republic), Ministry of Agriculture of the Czech Republic, Ministry of Innovation and Technology (Hungary), National Research, Development and Innovation Office (Hungary), Norwegian Biodiversity Information Centre, University of Oslo, Ministerio de Economía y Competitividad (España), Fundación Séneca, Ministry of Health of the Czech Republic, Evolutionary and Population Biology (IBED, FNWI), Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), Westerdijk Fungal Biodiversity Institute - Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Westerdijk Fungal Biodiversity Institute - Yeast Research, Westerdijk Fungal Biodiversity Institute - Collection, Westerdijk Fungal Biodiversity Institute - Food and Indoor Mycology, Crous P.W., Cowan D.A., Maggs-Kolling G., Yilmaz N., Thangavel R., Wingfield M.J., Noordeloos M.E., Dima B., Brandrud T.E., Jansen G.M., Morozova O.V., Vila J., Shivas R.G., Tan Y.P., Bishop-Hurley S., Lacey E., Marney T.S., Larsson E., Le Floch G., Lombard L., Nodet P., Hubka V., Alvarado P., Berraf-Tebbal A., Reyes J.D., Delgado G., Eichmeier A., Jordal J.B., Kachalkin A.V., Kubatova A., Macia-Vicente J.G., Malysheva E.F., Papp V., Rajeshkumar K.C., Sharma A., Spetik M., Szaboova D., Tomashevskaya M.A., Abad J.A., Abad Z.G., Alexandrova A.V., Anand G., Arenas F., Ashtekar N., Balashov S., Banares A., Baroncelli R., Bera I., Yu. Biketova A., Blomquist C.L., Boekhout T., Boertmann D., Bulyonkova T.M., Burgess T.I., Carnegie A.J., Cobo-Diaz J.F., Corriol G., Cunnington J.H., Da Cruz M.O., Damm U., Davoodian N., Desantiago A., Dearnaley J., De Freitas L.W.S., Dhileepan K., Dimitrov R., Di Piazza S., Fatima S., Fuljer F., Galera H., Ghosh A., Giraldo A., Glushakova A.M., Gorczak M., Gouliamova D.E., Gramaje D., Groenewald M., Gunsch C.K., Gutierrez A., Holdom D., Houbraken J., Ismailov A.B., Istel L., Iturriaga T., Jeppson M., Jurjevic Z., Kalinina L.B., Kapitonov V.I., Kautmanova I., Khalid A.N., Kiran M., Kiss L., Kovacs A., Kurose D., Kusan I., Lad S., Laessoe T., Lee H.B., Luangsa-Ard J.J., Lynch M., Mahamedi A.E., Malysheva V.F., Mateos A., Matocec N., Mesic A., Miller A.N., Mongkolsamrit S., Moreno G., Morte A., Mostowfizadeh-Ghalamfarsa R., Naseer A., Navarro-Rodenas A., Nguyen T.T.T., Noisripoom W., Ntandu J.E., Nuytinck J., Ostry V., Pankratov T.A., Pawlowska J., Pecenka J., Pham T.H.G., Polhorsky A., Posta A., Raudabaugh D.B., Reschke K., Rodriguez A., Romero M., Rooney-Latham S., Roux J., Sandoval-Denis M., Smith M.Th., Steinrucken T.V., Svetasheva T.Y., Tkalcec Z., Van Der Linde E.J., Vegte M.V.D., Vauras J., Verbeken A., Visagie C.M., Vitelli J.S., Volobuev S.V., Weill A., Wrzosek M., Zmitrovich I.V., Zvyagina E.A., and Groenewald J.Z.

Subjects
0106 biological sciences, Zoology and botany: 480 [VDP], 01 natural sciences, BLACK FUNGI, 030308 mycology & parasitology, MULTIPLE SEQUENCE ALIGNMENT, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 2. Zero hunger, 0303 health sciences, Rhizosphere, LSU, biology, Ecology, SPECIES-DIVERSITY, Ziziphus, Plant litter, Syzygium, visual_art, visual_art.visual_art_medium, Bark, GENERA, INHABITING, Systematic, ITS nrDNA barcodes, Evolution, Entoloma, Umbellularia, SYSTEMATICS, 03 medical and health sciences, Behavior and Systematics, New taxa, Systematics, Botany, ITS nrDNA barcode, LEATHERLEAF FERN, Zoologiske og botaniske fag: 480 [VDP], Biology, Ecology, Evolution, Behavior and Systematics, COLLETOTRICHUM-ACUTATUM, Biology and Life Sciences, IQ-TREE, INHABITING BLACK FUNGI, 15. Life on land, BAYESIAN PHYLOGENETIC INFERENCE, biology.organism_classification, Leucadendron, new taxa, systematics, GEN. NOV, SP. NOV, 010606 plant biology & botany
Abstract

Novel species of fungi described in this study include those from various countries as follows: Algeria, Phaeoacremonium adelophialidum from Vitis vinifera. Antarctica, Comoclathris antarctica from soil. Australia, Coniochaeta salicifolia as endophyte from healthy leaves of Geijera salicifolia, Eremothecium peggii in fruit of Citrus australis, Microdochium ratticaudae from stem of Sporobolus natalensis, Neocelosporium corymbiae on stems of Corymbia variegata, Phytophthora kelmanii from rhizosphere soil of Ptilotus pyramidatus, Pseudosydowia backhousiae on living leaves of Backhousia citriodora, Pseudosydowia indoor oopillyensis, Pseudosydowia louisecottisiae and Pseudosydowia queenslandica on living leaves of Eucalyptus sp. Brazil, Absidia montepascoalis from soil. Chile, Ilyonectria zarorii from soil under Maytenus boaria. Costa Rica, Colletotrichum filicis from an unidentified fern. Croatia, Mollisia endogranulata on deteriorated hardwood. Czech Republic, Arcopilus navicularis from tea bag with fruit tea, Neosetophoma buxi as endophyte from Buxus sempervirens, Xerochrysium bohemicum on surface of biscuits with chocolate glaze and filled with jam. France, Entoloma cyaneobasale on basic to calcareous soil, Fusarium aconidiale from Triticum aestivum, Fusarium juglandicola from buds of Juglans regia. Germany, Tetraploa endophytica as endophyte from Microthlaspi perfoliatum roots. India, Castanediella ambae on leaves of Mangifera indica, Lactifluus kanadii on soil under Castanopsis sp., Penicillium uttarakhandense from soil. Italy, Penicillium ferraniaense from compost. Namibia, Bezerromyces gobabebensis on leaves of unidentified succulent, Cladosporium stipagrostidicola on leaves of Stipagrostis sp., Cymostachys euphorbiae on leaves of Euphorbia sp., Deniquelata hypolithi from hypolith under a rock, Hysterobrevium walvisbayicola on leaves of unidentified tree, Knufia hypolithi and Knufia walvisbayicola from hypolith under a rock, Lapidomyces stipagrostidicola on leaves of Stipagrostis sp., Nothophaeotheca mirabibensis (incl. Nothophaeotheca gen. nov.) on persistent inflorescence remains of Blepharis obmitrata, Paramyrothecium salvadorae on twigs of Salvadora persica, Preussia procaviicola on dung of Procavia sp., Sordaria equicola on zebra dung, Volutella salvadorae on stems of Salvadora persica. Netherlands, Entoloma ammophilum on sandy soil, Entoloma pseudocruentatum on nutrient poor(acid)soil, Entoloma pudens on plant debris, amongst grasses. [...], Leslie W.S. de Freitas and colleagues express their gratitude to Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for scholarships provided to Leslie Freitas and for the research grant provided to André Luiz Santiago; their contribution was financed by the projects ‘Diversity of Mucoromycotina in the different ecosystems of the Atlantic Rainforest of Pernambuco’ (FACEPE–First Projects Program PPP/ FACEPE/CNPq–APQ–0842-2.12/14) and ‘Biology of conservation of fungi s.l. in areas of Atlantic Forest of Northeast Brazil’ (CNPq/ICMBio 421241/ 2017-9) H.B. Lee was supported by the Graduate Program for the Undiscovered Taxa of Korea (NIBR202130202). The study of O.V. Morozova, E.F. Malysheva, V.F. Malysheva, I.V. Zmitrovich, and L.B. Kalinina was carried out within the framework of a research project of the Komarov Botanical Institute RAS (АААА-А19-119020890079-6) using equipment of its Core Facility Centre ‘Cell and Molecular Technologies in Plant Science’. The work of O. V. Morozova, L.B. Kalinina, T. Yu. Svetasheva, and E.A. Zvyagina was financially supported by Russian Foundation for Basic Research project no. 20-04-00349. E.A. Zvyagina and T.Yu. Svetasheva are grateful to A.V. Alexandrova, A.E. Kovalenko, A.S. Baykalova for the loan of specimens, T.Y. James, E.F. Malysheva and V.F. Malysheva for sequencing. J.D. Reyes acknowledges B. Dima for comparing the holotype sequence of Cortinarius bonachei with the sequences in his database. A. Mateos and J.D. Reyes acknowledge L. Quijada for reviewing the phylogeny and S. de la Peña- Lastra and P. Alvarado for their support and help. Vladimir I. Kapitonov and colleagues are grateful to Brigitta Kiss for help with their molecular studies. This study was conducted under research projects of the Tobolsk Complex Scientific Station of the Ural Branch of the Russian Academy of Sciences (N АААА-А19-119011190112-5). E. Larsson acknowledges the Swedish Taxonomy Initiative, SLU Artdatabanken, Uppsala (dha.2019.4.3-13). The study of D.B. Raudabaugh and colleagues was supported by the Schmidt Science Fellows, in partnership with the Rhodes Trust. Gregorio Delgado is grateful to Michael Manning and Kamash Pillai (Eurofins EMLab P&K) for provision of laboratory facilities. Jose G. Maciá-Vicente acknowledges support from the German Research Foundation under grant MA7171/1-1, and from the Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz (LOEWE) of the state of Hesse within the framework of the Cluster for Integrative Fungal Research (IPF). Thanks are also due to the authorities of the Cabañeros National Park and Los Alcornocales Natural Park for granting the collection permit and for support during field work. The study of Alina V. Alexandrova was carried out as part of the Scientific Project of the State Order of the Government of Russian Federation to Lomonosov Moscow State University No. 121032300081-7. Michał Gorczak was financially supported by the Ministry of Science and Higher Education through the Faculty of Biology, University of Warsaw intramural grant DSM 0117600- 13. M. Gorczak acknowledges M. Klemens for sharing a photo of the Białowieża Forest logging site and M. Senderowicz for help with preparing the illustration. Ivona Kautmanová and D. Szabóová were funded by the Operational Program of Research and Development and co-financed with the European Fund for Regional Development (EFRD). ITMS 26230120004: ‘Building of research and development infrastructure for investigation of genetic biodiversity of organisms and joining IBOL initiative’. Ishika Bera, Aniket Ghosh, Jorinde Nuytinck and Annemieke Verbeken are grateful to the Director, Botanical Survey of India (Kolkata), Head of the Department of Botany & Microbiology & USIC Dept. HNB Garhwal University, Srinagar, Garhwal for providing research facilities. Ishika Bera and Aniket Ghosh acknowledge the staff of the forest department of Arunachal Pradesh for facilitating the macrofungal surveys to the restricted areas. Sergey Volobuev was supported by the Russian Science Foundation (RSF project N 19-77- 00085). Aleksey V. Kachalkin and colleagues were supported by the Russian Science Foundation (grant No. 19-74-10002). The study of Anna M. Glushakova was carried out as part of the Scientific Project of the State Order of the Government of Russian Federation to Lomonosov Moscow State University No. 121040800174-6. Tracey V. Steinrucken and colleagues were supported by AgriFutures Australia (Rural Industries Research and Development Corporation), through funding from the Australian Government Department of Agriculture, Water and the Environment, as part of its Rural Research and Development for Profit program (PRJ-010527). Neven Matočec and colleagues thank the Croatian Science Foundation for their financial support under the project grant HRZZ-IP-2018-01-1736 (ForFungiDNA). Ana Pošta thanks the Croatian Science Foundation for their support under the grant HRZZ-2018-09-7081. The research of Milan Spetik and co-authors was supported by Internal Grant of Mendel University in Brno No. IGAZF/ 2021-SI1003. K.C. Rajeshkumar thanks SERB, the Department of Science and Technology, Government of India for providing financial support under the project CRG/2020/000668 and the Director, Agharkar Research Institute for providing research facilities. Nikhil Ashtekar thanks CSIR-HRDG, INDIA, for financial support under the SRF fellowship (09/670(0090)/2020-EMRI), and acknowledges the support of the DIC Microscopy Facility, established by Dr Karthick Balasubramanian, B&P (Plants) Group, ARI, Pune. The research of Alla Eddine Mahamedi and co-authors was supported by project No. CZ.02.1.01/0.0/0.0/16_017/0002334, Czech Republic. Tereza Tejklová is thanked for providing useful literature. A. Polhorský and colleagues were supported by the Operational Program of Research and Development and co-financed with the European fund for Regional Development (EFRD), ITMS 26230120004: Building of research and development infrastructure for investigation of genetic biodiversity of organisms and joining IBOL initiative. Yu Pei Tan and colleagues thank R. Chen for her technical support. Ernest Lacey thanks the Cooperative Research Centres Projects scheme (CRCPFIVE000119) for its support. Suchada Mongkolsamrit and colleagues were financially supported by the Platform Technology Management Section, National Center for Genetic Engineering and Biotechnology (BIOTEC), Project Grant No. P19-50231. Dilnora Gouliamova and colleagues were supported by a grant from the Bulgarian Science Fund (KP-06-H31/19). The research of Timofey A. Pankratov was supported by the Russian Foundation for Basic Research (grant No. 19-04-00297a). Gabriel Moreno and colleagues wish to express their gratitude to L. Monje and A. Pueblas of the Department of Drawing and Scientific Photography at the University of Alcalá for their help in the digital preparation of the photographs, and to J. Rejos, curator of the AH herbarium, for his assistance with the specimens examined in the present study. Vit Hubka was supported by the Charles University Research Centre program No. 204069. Alena Kubátová was supported by The National Programme on Conservation and Utilization of Microbial Genetic Resources Important for Agriculture (Ministry of Agriculture of the Czech Republic). The Kits van Waveren Foundation (Rijksherbariumfonds Dr E. Kits van Waveren, Leiden, Netherlands) contributed substantially to the costs of sequencing and travelling expenses for M. Noordeloos. The work of B. Dima was supported by the ÚNKP-20-4 New National Excellence Program of the Ministry for Innovation and Technology from the source of the National Research, Development and Innovation Fund, and by the ELTE Thematic Excellence Programme 2020 supported by the National Research, Development and Innovation Office of Hungary (TKP2020-IKA-05). The Norwegian Entoloma studies received funding from the Norwegian Biodiversity Information Centre (NBIC), and the material was partly sequenced through NorBOL. Gunnhild Marthinsen and Katriina Bendiksen (Natural History Museum, University of Oslo, Norway) are acknowledged for performing the main parts of the Entoloma barcoding work. Asunción Morte is grateful to AEI/FEDER, UE (CGL2016-78946-R) and Fundación Séneca - Agencia de Ciencia y Tecnología de la Región de Murcia (20866/PI/18) for financial support. Vladimír Ostrý was supported by the Ministry of Health, Czech Republic - conceptual development of research organization (National Institute of Public Health – NIPH, IN 75010330). Konstanze Bensch (Westerdijk Fungal Biodiversity Institute, Utrecht) is thanked for correcting the spelling of various Latin epithets.

Published
2021

32. Molecular Detection of the Seed-Borne Pathogen Colletotrichum lupini Targeting the Hyper-Variable IGS Region of the Ribosomal Cluster

Author

Gaétan Le Floch, Susanna Pecchia, Benedetta Caggiano, Daniele Da Lio, Giovanni Cafà, Riccardo Baroncelli, Pecchia S., Caggiano B., Da Lio D., Cafa G., Le Floch G., and Baroncelli R.

Subjects
0106 biological sciences, 0301 basic medicine, Colletotrichum acutatum, legumes, Fungal pathogen, Plant Science, Biology, 01 natural sciences, 03 medical and health sciences, Lupinus, ribosomal intergenic spacer, medicine, lupins, Pathogen, Ecology, Evolution, Behavior and Systematics, Lupinu, Ecology, Botany, Sowing, food and beverages, IGS, Ribosomal RNA, biology.organism_classification, fungal pathogens, Yeast, Legume, Horticulture, 030104 developmental biology, Streptomycin, QK1-989, Lupin, Primer (molecular biology), 010606 plant biology & botany, medicine.drug
Abstract

Lupins anthracnose is a destructive seed and airborne disease caused by Colletotrichum lupini, affecting stems and pods. Primary seed infections as low as 0.01&ndash, 0.1% can cause very severe yield losses. One of the most effective management strategies is the development of a robust and sensitive seed detection assay to screen seed lots before planting. PCR-based detection systems exhibit higher levels of sensitivity than conventional techniques, but when applied to seed tests they require the extraction of PCR-quality DNA from target organisms in backgrounds of saprophytic organisms and inhibitory seed-derived compounds. To overcome these limitations, a new detection protocol for C. lupini based on a biological enrichment step followed by a PCR assay was developed. Several enrichment protocols were compared with Yeast Malt Broth amended with ampicillin, streptomycin, and lactic acid were the most efficient. A species-specific C. lupini primer pair was developed based on rDNA IGS sequences. The specificity was evaluated against 17 strains of C. lupini, 23 different Colletotrichum species, and 21 different organisms isolated from seeds of Lupinus albus cv. Multitalia, L. luteus cv. Mister, and L. angustifolius cv. Tango. The protocol described here enabled the detection of C. lupini in samples artificially infected with less than 1/10,000 infected seed.

Published
2019
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33. A novel metabarcoding approach to investigate Fusarium species composition in soil and plant samples

Author

José F. Cobo-Díaz, Riccardo Baroncelli, Gaétan Le Floch, Adeline Picot, Cobo-Diaz J.F., Baroncelli R., Le Floch G., and Picot A.

Subjects
0301 basic medicine, Fusarium, Operational taxonomic unit, molecular diversity, Soil test, 030106 microbiology, Applied Microbiology and Biotechnology, Microbiology, Zea mays, Fungal Proteins, 03 medical and health sciences, environmental Fusarium specie, Peptide Elongation Factor 1, Translation elongation, Botany, DNA Barcoding, Taxonomic, DNA, Fungal, Phylogeny, Soil Microbiology, Ecology, Phylogenetic tree, biology, Microbiota, food and beverages, Sequence Analysis, DNA, Amplicon, biology.organism_classification, 030104 developmental biology, metabarcoding primer pair, Fusarium communitie, EF1α-Fusarium database, Genus Fusarium
Abstract

The genus Fusarium contains more than 300 species, most of which are plant pathogens. Appropriate molecular tools for accurately and rapidly describing temporal and spatial shifts in Fusarium communities would be useful for the development of control strategies. Here, we present a new Fusarium-specific primer pair targeting the translation elongation factor 1-α (EF1α) gene with amplicons of ~430 bp, suitable for MiSeq metabarcoding sequencing. Mock Fusarium communities were used to evaluate its resolution and to optimize read filtering and downstream analyses. The use of the DADA2 pipeline coupled with operational taxonomic unit (OTU) picking at 98% similarity cut-off significantly increased the accuracy of read filtering. Building a phylogenetic tree using a manually curated database as a reference allowed taxonomic assignment at the species or species-complex level. This methodology was tested on soil and maize residue samples collected from crop fields. Up to 18 Fusarium OTUs, belonging to 17 species and 8 species complexes, were obtained, with F. oxysporum being the most abundant species in soil samples, while F. graminearum and F. avenaceum were the most abundant in maize residues. We demonstrated the high performance of this workflow which could be further used for profiling Fusarium species composition and dynamics during the cultivation cycle.

Published
2019

34. First Report of Colletotrichum fructicola Causing Apple Bitter Rot in Europe

Author

X. Crété, Morgane Chalopin, Riccardo Baroncelli, G. Le Floch, Patrice Nodet, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), Centre Expérimental Horticole de Marsillargues (CEHM), Nodet P., Chalopin M., Crete X., Baroncelli R., and Le Floch G.

Subjects
0106 biological sciences, 0301 basic medicine, Malus, Spots, biology, apple, Plant Science, 030108 mycology & parasitology, Anthracnose, Glomerella, Malus domestica, emerging disease, biology.organism_classification, 01 natural sciences, Conidium, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, 03 medical and health sciences, Horticulture, Colletotrichum acutatum, Colletotrichum, Leaf spot, Potato dextrose agar, Internal transcribed spacer, Agronomy and Crop Science, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 010606 plant biology & botany
Abstract

International audience; Bitter rot is one of the prevalent diseases of apple (Malus pumila Mill.) worldwide. The disease affects the fruit preharvest in orchards and/or postharvest in storage, resulting in considerable economic losses. Until recently the reported causal agents in Europe belong to the Colletotrichum acutatum species complex (Baroncelli et al. 2014; Nodet et al. 2016); however, species belonging to C. gloeosporioides species complex were reported in the United States (Munir et al. 2016), South America (Velho et al. 2018), Korea (Park et al. 2018), and recently in Belgium (Grammen et al. 2019). In September 2017, bitter rot symptoms were observed on apple fruit (cultivars Joya Cripps Red, Granny Smith, and Pink Lady) in four orchards in the region of Occitanie in France. The rot began as circular brown spots, 1 to 2 mm in diameter, which enlarged rapidly. Sixteen isolates were obtained from symptomatic apples by culturing pieces of necrotic tissue on potato dextrose agar. Cultures showed light-gray, cottony mycelium that became darker with age, with the reverse color being brownish and becoming black with age. Conidia were produced in small orange masses and were mainly cylindrical, with rounded ends. For all isolates, the production of perithecia was observed in culture, and asci and ascospores were observed under the microscope. The width and length of 50 conidia were examined and ranged from 3.1 to 4 µm (average 3.5 µm) and from 8 to 13 µm (average 10.5 µm), respectively. Based on these morphological characteristics, those isolates correspond to teleomorph of species belonging to C. gloeosporioides species complex (Weir et al. 2012). Total genomic DNA was extracted from the 16 isolates, and the internal transcribed spacer region of rDNA was amplified using the universal primers ITS4 and ITS5 and then sequenced. For all isolates, the resulting sequences were 100% identical to C. fructicola sequences obtained by a BLAST search in GenBank. Three other loci (partial GAPDH, TUB2, and ApMat genes) were amplified and sequenced to further characterize two isolates (UBOCC-A-118064 and UBOCC-A-118065; GenBank accession nos. MK114103 to MK114110, respectively). Multilocus phylogenetic analysis carried out with the obtained and reference sequences (Da Lio et al. 2018) revealed that the isolates clustered within C. fructicola, as suggested by the BLAST results; this is also consistent with their initial identification as C. gloeosporioides. To confirm Koch’s postulates, for the two characterized isolates, 10 ‘Golden Delicious’ apples were surface sterilized and then wound inoculated with 20 μl of a conidial suspension (105 conidia/ml). After 10 days of incubation at 20°C, symptoms identical to those initially observed developed around the inoculation point, whereas controls inoculated with water remained symptomless. Fungal thalli reisolated from the lesions were morphologically similar to the original isolate. To our knowledge, this is the first report in Europe of C. fructicola causing bitter rot on apple. According to Munir et al. (2016), C. fructicola was reported to be more aggressive than species belonging to the C. acutatum species complex such as C. fioriniae previously identified in France (Nodet et al. 2016); moreover, this species is associated with Glomerella leaf spot, an emerging leaf disease never described in Europe (Velho et al. 2018). All those points encourage the development of species-specific management strategies for this pathogen in European countries.

Published
2019

36. Combined Metabarcoding and Multi-locus approach for Genetic characterization of Colletotrichum species associated with common walnut (Juglans regia) anthracnose in France

Author

Da Lio, Daniele, Cobo-Díaz, José, Masson, Cyrielle, Chalopin, Morgane, Kebe, Djiby, Giraud, Michel, Verhaeghe, Agnes, Nodet, Patrice, Sarrocco, Sabrina, Le Floch, Gaétan, Baroncelli, Riccardo, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre Technique Interprofessionnel des Fruits et Légumes (CTIFL), Department of Agriculture, University of Pisa - Università di Pisa -Food and Environment, Da Lio D., Cobo-DIaz J.F., Masson C., Chalopin M., Kebe D., Giraud M., Verhaeghe A., Nodet P., Sarrocco S., Le Floch G., and Baroncelli R.

Subjects
Multidisciplinary, metabarcoding, microbiome, fungal populations, trees, Glomerella, pathogenic fungi, plant pathogens, lcsh:R, lcsh:Medicine, Genetic Variation, food and beverages, Juglans, Article, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Colletotrichum, DNA Barcoding, Taxonomic, Metagenome, lcsh:Q, France, lcsh:Science, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Plant Diseases
Abstract

International audience; Juglans regia (walnut) is a species belonging to the family Juglandaceae. Broadly spread in diverse temperate and subtropical regions, walnut is primarily cultivated for its nuts. In France, Colletotrichum sp. on walnut was detected for the first time in 2007; in 2011 the disease led to 50–70% losses in nut production. A combined approach of metabarcoding analysis and multi-locus genetic characterization of isolated strains has been used for taxonomic designation and to study the genetic variability of this pathogen in France. Evidence indicates that four Colletotrichum species are associated with walnut in France: 3 belong to the C. acutatum species complex and 1 to the C. gloeosporioides species complex. Results also show that C. godetiae is the most abundant species followed by C. fioriniae; while C. nymphaeae and another Colletotrichum sp. belonging to the C. gloeosporioides complex are found rarely. Representative isolates of detected species were also used to confirm pathogenicity on walnut fruits. The results show a high variability of lesion’s dimensions among isolates tested. This study highlights the genetic and pathogenic heterogeneity of Colletotrichum species associated with walnut anthracnose in France providing useful information for targeted treatments or selection of resistant cultivars, in order to better control the disease.

Published
2018

37. Whole-Genome Sequence of the Orchid Anthracnose Pathogen Colletotrichum orchidophilum

Author

Gaétan Le Floch, Serenella A. Sukno, Riccardo Baroncelli, Michael R. Thon, Giovanni Cafà, Sabrina Sarrocco, Baroncelli R., Sukno S.A., Sarrocco S., Cafa G., Le Floch G., Thon M.R., Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), Universidad de Salamanca, and Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali

Subjects
0106 biological sciences, 0301 basic medicine, Species complex, Physiology, Range (biology), Fungus, 01 natural sciences, Genome, 03 medical and health sciences, Botany, Orchidaceae, plant pathogens, pathogenic fungi, genome, genomics, bioinformatics, Glomerella, Colletotrichum, DNA, Fungal, Orchidaceae, Pathogen, ComputingMilieux_MISCELLANEOUS, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Plant Diseases, Whole genome sequencing, biology, Whole Genome Sequencing, fungi, Fungal genetics, food and beverages, General Medicine, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, 030104 developmental biology, Genome, Fungal, Agronomy and Crop Science, 010606 plant biology & botany
Abstract

Colletotrichum orchidophilum is a plant-pathogenic fungus infecting a wide range of plant species belonging to the family Orchidaceae. In addition to its economic impact, C. orchidophilum has been used in recent years in evolutionary studies because it represents the closest related species to the C. acutatum species complex. Here, we present the first-draft whole-genome sequence of C. orchidophilum IMI 309357, providing a resource for future research on anthracnose of Orchidaceae and other hosts.

Published
2018

38. The Colletotrichum acutatum Species Complex as a Model System to Study Evolution and Host Specialization in Plant Pathogens

Author

Serenella A. Sukno, Riccardo Baroncelli, Gaétan Le Floch, Pedro Talhinhas, Michael R. Thon, Flora Pensec, Baroncelli R., Talhinhas P., Pensec F., Sukno S.A., Le Floch G., Thon M.R., Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), and Instituto de Investigação Científica Tropical (IICT)

Subjects
0301 basic medicine, Microbiology (medical), Species complex, Colletotrichum acutatum, Evolution, fungal lifestyle, lcsh:QR1-502, Biology, Microbiology, lcsh:Microbiology, colletotrichum acutatum, 03 medical and health sciences, Phylogenetics, Genus, evolution, pathogenicity, Pathogenicity, Anthracnose, ComputingMilieux_MISCELLANEOUS, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Comparative genomics, anthracnose, Phylogenetic tree, Ecology, Host (biology), Fungal lifestyle, biology.organism_classification, 030104 developmental biology, Colletotrichum, Evolutionary biology
Abstract

Perspective Colletotrichum spp. infect a wide diversity of hosts, causing plant diseases on many economically important crops worldwide. The genus contains approximately 189 species organized into at least 11 major phylogenetic lineages, also known as species complexes. The Colletotrichum acutatum species complex is a diverse yet relatively closely related group of plant pathogenic fungi within this genus. Within the species complex we find a wide diversity of important traits such as host range and host preference, mode of reproduction and differences in the strategy used to infect their hosts. Research on fungal comparative genomics have attempted to find correlations in these traits and patterns of gene family evolution but such studies typically compare fungi from different genera or even different fungal Orders. The C. acutatum species complex contains most of this diversity within a group of relatively closely related species. This Perspective article presents a review of the current knowledge on C. acutatum phylogeny, biology, and pathology. It also demonstrates the suitability of C. acutatum for the study of gene family evolution on a fine scale to uncover evolutionary events in the genome that are associated with the evolution of phenotypic characters important for host interactions. info:eu-repo/semantics/publishedVersion

Published
2017

39. First report of pear bitter rot caused by Colletotrichum fioriniae in France

Author

Patrice Nodet, Daniele Da Lio, Amélie Weill, G. Le Floch, Riccardo Baroncelli, Da Lio D., Baroncelli R., Weill A., Le Floch G., Nodet P., Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), and Université de Brest (UBO)

Subjects
0106 biological sciences, 0301 basic medicine, Malus, PEAR, biology, Inoculation, food and beverages, Plant Science, 030108 mycology & parasitology, pear disease, emerging pathogens, plant pathogens, fungi, biology.organism_classification, 01 natural sciences, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Conidium, Spore, 03 medical and health sciences, Horticulture, Potato dextrose agar, Agronomy and Crop Science, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Mycelium, 010606 plant biology & botany, Black spot
Abstract

International audience; Bitter rot is a common disease mainly affecting apples (Malus domestica) worldwide, and resulting in considerable economic losses, but pears can also be affected (Ivic et al. 2013). Most of the reports refer to bitter rot of Chinese and Asian pears (Pyrus bretschneideri and P. pyrifolia) caused by C. acutatum sensu lato or C. fructicola (Jiang et al. 2014; Kim et al. 2007; Li et al. 2013). To our knowledge, the only report of bitter rot on European pears (P. communis) was done by Ivic et al. (2013) in Croatia and the causal agent was identified as C. fioriniae. In the last 4 to 5 years, anthracnose symptoms have been repeatedly observed on the pear cultivar Beurré Hardy in September during harvest in an orchard near Brest, France. Lesions were round, 1 to 4 cm in diameter, brown, and dry, with acervuli, producing orange spore masses in concentric rings. Two fungal isolates were obtained (in 2015 and 2016, respectively) from symptomatic pears by culturing necrotic tissue pieces on potato dextrose agar (PDA) at 25°C in the dark. Cultures were light gray, with cottony aerial mycelium becoming darker with age and reverse ranging from brownish pink to dark gray with black spots. Cultures have dark melanized structures similar to acervuli that oozed orange-colored conidia. Conidia were cylindrical to fusiform, pointed at one or both ends, and measured 10.0 to 14.0 μm × 3.0 to 3.5 μm. Both cultural and morphological characteristics were similar to those described for C. acutatum sensu lato (Damm et al. 2012). Total genomic DNA was extracted and the rDNA ITS region was amplified using universal primers ITS4 and ITS5 then sequenced. For both isolates (UBOCC-A-116033 and UBOCC-A-116034), resulting sequences were 100% identical to C. acutatum species complex sequences. Based on Damm et al. (2012), strains were further characterized by sequencing partial ACT, CHS-1, GAPDH, HIS3, and TUB2 genes (GenBank accession nos. KY344741–52). Multilocus phylogenetic analyses carried out with the obtained and reference sequences (Damm et al. 2012) revealed that both isolates clustered within C. fioriniae, as observed using BLAST; this result was consistent with their initial identification as belonging to the C. acutatum species complex. Koch’s postulates were performed on 10 ‘Comice’ pears for each isolate. Surface sterilized fruits were wound-inoculated with 20 μl of a conidial suspension (105 conidia ml–1). After 10 days incubation at 20°C, symptoms identical to those initially observed developed around the inoculation point, while controls inoculated with water remained symptomless. Fungal colonies reisolated from the lesions were morphologically similar to the original isolates. To our knowledge, this is the first report of pear bitter rot caused by C. fioriniae in France. Moreover, to date, bitter rot was not considered as a major problem for pear growing, but as pears are the eighth largest fruit crop in production yield worldwide, pear bitter rot caused by Colletotrichum species may become a major problem in the future and require further investigation.

Published
2017

40. Gene family expansions and contractions are associated with host range in plant pathogens of the genus Colletotrichum

Author

Giovanni Vannacci, Michael R. Thon, Daniel Buchvaldt Amby, Sabrina Sarrocco, Antonio Zapparata, Gaétan Le Floch, Surapareddy Sreenivasaprasad, Riccardo Baroncelli, Eric B. Holub, Serenella A. Sukno, Richard J. Harrison, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), University of Copenhagen = Københavns Universitet (KU), Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, University of Warwick [Coventry], Universidad de Salamanca, Baroncelli R., Amby D.B., Zapparata A., Sarrocco S., Vannacci G., Le Floch G., Harrison R.J., Holub E., Sukno S.A., Sreenivasaprasad S., and Thon M.R.

Subjects
0301 basic medicine, Species complex, Fungal genomic, Genes, Fungal, Genome, Host Specificity, Evolution, Molecular, Necrosis, 03 medical and health sciences, Colletotrichum acutatum, Phylogenetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Plant pathogen, Colletotrichum, Genetics, Cluster Analysis, Gene family, Fungal genomics, Colletotrichum spp, Anthracnose, SB, Phylogeny, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 2. Zero hunger, Phylogenetic tree, biology, QK, fungi, Computational Biology, High-Throughput Nucleotide Sequencing, food and beverages, Molecular Sequence Annotation, Genomics, Sordariomycetes, biology.organism_classification, CAZyme, Biotechnology, 030104 developmental biology, Multigene Family, Host-Pathogen Interactions, Genome, Fungal, Research Article
Abstract

Background Many species belonging to the genus Colletotrichum cause anthracnose disease on a wide range of plant species. In addition to their economic impact, the genus Colletotrichum is a useful model for the study of the evolution of host specificity, speciation and reproductive behaviors. Genome projects of Colletotrichum species have already opened a new era for studying the evolution of pathogenesis in fungi. Results We sequenced and annotated the genomes of four strains in the Colletotrichum acutatum species complex (CAsc), a clade of broad host range pathogens within the genus. The four CAsc proteomes and secretomes along with those representing an additional 13 species (six Colletotrichum spp. and seven other Sordariomycetes) were classified into protein families using a variety of tools. Hierarchical clustering of gene family and functional domain assignments, and phylogenetic analyses revealed lineage specific losses of carbohydrate-active enzymes (CAZymes) and proteases encoding genes in Colletotrichum species that have narrow host range as well as duplications of these families in the CAsc. We also found a lineage specific expansion of necrosis and ethylene-inducing peptide 1 (Nep1)-like protein (NLPs) families within the CAsc. Conclusions This study illustrates the plasticity of Colletotrichum genomes, and shows that major changes in host range are associated with relatively recent changes in gene content. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2917-6) contains supplementary material, which is available to authorized users.

Published
2016

41. First Report of Apple Bitter Rot Caused by Colletotrichum fioriniae in Brittany, France

Author

Riccardo Baroncelli, Patrice Nodet, D. Faugère, G. Le Floch, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), Nodet P., Baroncelli R., Faugere D., and Le Floch G.

Subjects
0106 biological sciences, 0301 basic medicine, emerging disease, fungi, plant pathogens, phylogenetics, Malus, Glomerella, fungi, Plant Science, 030108 mycology & parasitology, Biology, Colletotrichum fioriniae, 01 natural sciences, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, 03 medical and health sciences, Botany, Agronomy and Crop Science, ComputingMilieux_MISCELLANEOUS, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 010606 plant biology & botany
Abstract

France is the third largest European producer of apples (Malus domestica), after Poland and Italy, with 2.1 million tons yearly (Eurostat 2015), and the largest producer of European cider apples, with 8,500 ha and 250,000 tons of fruit. Cider apples from Brittany represent over a quarter of the national tonnage (Anonymous 2012). Apple bitter rot symptoms have been observed on ‘Galeuse’ apples (a local variety in Brittany) for nearly 5 to 7 years and again in September 2015, during harvest at one apple orchard near Brest, France. Lesions were round, 1 to 4 cm in diameter, brown and dry with acervuli, producing orange spore masses in concentric rings. Fungal isolates were obtained from symptomatic apples by culturing necrotic tissue pieces on potato dextrose agar at 25°C in the dark. Cultures were light gray, with cottony aerial mycelium becoming darker with age and with reverse colors ranging from brownish pink to dark gray with black spots. Cultures had dark melanized structures similar to acervuli that oozed orange-colored conidia. Conidia were cylindrical to fusiform, pointed at one or both ends, and 10.0 to 14.0 μm × 3.0 to 3.5 μm. Both cultural and morphological characteristics were similar to those described for Colletotrichum acutatum sensu lato (Damm et al. 2012). Total genomic DNA was extracted and the ITS region of rDNA was amplified using the universal primers ITS4 and ITS5, then sequenced. The resulting sequence was 100% identical to C. acutatum species complex sequences obtained by a BLAST search in GenBank. Based on Damm et al. (2012), five other loci were used to further characterize the isolate: partial GAPDH, CHS-1, HIS3, ACT, and TUB2 genes sequences were amplified and sequenced. Sequences were deposited in GenBank (Accession Nos. KT887552 for ITS, KT887551 for TUB, KT887555 for CHS, KT887553 for HIS3, KT887556 for ACT, and KT887554 for GAPDH). The multilocus phylogenetic analysis carried out with the obtained sequences and reference sequences (Damm et al. 2012) revealed that the isolate clustered within C. fioriniae, as also suggested by the BLAST results, and consistent with the initial identification as C. acutatum. Koch’s postulates were performed on 10 ‘Golden Delicious’ apples. Surface sterilized fruits were wound-inoculated with 20 μl of a conidial suspension (105 conidia/ml). After 10 days incubating at 20°C, symptoms identical to those initially observed developed around the inoculation point, while controls inoculated with water remained symptomless. Fungal colonies reisolated from the lesions were morphologically similar to the original isolate. Previous studies have demonstrated that this pathogen is present worldwide on Malus spp., and apple bitter rot is considered one of the most important diseases in the United States (Ivic et al. 2013). In Europe, there are increasing numbers of reports ofColletotrichum species on apples (Ivic et al. 2013; Baroncelli et al. 2014), but to our knowledge, this is the first report in France of anthracnose on apples caused by C. fioriniae. In Europe, bitter rot caused by C. acutatum species may become a major problem and require additional investigation.

Published
2016

42. L'interprétation des traités établissant la frontière

Author

STARITA, Massimo, D'Argent, P, Alland, D, Vijffels, A, Khan, D-E, Starita, M, Mbengue, M, Kranz, J, Couvreur, P, Gautier, P, Reichler, P, Hafner, G, Le Floch, G, Reinisch, A, Stahn, C, Besson, S, Uerpmann-Wittzack, R, Hoffmeister, F, Benlolo-Carabot, M, and STARITA, Massimo

Subjects
frontiere - interpretazione - diritto dei trattati, Settore IUS/13 - Diritto Internazionale, international borders - interpretation - law of treaties, frontières - interprétation - droit des traités
Abstract

Il lavoro si occupa del problema se l'interpretazione dei trattati che stabiliscono frontiere è sottoposta a principi particolari o se, al contrario, segue i principi comuni applicabili all'interpretazione dei trattati. La tesi esposta è che le particolarità dell'interpretazione in questo settore sono due. La prima cpmsoste nell'applicazione, accanto ai principi generali di natura metodologica fissati negli articoli 31-33 della Convenzione di Vienna sul diritto dei trattati, di un principio interpretativo sostanziale, e cioè il cd. principio della stabilità delle frontiere, anche se il suo ambito di applicazione è più ristretto di quanto possa a prima vista ritenersi. La seconda peculiarità consiste nel metodo interpretativo seguito dall'interprete, che si discosta, in una certa misura almeno, dalla teoria del sillogismo giuridico. Le problème que l'on se pose dans cet exposé est de savoir si l'interprétation des traités établissant des frontières est soumisse à des principes interprétaifs particuliers ou si, au contraire, elle suit les principes communs qui sont applicables aux traités. La thèse proposée est que les particularités sont au nombre de deux. La première consiste dans l'application, à coté de des principes généraux de nature méthodologiques qui sont fixés dans les articles 31-33 de la Convention de Vienne, d'un principe interprétatif substantiel, à savoir le principe de la stabilitè des frontières, meme si la portée de ce principe est plus restreinte qu'il peut apparaitre à première vue. La deuxième particularité concerne la méthode suivie par l'interprète, qui s'éloigne, dans une certaine mesure, de la théorie du syllogisme juridique.

Published
2016

43. Shifts in Fusarium Communities and Mycotoxins in Maize Residues, Soils, and Wheat Grains throughout the Wheat Cycle: Implications for Fusarium Head Blight Epidemiology.

Author

Nguyen TBH, Henri-Sanvoisin A, Coton M, Le Floch G, and Picot A

Abstract

Fusarium Head Blight (FHB), predominantly caused by Fusarium species, is a devastating cereal disease worldwide. While considerable research has focused on Fusarium communities in grains, less attention has been given to residues and soil, the primary inoculum sources. Knowledge of Fusarium spp. diversity, dynamics, and mycotoxin accumulation in these substrates is crucial for assessing their contribution to wheat head infection and the complex interactions among Fusarium communities throughout the wheat cycle. We monitored six minimum-tillage wheat fields, with maize as the preceding crop, over two years. Soils, maize residues, and wheat grains were sampled at four stages. Fusarium composition was analyzed using a culture-dependent method, species-specific qPCR, and EF1α region metabarcoding sequencing, enabling species-level resolution. The Fusarium communities were primarily influenced by substrate type, accounting for 35.8% of variance, followed by sampling location (8.1%) and sampling stage (3.2%). Among the 32 identified species, F. poae and F. graminearum dominated grains, with mean relative abundances of 47% and 29%, respectively. Conversely, residues were mainly contaminated by F. graminearum , with a low presence of F. poae , as confirmed by species-specific qPCR. Notably, during periods of high FHB pressure, such as in 2021, F. graminearum was the dominant species in grains. However, in the following year, F. poae outcompeted F. graminearum , resulting in reduced disease pressure, consistent with the lower pathogenicity of F. poae . Source Tracker analysis indicated that residues were a more significant source of Fusarium contamination on wheat in 2021 compared to 2022, suggesting that F. graminearum in 2021 primarily originated from residues, whereas F. poae 's sources of infection need further investigation. Additionally, multiple mycotoxins were detected and quantified in maize residues during the wheat cycle, raising the question of their ecological role and impact on the soil microbiota.

Published
2024
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44. Genetic diversity and population structure of Botryosphaeria dothidea and Neofusicoccum parvum on English walnut (Juglans regia L.) in France.

Author

Belair M, Picot A, Lepais O, Masson C, Hébrard MN, Moronvalle A, Comont G, Gabri Martin VM, Tréguer S, Laloum Y, Corio-Costet MF, Michailides TJ, Moral J, Le Floch G, and Pensec F

Subjects
France, Genotype, Juglans microbiology, Ascomycota genetics, Ascomycota classification, Genetic Variation, Plant Diseases microbiology, Microsatellite Repeats genetics
Abstract

Botryosphaeriaceae species are the major causal agents of walnut dieback worldwide, along with Diaporthe species. Botryosphaeria dothidea and Neofusicoccum parvum are the only two Botryosphaeriaceae species associated with this recently emergent disease in France, and little is known about their diversity, structure, origin and dispersion in French walnut orchards. A total of 381 isolates of both species were genetically typed using a sequence-based microsatellite genotyping (SSR-seq) method. This analysis revealed a low genetic diversity and a high clonality of these populations, in agreement with their clonal mode of reproduction. The genetic similarity among populations, regardless of the tissue type and the presence of symptoms, supports the hypothesis that these pathogens can move between fruits and twigs and display latent pathogen lifestyles. Contrasting genetic patterns between N. parvum populations from Californian and Spanish walnut orchards and the French ones suggested no conclusive evidence for pathogen transmission from infected materials. The high genetic similarity with French vineyards populations suggested instead putative transmission between these hosts, which was also observed with B. dothidea populations. Overall, this study provides critical insight into the epidemiology of two important pathogens involved in the emerging dieback of French walnut orchards, including their distribution, potential to mate, putative origin and disease pathways., (© 2024. The Author(s).)

Published
2024
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45. New insights into mycotoxin risk management through fungal population genetics and genomics.

Author

Nguyen TBH, Foulongne-Oriol M, Jany JL, le Floch G, and Picot A

Abstract

Mycotoxin contamination of food and feed is a major global concern. Chronic or acute dietary exposure to contaminated food and feed can negatively affect both human and animal health. Contamination occurs through plant infection by toxigenic fungi, primarily Aspergillus and Fusarium spp., either before or after harvest. Despite the application of various management strategies, controlling these pathogens remains a major challenge primarily because of their ability to adapt to environmental changes and selection pressures. Understanding the genetic structure of plant pathogen populations is pivotal for gaining new insights into their biology and epidemiology, as well as for understanding the mechanisms behind their adaptability. Such deeper understanding is crucial for developing effective and preemptive management strategies tailored to the evolving nature of pathogenic populations. This review focuses on the population-level variations within the two most economically significant toxigenic fungal genera according to space, host, and pathogenicity. Outcomes in terms of migration patterns, gene flow within populations, mating abilities, and the potential for host jumps are examined. We also discuss effective yet often underutilized applications of population genetics and genomics to address practical challenges in the epidemiology and disease control of toxigenic fungi.

Published
2024
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46. Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi.

Author

Baroncelli R, Cobo-Díaz JF, Benocci T, Peng M, Battaglia E, Haridas S, Andreopoulos W, LaButti K, Pangilinan J, Lipzen A, Koriabine M, Bauer D, Le Floch G, Mäkelä MR, Drula E, Henrissat B, Grigoriev IV, Crouch JA, de Vries RP, Sukno SA, and Thon MR

Subjects
Phylogeny, Adaptation, Physiological genetics, Gene Expression Profiling methods, Plant Diseases microbiology, Plant Diseases genetics, Colletotrichum genetics, Colletotrichum pathogenicity, Transcriptome, Genome, Fungal, Evolution, Molecular
Abstract

Background: Colletotrichum fungi infect a wide diversity of monocot and dicot hosts, causing diseases on almost all economically important plants worldwide. Colletotrichum is also a suitable model for studying gene family evolution on a fine scale to uncover events in the genome associated with biological changes., Results: Here we present the genome sequences of 30 Colletotrichum species covering the diversity within the genus. Evolutionary analyses revealed that the Colletotrichum ancestor diverged in the late Cretaceous in parallel with the diversification of flowering plants. We provide evidence of independent host jumps from dicots to monocots during the evolution of Colletotrichum, coinciding with a progressive shrinking of the plant cell wall degradative arsenal and expansions in lineage-specific gene families. Comparative transcriptomics of 4 species adapted to different hosts revealed similarity in gene content but high diversity in the modulation of their transcription profiles on different plant substrates. Combining genomics and transcriptomics, we identified a set of core genes such as specific transcription factors, putatively involved in plant cell wall degradation., Conclusions: These results indicate that the ancestral Colletotrichum were associated with dicot plants and certain branches progressively adapted to different monocot hosts, reshaping the gene content and its regulation., (© The Author(s) 2024. Published by Oxford University Press GigaScience.)

Published
2024
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47. Food transport in Reptilia: a comparative viewpoint.

Author

Bels V, Le Floch G, Kirchhoff F, Gastebois G, Davenport J, and Baguette M

Subjects
Animals, Vertebrates, Reptiles
Abstract

Reptilia exploit a large diversity of food resources from plant materials to living mobile prey. They are among the first tetrapods that needed to drink to maintain their water homeostasis. Here were compare the feeding and drinking mechanisms in Reptilia through an empirical approach based on the available data to open perspectives in our understanding of the evolution of the various mechanisms determined in these Tetrapoda for exploiting solid and liquid food resources. This article is part of the theme issue 'Food processing and nutritional assimilation in animals'.

Published
2023
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48. Profiling Walnut Fungal Pathobiome Associated with Walnut Dieback Using Community-Targeted DNA Metabarcoding.

Author

Belair M, Pensec F, Jany JL, Le Floch G, and Picot A

Abstract

Walnut dieback can be caused by several fungal pathogenic species, which are associated with symptoms ranging from branch dieback to fruit necrosis and blight, challenging the one pathogen-one disease concept. Therefore, an accurate and extensive description of the walnut fungal pathobiome is crucial. To this end, DNA metabarcoding represents a powerful approach provided that bioinformatic pipelines are evaluated to avoid misinterpretation. In this context, this study aimed to determine (i) the performance of five primer pairs targeting the ITS region in amplifying genera of interest and estimating their relative abundance based on mock communities and (ii) the degree of taxonomic resolution using phylogenetic trees. Furthermore, our pipelines were also applied to DNA sequences from symptomatic walnut husks and twigs. Overall, our results showed that the ITS2 region was a better barcode than ITS1 and ITS, resulting in significantly higher sensitivity and/or similarity of composition values. The ITS3/ITS4_KYO1 primer set allowed to cover a wider range of fungal diversity, compared to the other primer sets also targeting the ITS2 region, namely, GTAA and GTAAm. Adding an extraction step to the ITS2 sequence influenced both positively and negatively the taxonomic resolution at the genus and species level, depending on the primer pair considered. Taken together, these results suggested that Kyo set without ITS2 extraction was the best pipeline to assess the broadest fungal diversity, with a more accurate taxonomic assignment, in walnut organs with dieback symptoms.

Published
2023
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49. First report of grapefruit rot caused by Colletotrichum gloeosporioides and C. karsti in France.

Author

Nodet P, Da Lio D, Dubreuil N, Leboulanger A, and Le Floch G

Abstract

The grapefruit ( Citrus paradisi ) is a citrus hybrid tree ( C. maxima & C. sinensis ). Due to nutritional value and its bioactive compounds, the fruits are recognized as a functional food, valued as promoting health. French grapefruit production is low (7.5 Kt/year) but is confined to a restricted area in Corsica and benefits from a quality label, the economic impact of its cultivation being therefore locally significant. Since 2015 previously unreported symptoms have been repeatedly observed on grapefruits in more than half of the orchards in Corsica, with an incidence of 30% of fruits altered. Brown to black circular spots were observed on fruits and leaves, surrounded by chlorotic halos on the latter. On the mature fruit, lesions were round, 4 to 10 mm in diameter, brown and dry (e-Xtra 1). Although the lesions are superficial, the fruits cannot be marketed due to constraints linked to the quality label. 75 fungal isolates were obtained from symptomatic fruits or leaves collected in Corsica (in 2016, 2017, and 2021). Cultures obtained after 7 days on PDA at 25°C, were white to light grey in colour, forming concentric rings or dark spots on the agar surface. We did not observe any notable difference among the isolates except some evolved towards a more marked grey. Colonies tend to form a cottony aerial mycelium and orange conidial masses appear with age. The conidia were hyaline, aseptate, cylindrical with ends rounded, and measured 14.9 ± 0.95 µm length and 5.1 ± 0.45 µm width (n = 50). Cultural and morphological characteristics were similar to those described for C. gloeosporioides s. lat. or C. boninense s. lat. (Weir et al. 2012 ; Damm et al. 2012). Total genomic DNA was extracted from all isolates, and the ITS region of rDNA was amplified with ITS 5 & 4 primers, then sequenced (GenBank Accession Nos. OQ509805-808). For 90% of isolates GenBank BLASTn results were 100% identical to C. gloeosporioides isolates sequences, whereas for other isolates the resulting sequences were 100% identical to C. karsti or C. boninense isolates sequences. Four strains (three C. gloeosporioides with light colour differences, in order to see if there was diversity among isolates of C. gloeosporioides s. lato ; and one C. karsti ) were further characterized by sequencing partial actin [ACT], calmodulin [CAL], chitin synthase [CHS-1], glyceraldehyde-3-phosphate dehydrogenase [GAPDH], β-tubulin 2 [TUB2], for all strains ; glutamine synthetase [GS], Apn2-Mat1-2-1 intergenic spacer and partial mating type (Mat1-2) gene [ApMAT] for C. gloeosporioides s. lat. , and HIS3 for C. boninense s. lat. (Weir et al. 2012 ; Silva et al, 2012) (GenBank Accession Nos. OQ509805-808 & OQ507698-724). Multilocus phylogenetic analyses carried out with the obtained and Genbank available sequences confirmed that 3 isolates (UBOCC-A-116036, -116038, & -116039) clustered within C. gloeosporioides s. s. , while the other (UBOCC-A-116037) clustered within C. karsti (e-Xtra 2) 'Star ruby' grapefruits were surface sterilized then wound-inoculated with 20 μl of a conidial suspension (10 5 conidia ml -1 ) of UBOCC-A-116036 & 116037 isolates or 20 μl sterile water for control (ten fruits for each isolate or control). After 10 days incubation at 20°C, symptoms, identical to those initially observed, developed around the inoculation point, while controls inoculated with water remained symptomless. Fungal colonies re-isolated from the lesions were morphologically like the original isolates. Recently, various infections caused by some Colletotrichum sp. have strongly compromised citrus production in different Mediterranean countries: ie Italy (Aiello et al. 2015), Portugal (Ramos et al. 2016), Tunisia (Ben Hadj Daoud et al. 2019), Turkey (Uysal et al. 2022). In these studies, C. gloeosporioides s. s. and C. karsti were identified as the causal agents. These two species were the predominant Colletotrichum sp. associated with Citrus and allied genera in Europe (Guarnaccia et al. 2017). To our knowledge, our study is the first report of C. gloeosporioides and C. karsti causing anthracnose on grapefruit in France, which confirms the incidence of these two pathogens on the Mediterranean rim. Given the economic importance of citrus cultivation in the Mediterranean region, the presence of Colletotrichum spp. should deserves to be monitored, and a control strategy should be considered.

Published
2023
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50. Influence of Maize Residues in Shaping Soil Microbiota and Fusarium spp. Communities.

Author

Cobo-Díaz JF, Legrand F, Le Floch G, and Picot A

Subjects
Plant Diseases microbiology, Soil chemistry, Zea mays microbiology, Ascomycota, Fusarium genetics, Microbiota
Abstract

Fusarium head blight (FHB) is a devastating fungal disease of small grain cereals including wheat. Causal fungal agents colonize various components of the field during their life cycle including previous crop residues, soil, and grains. Although soil and residues constitute the main inoculum source, these components have received much less attention than grains. This study aimed at disentangling the role of previous crop residues in shaping soil microbiota, including Fusarium spp. communities, in fields under wheat-maize rotation. Such knowledge may contribute to better understand the complex interactions between Fusarium spp. and soil microbiota. Dynamics of bacterial and fungal communities, with a special focus on Fusarium spp., were monitored in soils at 3 time points: during wheat cultivation (April 2015 and 2017) and after maize harvest (November 2016) and in maize residues taken from fields after harvest. Shifts in microbiota were also evaluated under mesocosm experiments using soils amended with maize residues. Fusarium graminearum and F. avenaceum were predominant on maize residues but did not remain in soils during wheat cultivation. Differences in soil bacterial diversity and compositions among years were much lower than variation between fields, suggesting that bacterial communities are field-specific and more conserved over time. In contrast, soil fungal diversity and compositions were more influenced by sampling time. Maize residues, left after harvest, led to a soil enrichment with several fungal genera, including Epicoccum, Fusarium, Vishniacozyma, Papiliotrema, Sarocladium, Xenobotryosphaeria, Ramularia, Cladosporium, Cryptococcus, and Bullera, but not with bacterial genera. Likewise, under mesocosm conditions, the addition of maize residues had a stronger influence on fungal communities than on bacterial communities. In particular, addition of maize significantly increased soil fungal richness, while bacteria were much less prone to changes. Based on co-occurrence networks, OTUs negatively correlated to Fusarium spp. were identified, such as those assigned to Epicoccum and Vishniacozyma. Altogether, our results allowed to gain a deeper insight into the complex microbiota interactions in soils, with bacteria and fungi responding differently to environmental disturbances., (© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Published
2022
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