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35 results on '"Coutinho, P.M."'

1. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

Author

Tuskan, G.A., DiFazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Aerts, A., Bhalerao, R.R., Bhalerao, R.P., Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Carlson, J., Chalot, M., Chapman, J., Chen, G.-L., Cooper, D., Coutinho, P.M., Couturier, J., Covert, S., Cronk, Q., Cunningham, R., Davis, J., Degroeve, S., Dejardin, A., dePamphillis, C., Detter, J., Dirks, B., Dubchak, I., Duplessis, S., Ehiting, J., Ellis, B., Gendler, K., Goodstein, D., Gribskov, M., Grimwood, J., Groover, A., Gunter, L., Hamberger, B., Heinze, B., Helariutta, Y., Henrissat, B., Holligan, D., Holt, R., Huang, W., Islam-Faridi, N., Jones, S., Jones-Rhoades, M., Jorgensen, R., Joshi, C., Kangasjarvi, J., Karlsson, J., Kelleher, C., Kirkpatrick, R., Kirst, M., Kohler, A., Kalluri, U., Larimer, F., Leebens-Mack, J., Leple, J.-C., Locascio, P., Lou, Y., Lucas, S., Martin, F., Montanini, B., Napoli, C., Nelson, D.R., Nelson, D., Nieminen, K., Nilsson, O., Peter, G., Philippe, R., Pilate, G., Poliakov, A., Razumovskaya, J., Richardson, P., Rinaldi, C., Ritland, K., Rouze, P., Ryaboy, D., Schmutz, J., Schrader, J., Segerman, B., Shin, H., Siddiqui, A., Sterky, F., Terry, A., Tsai, C., Uberbacher, E., Unneberg, P., and Vahala, J.

Subjects
Basic biological sciences
Published
2006

2. Botrytis cinerea B05.10 Genome sequencing

Author

Amselem, J., Cuomo, C.A., van Kan, J.A.L., Viaud, M., Benito, E.P., Couloux, A., Coutinho, P.M., de Vries, R.P., Dyer, P.S., Fillinger, S., Fournier, E., Gout, L., Hahn, M., Kohn, L., Lapalu, N., Plummer, K.M., Pradier, J.M., Quévillon, E., Sharon, A., Simon, A., ten Have, A., Tudzynski, B., Tudzynski, P., Wincker, P., Andrew, M., Anthouard, V., Beever, R.E., Beffa, R., Benoit, I., Bouzid, O., Brault, B., Chen, Z., Choquer, M., Collemare, J., Cotton, P., Danchin, E.G., Da Silva, C., Gautier, A., Giraud, C., Giraud, T., Gonzalez, C., Grossetete, S., Güldener, U., Henrissat, B., Howlett, B.J., Kodira, C., Kretschmer, M., Lappartient, A., Leroch, M., Levis, C., Mauceli, E., Neuvéglise, C., Oeser, B., Pearson, M., Poulain, J., Poussereau, N., Quesneville, H., Rascle, C., Schumacher, J., Ségurens, B., Sexton, A., Silva, E., Sirven, C., Soanes, D.M., Talbot, N.J., Templeton, M., Yandava, C., Yarden, O., Zeng, Q., Rollins, J.A., Lebrun, M.H., Dickman, M., Amselem, J., Cuomo, C.A., van Kan, J.A.L., Viaud, M., Benito, E.P., Couloux, A., Coutinho, P.M., de Vries, R.P., Dyer, P.S., Fillinger, S., Fournier, E., Gout, L., Hahn, M., Kohn, L., Lapalu, N., Plummer, K.M., Pradier, J.M., Quévillon, E., Sharon, A., Simon, A., ten Have, A., Tudzynski, B., Tudzynski, P., Wincker, P., Andrew, M., Anthouard, V., Beever, R.E., Beffa, R., Benoit, I., Bouzid, O., Brault, B., Chen, Z., Choquer, M., Collemare, J., Cotton, P., Danchin, E.G., Da Silva, C., Gautier, A., Giraud, C., Giraud, T., Gonzalez, C., Grossetete, S., Güldener, U., Henrissat, B., Howlett, B.J., Kodira, C., Kretschmer, M., Lappartient, A., Leroch, M., Levis, C., Mauceli, E., Neuvéglise, C., Oeser, B., Pearson, M., Poulain, J., Poussereau, N., Quesneville, H., Rascle, C., Schumacher, J., Ségurens, B., Sexton, A., Silva, E., Sirven, C., Soanes, D.M., Talbot, N.J., Templeton, M., Yandava, C., Yarden, O., Zeng, Q., Rollins, J.A., Lebrun, M.H., and Dickman, M.

Abstract

Botrytis cinhttp://intrawebdev2.be-md.ncbi.nlm.nih.gov/projects/bp/bpedit.cgi?pid=264284#TabMainerea is an ascomycete fungus causing grey mould disease on many crops and harvested products (e.g. grape, strawberry, cucumber, rose), Botrytis cinhttp://intrawebdev2.be-md.ncbi.nlm.nih.gov/projects/bp/bpedit.cgi?pid=264284#TabMainerea is an ascomycete fungus causing grey mould disease on many crops and harvested products (e.g. grape, strawberry, cucumber, rose)

Published
2015

3. Genomic sequence of the wood–rotting Schizophyllum commune strain H4–8: the model organism to study mushroom formation

Author

Ohm, R.A., de Jong, J.F., Lugones, L.G., Aerts, A., Kothe, E., De Vries, R.P., Record, E., Baker, S.E., Bartholomew, K.A., Coutinho, P.M., Erdmann, S., Fowler, T.J., Gathman, A.C., Henrissat, B., Knabe, N.., Kües, U., Levasseur, A., Lilly, W.W., Lindquist, E., Lucas, S., Magnuson, J.K., Piumi, F., Raudaskoski, M., Salamov, A., Schmutz, F., Schwarze, F.W.M.R., Stajich, J., van Kuyk, P.A., Horton, J.S., Grigoriev, I.V., and Wösten, H.A.B.

Published
2010

4. Genome sequence of the necrotrophic plant pathogen, Pythium ultimum, reveals original pathogenicity mechanisms and effector repertoire

Author

Lévesque, C.A., Brouwer, H., Cano, L., Hamilton, J.P., Holt, C., Huitema, E., Raffaele, S., Robideau, G.P., Thines, M., Win, J., Zerillo, M., Beakes, G.W., Boore, J.L., Busam, D., Dumas, B., Ferriera, S., Fuerstenberg, S.I., Gachon, C.M.M., Gaulin, E., Govers, F., Grenville-Briggs, L., Horner, N., Hostetler, J., Jiang, R.H.Y., Johnson, J., Krajaejun, T., Lin, H., Meijer, H.J.G., Moore, B., Morris, P., Phuntmart, V., Puiu, D., Stajich, J.E., Tripathy, S., Wawra, S., van West, P., Whitty, B.R., Coutinho, P.M., Henrissat, B., Martin, F., Thomas, P.D., Tyler, B.M., De Vries, R.P., Kamoun, S., Yandell, M., Tisserat, N., and Buell, C.R.

Published
2010

6. Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus

Author

Patyshakuliyeva, A, Jurak, E., Kohler, A., Baker, A., Battaglia, E., de Bruijn, W., Burton, K.S., Challen, M.P., Coutinho, P.M., Eastwood, D.C., Gruben, B.S., Makela, M.R., Martin, F., Nadal, M., van den Brink, J., Wiebenga, A., Zhou, M., Henrissat, B., Kabel, M., Gruppen, H., de Vries, R.P., Patyshakuliyeva, A, Jurak, E., Kohler, A., Baker, A., Battaglia, E., de Bruijn, W., Burton, K.S., Challen, M.P., Coutinho, P.M., Eastwood, D.C., Gruben, B.S., Makela, M.R., Martin, F., Nadal, M., van den Brink, J., Wiebenga, A., Zhou, M., Henrissat, B., Kabel, M., Gruppen, H., and de Vries, R.P.

Abstract

BACKGROUND: Agaricus bisporus is commercially grown on compost, in which the available carbon sources consist mainly of plant-derived polysaccharides that are built out of various different constituent monosaccharides. The major constituent monosaccharides of these polysaccharides are glucose, xylose, and arabinose, while smaller amounts of galactose, glucuronic acid, rhamnose and mannose are also present. RESULTS: In this study, genes encoding putative enzymes from carbon metabolism were identified and their expression was studied in different growth stages of A. bisporus. We correlated the expression of genes encoding plant and fungal polysaccharide modifying enzymes identified in the A. bisporus genome to the soluble carbohydrates and the composition of mycelium grown compost, casing layer and fruiting bodies. CONCLUSIONS: The compost grown vegetative mycelium of A. bisporus consumes a wide variety of monosaccharides. However, in fruiting bodies only hexose catabolism occurs, and no accumulation of other sugars was observed. This suggests that only hexoses or their conversion products are transported from the vegetative mycelium to the fruiting body, while the other sugars likely provide energy for growth and maintenance of the vegetative mycelium. Clear correlations were found between expression of the genes and composition of carbohydrates. Genes encoding plant cell wall polysaccharide degrading enzymes were mainly expressed in compost-grown mycelium, and largely absent in fruiting bodies. In contrast, genes encoding fungal cell wall polysaccharide modifying enzymes were expressed in both fruiting bodies and vegetative mycelium, but different gene sets were expressed in these samples., BACKGROUND: Agaricus bisporus is commercially grown on compost, in which the available carbon sources consist mainly of plant-derived polysaccharides that are built out of various different constituent monosaccharides. The major constituent monosaccharides of these polysaccharides are glucose, xylose, and arabinose, while smaller amounts of galactose, glucuronic acid, rhamnose and mannose are also present. RESULTS: In this study, genes encoding putative enzymes from carbon metabolism were identified and their expression was studied in different growth stages of A. bisporus. We correlated the expression of genes encoding plant and fungal polysaccharide modifying enzymes identified in the A. bisporus genome to the soluble carbohydrates and the composition of mycelium grown compost, casing layer and fruiting bodies. CONCLUSIONS: The compost grown vegetative mycelium of A. bisporus consumes a wide variety of monosaccharides. However, in fruiting bodies only hexose catabolism occurs, and no accumulation of other sugars was observed. This suggests that only hexoses or their conversion products are transported from the vegetative mycelium to the fruiting body, while the other sugars likely provide energy for growth and maintenance of the vegetative mycelium. Clear correlations were found between expression of the genes and composition of carbohydrates. Genes encoding plant cell wall polysaccharide degrading enzymes were mainly expressed in compost-grown mycelium, and largely absent in fruiting bodies. In contrast, genes encoding fungal cell wall polysaccharide modifying enzymes were expressed in both fruiting bodies and vegetative mycelium, but different gene sets were expressed in these samples.

Published
2013

7. The rational design of an iminosugar inhibitor able to mimic substrate distortion occurring during retaining-cellulase hydrolysis

Author

Fort, S., Coutinho, P.M., Schulein, M., Nardin, R., Cottaz, S., Driguez, H., Centre de Recherches sur les Macromolécules Végétales (CERMAV), and Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)

Subjects
ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2001

8. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

Author

Morin, E., Kohler, A., Baker, A.R., Foulongne-Oriol, M., Lombard, V., Nagy, L.G., Ohm, R.A., Patyshakuliyeva, A, Brun, A., Aerts, A.L., Bailey, A.M., Billette, C., Coutinho, P.M., Deakin, G., Doddapaneni, H., Floudas, D., Grimwood, J., Hilden, K., Kues, U., LaButti, K.M., Lapidus, A., Lindquist, E.A., Lucas, S.M., Murat, C., Riley, R.W., Salamov, A.A., Schmutz, J., Subramanian, V., Wosten, H.A., Xu, J., Eastwood, D.C., Foster, G.D., Sonnenberg, A.S., Cullen, D., de Vries, R.P., Lundell, T., Hibbett, D.S., Henrissat, B., Burton, K.S., Kerrigan, R.W., Challen, M.P., Grigoriev, I.V., Martin, F., Morin, E., Kohler, A., Baker, A.R., Foulongne-Oriol, M., Lombard, V., Nagy, L.G., Ohm, R.A., Patyshakuliyeva, A, Brun, A., Aerts, A.L., Bailey, A.M., Billette, C., Coutinho, P.M., Deakin, G., Doddapaneni, H., Floudas, D., Grimwood, J., Hilden, K., Kues, U., LaButti, K.M., Lapidus, A., Lindquist, E.A., Lucas, S.M., Murat, C., Riley, R.W., Salamov, A.A., Schmutz, J., Subramanian, V., Wosten, H.A., Xu, J., Eastwood, D.C., Foster, G.D., Sonnenberg, A.S., Cullen, D., de Vries, R.P., Lundell, T., Hibbett, D.S., Henrissat, B., Burton, K.S., Kerrigan, R.W., Challen, M.P., Grigoriev, I.V., and Martin, F.

Abstract

Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the “button mushroom” forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.

Published
2012

9. Degradation of different pectins by fungi: correlations and contrasts between the pectinolytic enzyme sets identified in genomes and the growth on pectins of different origin

Author

Benoit, I., Coutinho, P.M., Schols, H.A., Gerlach, J.P., Henrissat, B., de Vries, R.P., Benoit, I., Coutinho, P.M., Schols, H.A., Gerlach, J.P., Henrissat, B., and de Vries, R.P.

Abstract

Background Pectins are diverse and very complex biomolecules and their structure depends on the plant species and tissue. It was previously shown that derivatives of pectic polymers and oligosaccharides from pectins have positive effects on human health. To obtain specific pectic oligosaccharides, highly defined enzymatic mixes are required. Filamentous fungi are specialized in plant cell wall degradation and some produce a broad range of pectinases. They may therefore shed light on the enzyme mixes needed for partial hydrolysis. Results The growth profiles of 12 fungi on four pectins and four structural elements of pectins show that the presence/absence of pectinolytic genes in the fungal genome clearly correlates with their ability to degrade pectins. However, this correlation is less clear when we zoom in to the pectic structural elements. Conclusions This study highlights the complexity of the mechanisms involved in fungal degradation of complex carbon sources such as pectins. Mining genomes and comparative genomics are promising first steps towards the production of specific pectinolytic fractions., Background Pectins are diverse and very complex biomolecules and their structure depends on the plant species and tissue. It was previously shown that derivatives of pectic polymers and oligosaccharides from pectins have positive effects on human health. To obtain specific pectic oligosaccharides, highly defined enzymatic mixes are required. Filamentous fungi are specialized in plant cell wall degradation and some produce a broad range of pectinases. They may therefore shed light on the enzyme mixes needed for partial hydrolysis. Results The growth profiles of 12 fungi on four pectins and four structural elements of pectins show that the presence/absence of pectinolytic genes in the fungal genome clearly correlates with their ability to degrade pectins. However, this correlation is less clear when we zoom in to the pectic structural elements. Conclusions This study highlights the complexity of the mechanisms involved in fungal degradation of complex carbon sources such as pectins. Mining genomes and comparative genomics are promising first steps towards the production of specific pectinolytic fractions.

Published
2012

10. Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis

Author

Fernandez-Fueyo, E., Ruiz-Duenas, F.J., Ferreira, P., Floudas, D., Hibbett, D.S., Canessa, P., Larrondo, L.F., James, T.Y., Seelenfreund, D., Lobos, S., Polanco, R., Tello, M., Honda, Y., Watanabe, T., Ryu, J.S., Kubicek, C.P., Schmoll, M., Gaskell, J., Hammel, K.E., St John, F.J., Vanden Wymelenberg, A., Sabat, G., Splinter BonDurant, S., Syed, K., Yadav, J.S., Doddapaneni, H., Subramanian, V., Lavin, J.L., Oguiza, J.A., Perez, G., Pisabarro, A.G., Ramirez, L., Santoyo, F., Master, E., Coutinho, P.M., Henrissat, B., Lombard, V., Magnuson, J.K., Kues, U., Hori, C., Igarashi, K., Samejima, M., Held, B.W., Barry, K.W., LaButti, K.M., Lapidus, A., Lindquist, E.A., Lucas, S.M., Riley, R., Salamov, A.A., Hoffmeister, D., Schwenk, D., Hadar, Y., Yarden, O., de Vries, R.P., Wiebenga, A., Stenlid, J., Eastwood, D., Grigoriev, I.V., Berka, R.M., Blanchette, R.A., Kersten, P., Martinez, A.T., Vicuna, R., Cullen, D., Fernandez-Fueyo, E., Ruiz-Duenas, F.J., Ferreira, P., Floudas, D., Hibbett, D.S., Canessa, P., Larrondo, L.F., James, T.Y., Seelenfreund, D., Lobos, S., Polanco, R., Tello, M., Honda, Y., Watanabe, T., Ryu, J.S., Kubicek, C.P., Schmoll, M., Gaskell, J., Hammel, K.E., St John, F.J., Vanden Wymelenberg, A., Sabat, G., Splinter BonDurant, S., Syed, K., Yadav, J.S., Doddapaneni, H., Subramanian, V., Lavin, J.L., Oguiza, J.A., Perez, G., Pisabarro, A.G., Ramirez, L., Santoyo, F., Master, E., Coutinho, P.M., Henrissat, B., Lombard, V., Magnuson, J.K., Kues, U., Hori, C., Igarashi, K., Samejima, M., Held, B.W., Barry, K.W., LaButti, K.M., Lapidus, A., Lindquist, E.A., Lucas, S.M., Riley, R., Salamov, A.A., Hoffmeister, D., Schwenk, D., Hadar, Y., Yarden, O., de Vries, R.P., Wiebenga, A., Stenlid, J., Eastwood, D., Grigoriev, I.V., Berka, R.M., Blanchette, R.A., Kersten, P., Martinez, A.T., Vicuna, R., and Cullen, D.

Abstract

Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium simultaneously degrades lignin and cellulose, whereas the closely related species, Ceriporiopsis subvermispora, also depolymerizes lignin but may do so with relatively little cellulose degradation. To investigate the basis for selective ligninolysis, we conducted comparative genome analysis of C. subvermispora and P. chrysosporium. Genes encoding manganese peroxidase numbered 13 and five in C. subvermispora and P. chrysosporium, respectively. In addition, the C. subvermispora genome contains at least seven genes predicted to encode laccases, whereas the P. chrysosporium genome contains none. We also observed expansion of the number of C. subvermispora desaturase-encoding genes putatively involved in lipid metabolism. Microarray-based transcriptome analysis showed substantial up-regulation of several desaturase and MnP genes in wood-containing medium. MS identified MnP proteins in C. subvermispora culture filtrates, but none in P. chrysosporium cultures. These results support the importance of MnP and a lignin degradation mechanism whereby cleavage of the dominant nonphenolic structures is mediated by lipid peroxidation products. Two C. subvermispora genes were predicted to encode peroxidases structurally similar to P. chrysosporium lignin peroxidase and, following heterologous expression in Escherichia coli, the enzymes were shown to oxidize high redox potential substrates, but not Mn2+. Apart from oxidative lignin degradation, we also examined cellulolytic and hemicellulolytic systems in both fungi. In summary, the C. subvermispora genetic inventory and expression patterns exhibit increased oxidoreductase potential and diminished cellulolytic capability relative to P. chrysosporium., Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium simultaneously degrades lignin and cellulose, whereas the closely related species, Ceriporiopsis subvermispora, also depolymerizes lignin but may do so with relatively little cellulose degradation. To investigate the basis for selective ligninolysis, we conducted comparative genome analysis of C. subvermispora and P. chrysosporium. Genes encoding manganese peroxidase numbered 13 and five in C. subvermispora and P. chrysosporium, respectively. In addition, the C. subvermispora genome contains at least seven genes predicted to encode laccases, whereas the P. chrysosporium genome contains none. We also observed expansion of the number of C. subvermispora desaturase-encoding genes putatively involved in lipid metabolism. Microarray-based transcriptome analysis showed substantial up-regulation of several desaturase and MnP genes in wood-containing medium. MS identified MnP proteins in C. subvermispora culture filtrates, but none in P. chrysosporium cultures. These results support the importance of MnP and a lignin degradation mechanism whereby cleavage of the dominant nonphenolic structures is mediated by lipid peroxidation products. Two C. subvermispora genes were predicted to encode peroxidases structurally similar to P. chrysosporium lignin peroxidase and, following heterologous expression in Escherichia coli, the enzymes were shown to oxidize high redox potential substrates, but not Mn2+. Apart from oxidative lignin degradation, we also examined cellulolytic and hemicellulolytic systems in both fungi. In summary, the C. subvermispora genetic inventory and expression patterns exhibit increased oxidoreductase potential and diminished cellulolytic capability relative to P. chrysosporium.

Published
2012

11. Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen

Author

Olson, A., Aerts, A., Asiegbu, F., Belbahri, L., Bouzid, O., Broberg, A., Canback, B., Coutinho, P.M., Cullen, D., Dalman, K., Deflorio, G., van Diepen, L.T., Dunand, C., Duplessis, S., Durling, M., Gonthier, P., Grimwood, J., Fossdal, C.G., Hansson, D., Henrissat, B., Hietala, A., Himmelstrand, K., Hoffmeister, D., Hogberg, N., James, T.Y., Karlsson, M., Kohler, A., Kues, U., Lee, Y.H., Lin, Y.C., Lind, M., Lindquist, E., Lombard, V., Lucas, S., Lunden, K., Morin, E., Murat, C., Park, J., Raffaello, T., Rouze, P., Salamov, A., Schmutz, J., Solheim, H., Stahlberg, J., Velez, H., de Vries, R.P., Wiebenga, A., Woodward, S., Yakovlev, I., Garbelotto, M., Martin, F., Grigoriev, I.V., Stenlid, J., Olson, A., Aerts, A., Asiegbu, F., Belbahri, L., Bouzid, O., Broberg, A., Canback, B., Coutinho, P.M., Cullen, D., Dalman, K., Deflorio, G., van Diepen, L.T., Dunand, C., Duplessis, S., Durling, M., Gonthier, P., Grimwood, J., Fossdal, C.G., Hansson, D., Henrissat, B., Hietala, A., Himmelstrand, K., Hoffmeister, D., Hogberg, N., James, T.Y., Karlsson, M., Kohler, A., Kues, U., Lee, Y.H., Lin, Y.C., Lind, M., Lindquist, E., Lombard, V., Lucas, S., Lunden, K., Morin, E., Murat, C., Park, J., Raffaello, T., Rouze, P., Salamov, A., Schmutz, J., Solheim, H., Stahlberg, J., Velez, H., de Vries, R.P., Wiebenga, A., Woodward, S., Yakovlev, I., Garbelotto, M., Martin, F., Grigoriev, I.V., and Stenlid, J.

Published
2012

12. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes

Author

Floudas, D., Binder, M., Riley, R., Barry, K., Blanchette, R.A., Henrissat, B., Martinez, A.T., Otillar, R., Spatafora, J.W., Yadav, J.S., Aerts, A., Benoit, I., Boyd, A., Carlson, A., Copeland, A., Coutinho, P.M., de Vries, R.P., Ferreira, P., Findley, K., Foster, B., Gaskell, J., Glotzer, D., Gorecki, P., Heitman, J., Hesse, C., Hori, C., Igarashi, K., Jurgens, J.A., Kallen, N., Kersten, P., Kohler, A., Kues, U., Kumar, T.K., Kuo, A., LaButti, K., Larrondo, L.F., Lindquist, E., Ling, A., Lombard, V., Lucas, S., Lundell, T., Martin, R., McLaughlin, D.J., Morgenstern, I., Morin, E., Murat, C., Nagy, L.G., Nolan, M., Ohm, R.A., Patyshakuliyeva, A, Rokas, A., Ruiz-Duenas, F.J., Sabat, G., Salamov, A., Samejima, M., Schmutz, J., Slot, J.C., St John, F., Stenlid, J., Sun, H., Sun, S., Syed, K., Tsang, A., Wiebenga, A., Young, D., Pisabarro, A., Eastwood, D.C., Martin, F., Cullen, D., Grigoriev, I.V., Hibbett, D.S., Floudas, D., Binder, M., Riley, R., Barry, K., Blanchette, R.A., Henrissat, B., Martinez, A.T., Otillar, R., Spatafora, J.W., Yadav, J.S., Aerts, A., Benoit, I., Boyd, A., Carlson, A., Copeland, A., Coutinho, P.M., de Vries, R.P., Ferreira, P., Findley, K., Foster, B., Gaskell, J., Glotzer, D., Gorecki, P., Heitman, J., Hesse, C., Hori, C., Igarashi, K., Jurgens, J.A., Kallen, N., Kersten, P., Kohler, A., Kues, U., Kumar, T.K., Kuo, A., LaButti, K., Larrondo, L.F., Lindquist, E., Ling, A., Lombard, V., Lucas, S., Lundell, T., Martin, R., McLaughlin, D.J., Morgenstern, I., Morin, E., Murat, C., Nagy, L.G., Nolan, M., Ohm, R.A., Patyshakuliyeva, A, Rokas, A., Ruiz-Duenas, F.J., Sabat, G., Salamov, A., Samejima, M., Schmutz, J., Slot, J.C., St John, F., Stenlid, J., Sun, H., Sun, S., Syed, K., Tsang, A., Wiebenga, A., Young, D., Pisabarro, A., Eastwood, D.C., Martin, F., Cullen, D., Grigoriev, I.V., and Hibbett, D.S.

Published
2012

13. Degradation of different pectins by fungi:correlations and contrasts between the pectinolytic enzyme sets identified in genomes and the growth on pectins of different origin

Author

Benoit, I., Coutinho, P.M., Schols, H.A., Gerlach, G.F., Henrissat, B., de Vries, R.P., Benoit, I., Coutinho, P.M., Schols, H.A., Gerlach, G.F., Henrissat, B., and de Vries, R.P.

Abstract

Background: Pectins are diverse and very complex biomolecules and their structure depends on the plant speciesand tissue. It was previously shown that derivatives of pectic polymers and oligosaccharides from pectins havepositive effects on human health. To obtain specific pectic oligosaccharides, highly defined enzymatic mixes arerequired. Filamentous fungi are specialized in plant cell wall degradation and some produce a broad range ofpectinases. They may therefore shed light on the enzyme mixes needed for partial hydrolysis.Results: The growth profiles of 12 fungi on four pectins and four structural elements of pectins show that thepresence/absence of pectinolytic genes in the fungal genome clearly correlates with their ability to degradepectins. However, this correlation is less clear when we zoom in to the pectic structural elements.Conclusions: This study highlights the complexity of the mechanisms involved in fungal degradation of complexcarbon sources such as pectins. Mining genomes and comparative genomics are promising first steps towards theproduction of specific pectinolytic fractions.

Published
2012

14. Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis

Author

Goodwin, S.B., Ben M'Barek, S., Dhillon, B., Wittenberg, A.H.J., Crane, C.F., Hane, J.K., Foster, A.J., Van der Lee, T.A.J., Grimwood, J., Aerts, A., Antoniw, J., Bailey, A., Bluhm, B., Bowler, J., Bristow, J., van der Burgt, A., Canto-Canché, B., Churchill, A.C.L., Conde-Ferràez, L., Cools, H.J., Coutinho, P.M., Csukai, M., Dehal, P., De Wit, P., Donzelli, B., van de Geest, H.C., van Ham, R.C.H.J., Hammond-Kosack, K.E., Henrissat, B., Kilian, A., Kobayashi, A.K., Koopmann, E., Kourmpetis, Y., Kuzniar, A., Lindquist, E., Lombard, V., Maliepaard, C., Martins, N., Mehrabi, R., Nap, J.P.H., Ponomarenko, A., Rudd, J.J., Salamov, A., Schmutz, J., Schouten, H., Shapiro, H., Stergiopoulos, I., Torriani, S.F.F., Tu, H., de Vries, R.P., Waalwijk, C., Ware, S.B., Wiebenga, A., Zwiers, L-H, Oliver, R.P., Grigoriev, I.V., Kema, G.H.J., Goodwin, S.B., Ben M'Barek, S., Dhillon, B., Wittenberg, A.H.J., Crane, C.F., Hane, J.K., Foster, A.J., Van der Lee, T.A.J., Grimwood, J., Aerts, A., Antoniw, J., Bailey, A., Bluhm, B., Bowler, J., Bristow, J., van der Burgt, A., Canto-Canché, B., Churchill, A.C.L., Conde-Ferràez, L., Cools, H.J., Coutinho, P.M., Csukai, M., Dehal, P., De Wit, P., Donzelli, B., van de Geest, H.C., van Ham, R.C.H.J., Hammond-Kosack, K.E., Henrissat, B., Kilian, A., Kobayashi, A.K., Koopmann, E., Kourmpetis, Y., Kuzniar, A., Lindquist, E., Lombard, V., Maliepaard, C., Martins, N., Mehrabi, R., Nap, J.P.H., Ponomarenko, A., Rudd, J.J., Salamov, A., Schmutz, J., Schouten, H., Shapiro, H., Stergiopoulos, I., Torriani, S.F.F., Tu, H., de Vries, R.P., Waalwijk, C., Ware, S.B., Wiebenga, A., Zwiers, L-H, Oliver, R.P., Grigoriev, I.V., and Kema, G.H.J.

Abstract

The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This disease is economically important in most wheat-growing areas worldwide and threatens global food production. Control of the disease has been hampered by a limited understanding of the genetic and biochemical bases of pathogenicity, including mechanisms of infection and of resistance in the host. Unlike most other plant pathogens, M. graminicola has a long latent period during which it evades host defenses. Although this type of stealth pathogenicity occurs commonly in Mycosphaerella and other Dothideomycetes, the largest class of plant-pathogenic fungi, its genetic basis is not known. To address this problem, the genome of M. graminicola was sequenced completely. The finished genome contains 21 chromosomes, eight of which could be lost with no visible effect on the fungus and thus are dispensable. This eight-chromosome dispensome is dynamic in field and progeny isolates, is different from the core genome in gene and repeat content, and appears to have originated by ancient horizontal transfer from an unknown donor. Synteny plots of the M. graminicola chromosomes versus those of the only other sequenced Dothideomycete, Stagonospora nodorum, revealed conservation of gene content but not order or orientation, suggesting a high rate of intra-chromosomal rearrangement in one or both species. This observed “mesosynteny” is very different from synteny seen between other organisms. A surprising feature of the M. graminicola genome compared to other sequenced plant pathogens was that it contained very few genes for enzymes that break down plant cell walls, which was more similar to endophytes than to pathogens. The stealth pathogenesis of M. graminicola probably involves degradation of proteins rather than carbohydrates to evade host defenses during the biotrophic stage of infection and m

Published
2011

15. The Plant Cell Wall-Decomposing Machinery Underlies the Functional Diversity of Forest Fungi

Author

Eastwood, D.C., Floudas, D., Binder, M., Majcherczyk, A., Schneider, P., Aerts, A., Asiegbu, F.O., Baker, S.E., Barry, K., Bendiksby, M., Blumentritt, M., Coutinho, P.M., Cullen, D., De Vries, R.P., Gathman, A.C., Goodell, B., Henrissat, B., Ihrmark, K., Kauserud, H., Kohler, A., LaButti, K., Lapidus, A., Lavin, J.L., Lee, Y.A., Lindquist, E., Lilly, W.W., Lucas, S., Morin, E., Murat, C., Oguiza, J.A., Park, J., Pisabarro, A.G., Riley, R., Rosling, A., Salamov, A., Schmidt, O., Schmutz, J., Skrede, I., Stenlid, J., Wiebenga, A., Xie, X., Kuees, U., Hibbett, D.S., Hoffmeister, D., Hogberg, N., Martin, F., Grigoriev, I.V., Watkinson, S.C., Eastwood, D.C., Floudas, D., Binder, M., Majcherczyk, A., Schneider, P., Aerts, A., Asiegbu, F.O., Baker, S.E., Barry, K., Bendiksby, M., Blumentritt, M., Coutinho, P.M., Cullen, D., De Vries, R.P., Gathman, A.C., Goodell, B., Henrissat, B., Ihrmark, K., Kauserud, H., Kohler, A., LaButti, K., Lapidus, A., Lavin, J.L., Lee, Y.A., Lindquist, E., Lilly, W.W., Lucas, S., Morin, E., Murat, C., Oguiza, J.A., Park, J., Pisabarro, A.G., Riley, R., Rosling, A., Salamov, A., Schmidt, O., Schmutz, J., Skrede, I., Stenlid, J., Wiebenga, A., Xie, X., Kuees, U., Hibbett, D.S., Hoffmeister, D., Hogberg, N., Martin, F., Grigoriev, I.V., and Watkinson, S.C.

Published
2011

18. Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Author

Amselem, J., Cuomo, C.A., van Kan, Jan A. L., Viaud, Muriel, Benito, E.P., Couloux, A., Coutinho, P.M., de Vries, R.P., Dyer, P.S., Fillinger, S., Fournier, E., Gout, L., Hahn, M.W., Kohn, Linda, Lapalu, Nicolas, Plummer, Kim M., Pradier, Jean-Marc, Quevillon, Emmanuel, Sharon, Amir, Simon, Adeline, ten Have, A., Tudzynski, Bettina, Tudzynski, Paul, Wincker, Patrick, Andrew, M., Anthouard, V., Beever, R.E., Beffa, R., Benoit, I., Bouzid, O., Brault, B., Chen, Z., Choquer, M., Collemare, J., Cotton, P.A., Danchin, Etienne G., Da Silva, Corinne, Gautier, A., Giraud, C., Giraud, T., Gonzalez, C., Grossetete, S., Gueldener, U., Henrissat, B., Howlett, B.J., Kodira, Chinnappa, Kretschmer, Matthias, Lappartient, Anne, Leroch, Michaela, Levis, Caroline, Mauceli, Evan, Neuveglise, Cecile, Oeser, Birgitt, Pearson, Matthew, Poulain, Julie, Poussereau, Nathalie, Quesneville, Hadi, Rascle, Christine, Schumacher, Julia, Segurens, Beatrice, Sexton, Adrienne, Silva, E.I.L., Sirven, Catherine, Soanes, Darren M., Talbot, Nicholas J., Templeton, Matt, Yandava, Chandri, Yarden, Oded, Zeng, Qiandong, Rollins, Jeffrey A., Lebrun, M.H., Dickman, M., Amselem, J., Cuomo, C.A., van Kan, Jan A. L., Viaud, Muriel, Benito, E.P., Couloux, A., Coutinho, P.M., de Vries, R.P., Dyer, P.S., Fillinger, S., Fournier, E., Gout, L., Hahn, M.W., Kohn, Linda, Lapalu, Nicolas, Plummer, Kim M., Pradier, Jean-Marc, Quevillon, Emmanuel, Sharon, Amir, Simon, Adeline, ten Have, A., Tudzynski, Bettina, Tudzynski, Paul, Wincker, Patrick, Andrew, M., Anthouard, V., Beever, R.E., Beffa, R., Benoit, I., Bouzid, O., Brault, B., Chen, Z., Choquer, M., Collemare, J., Cotton, P.A., Danchin, Etienne G., Da Silva, Corinne, Gautier, A., Giraud, C., Giraud, T., Gonzalez, C., Grossetete, S., Gueldener, U., Henrissat, B., Howlett, B.J., Kodira, Chinnappa, Kretschmer, Matthias, Lappartient, Anne, Leroch, Michaela, Levis, Caroline, Mauceli, Evan, Neuveglise, Cecile, Oeser, Birgitt, Pearson, Matthew, Poulain, Julie, Poussereau, Nathalie, Quesneville, Hadi, Rascle, Christine, Schumacher, Julia, Segurens, Beatrice, Sexton, Adrienne, Silva, E.I.L., Sirven, Catherine, Soanes, Darren M., Talbot, Nicholas J., Templeton, Matt, Yandava, Chandri, Yarden, Oded, Zeng, Qiandong, Rollins, Jeffrey A., Lebrun, M.H., and Dickman, M.

Published
2011

19. Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

Author

Berka, R.M., Grigoriev, I.V., Otillar, Robert, Salamov, A., Grimwood, J., Reid, Ian, Ishmael, N., John, T., Darmond, C., Moisan, Marie-Claude, Henrissat, B., Coutinho, P.M., Lombard, Vincent, Natvig, Donald O., Lindquist, E., Schmutz, Jeremy, Lucas, S., Harris, P.C., Powlowski, Justin, Bellemare, A., Taylor, David, Butler, G., de Vries, R.P., Allijn, I.E., van den Brink, J., Ushinsky, Sophia, Storms, Reginald, Powell, Amy J., Paulsen, Ian T., Elbourne, L.D.H., Baker, S.E., Magnuson, J.K., LaBoissiere, Sylvie, Clutterbuck, A.J., Martinez, Diego, Wogulis, Mark, de Leon, Alfredo Lopez, Rey, Michael W., Tsang, Adrian, Berka, R.M., Grigoriev, I.V., Otillar, Robert, Salamov, A., Grimwood, J., Reid, Ian, Ishmael, N., John, T., Darmond, C., Moisan, Marie-Claude, Henrissat, B., Coutinho, P.M., Lombard, Vincent, Natvig, Donald O., Lindquist, E., Schmutz, Jeremy, Lucas, S., Harris, P.C., Powlowski, Justin, Bellemare, A., Taylor, David, Butler, G., de Vries, R.P., Allijn, I.E., van den Brink, J., Ushinsky, Sophia, Storms, Reginald, Powell, Amy J., Paulsen, Ian T., Elbourne, L.D.H., Baker, S.E., Magnuson, J.K., LaBoissiere, Sylvie, Clutterbuck, A.J., Martinez, Diego, Wogulis, Mark, de Leon, Alfredo Lopez, Rey, Michael W., and Tsang, Adrian

Published
2011

22. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

Author

Pel, H.J., Winde, J.H. de, Archer, D.B., Dyer, P.S., Hofmann, G., Schaap, P.J., Turner, G., Vries, R.P. de, Albang, R., Albermann, K., Andersen, M.R., Bendtsen, J.D., Benen, J.A., Berg, M. van den, Breestraat, S., Caddick, M.X., Contreras, R., Cornell, M., Coutinho, P.M., Danchin, E.G., Debets, A.J., Dekker, P., Dijck, P.W. van, Dijk, A. van, Dijkhuizen, L., Driessen, A.J., D'Enfert, C., Geysens, S., Goosen, C., Groot, G.S., Groot, P.W. de, Guillemette, T., Henrissat, B., Herweijer, M., Hombergh, J.P. van den, Hondel, C.A. van den, Heijden, R.T.J.M. van der, Kaaij, R.M. van der, Klis, F.M., Kools, H.J., Kubicek, C.P., Kuyk, P.A. van, Lauber, J., Lu, X., Maarel, M.J. van der, Meulenberg, R., Menke, H., Mortimer, M.A., Nielsen, J., Oliver, S.G., Olsthoorn, M., Pal, K., Peij, N.N. van, Ram, A.F., Rinas, U., Roubos, J.A., Sagt, C.M., Schmoll, M., Sun, J., Ussery, D., Varga, J., Vervecken, W., Vondervoort, P.J. van de, Wedler, H., Wosten, H.A., Zeng, A.P., Ooyen, A.J. van, Visser, J.C., Stam, H., Pel, H.J., Winde, J.H. de, Archer, D.B., Dyer, P.S., Hofmann, G., Schaap, P.J., Turner, G., Vries, R.P. de, Albang, R., Albermann, K., Andersen, M.R., Bendtsen, J.D., Benen, J.A., Berg, M. van den, Breestraat, S., Caddick, M.X., Contreras, R., Cornell, M., Coutinho, P.M., Danchin, E.G., Debets, A.J., Dekker, P., Dijck, P.W. van, Dijk, A. van, Dijkhuizen, L., Driessen, A.J., D'Enfert, C., Geysens, S., Goosen, C., Groot, G.S., Groot, P.W. de, Guillemette, T., Henrissat, B., Herweijer, M., Hombergh, J.P. van den, Hondel, C.A. van den, Heijden, R.T.J.M. van der, Kaaij, R.M. van der, Klis, F.M., Kools, H.J., Kubicek, C.P., Kuyk, P.A. van, Lauber, J., Lu, X., Maarel, M.J. van der, Meulenberg, R., Menke, H., Mortimer, M.A., Nielsen, J., Oliver, S.G., Olsthoorn, M., Pal, K., Peij, N.N. van, Ram, A.F., Rinas, U., Roubos, J.A., Sagt, C.M., Schmoll, M., Sun, J., Ussery, D., Varga, J., Vervecken, W., Vondervoort, P.J. van de, Wedler, H., Wosten, H.A., Zeng, A.P., Ooyen, A.J. van, Visser, J.C., and Stam, H.

Abstract

Contains fulltext : 51722.pdf (publisher's version ) (Closed access), The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis.

Published
2007

23. CBM62 in complex with 6-alpha-D-Galactosyl-mannotriose

Author

Montanier, C.Y., primary, Correia, M.A.S., additional, Flint, J.E., additional, Zhu, Y., additional, McKee, L.S., additional, Prates, J.A.M., additional, Polizzi, S.J., additional, Coutinho, P.M., additional, Henrissat, B., additional, Fontes, C.M.G.A., additional, and Gilbert, H.J., additional

Published
2011
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24. CBM62 FROM CLOSTRIDIUM THERMOCELLUM XYL5A

Author

Montanier, C.Y., primary, Correia, M.A.S., additional, Flint, J.E., additional, Zhu, Y., additional, Basle, A., additional, Mckee, L.S., additional, Prates, J.A.M., additional, Polizzi, S.J., additional, Coutinho, P.M., additional, Henrissat, B., additional, Fontes, C.M.G.A., additional, and Gilbert, H.J., additional

Published
2011
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25. CBM62 in complex with xyloglucan oligosaccharide

Author

Montanier, C.Y., primary, Correia, M.A.S., additional, Flint, J.E., additional, Zhu, Y., additional, McKee, L.S., additional, Prates, J.A.M., additional, Polizzi, J., additional, Coutinho, P.M., additional, Henrissat, B., additional, Fontes, C.M.G.A., additional, and Gilbert, H.J., additional

Published
2011
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26. CBM62 in complex with arabinobiose

Author

Montanier, C.Y., primary, Correia, M.A.S., additional, Flint, J.E., additional, Zhu, Y., additional, McKee, L.S., additional, Prates, J.A.M., additional, Polizzi, J., additional, Coutinho, P.M., additional, Henrissat, B., additional, Fontes, C.M.G.A., additional, and Gilbert, H.J., additional

Published
2011
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35. Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

Author

Francis Martin, Annegret Kohler, Claude Murat, Raffaella Balestrini, Pedro M. Coutinho, Olivier Jaillon, Barbara Montanini, Emmanuelle Morin, Benjamin Noel, Riccardo Percudani, Bettina Porcel, Andrea Rubini, Antonella Amicucci, Joelle Amselem, Véronique Anthouard, Sergio Arcioni, François Artiguenave, Jean-Marc Aury, Paola Ballario, Angelo Bolchi, Andrea Brenna, Annick Brun, Marc Buée, Brandi Cantarel, Gérard Chevalier, Arnaud Couloux, Corinne Da Silva, France Denoeud, Sébastien Duplessis, Stefano Ghignone, Benoît Hilselberger, Mirco Iotti, Benoît Marçais, Antonietta Mello, Michele Miranda, Giovanni Pacioni, Hadi Quesneville, Claudia Riccioni, Roberta Ruotolo, Richard Splivallo, Vilberto Stocchi, Emilie Tisserant, Arturo Roberto Viscomi, Alessandra Zambonelli, Elisa Zampieri, Bernard Henrissat, Marc-Henri Lebrun, Francesco Paolocci, Paola Bonfante, Simone Ottonello, Patrick Wincker, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Istituto per la Protezione Sostenibile delle Piante (CNR-IPSP), UOS Torino, Architecture et fonction des Macromolécules Biologiques - UMR 6098 (AFMB), Université de Provence - Aix-Marseille 1-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Dipartimento di Biochimica e Biologia Molecolare, Università degli studi di Parma [Parme, Italie], Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Consiglio Nazionale delle Ricerche [Milano] (CNR), Dipartimento di Scienze Biomolecolari Universita di Urbino (DISB), Università degli Studi di Urbino 'Carlo Bo', Institut National de la Recherche Agronomique (INRA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Dipartimento di Genetica e Biologia Molecolare, Università degli Studi di Roma 'La Sapienza' [Rome], Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Università degli Studi di Bologna, Dipartimento di Biologia Vegetale, Università degli studi di Torino (UNITO), Dipartimento di Biologia di Base ed Applicata, Aquila University, Università degli Studi dell'Aquila [L'Aquila] (UNIVAQ.IT), Unité de Recherche Génomique Info (URGI), CNR IGV, Consiglio Nazionale delle Ricerche (CNR), University of Goettingen, Consiglio Nazionale delle Ricerche [Torino] (CNR), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Istituto di Scienze e Tecnologie Molecolari = Institute of Molecular Science and Technologies (ISTM-CNR [Perugia - Milano]), ANR-06-BLAN-0399,FungEffector,A genome-wide survey of secreted proteins as effectors of symbiosis and pathogenicity in plant-associated fungi(2006), European Project: 33958,EVOLTREE, Martin, Francis, Murat-Furminieux, Claude, Martin F., Kohler A., Murat C., Balestrini R., Coutinho P.M., Jaillon O., Montanini B., Morin E., Noel B., Percudani R., Porcel B., Rubini A., Amicucci A., Amselem J., Anthouard V., Arcioni S., Artiguenave F., Aury J.M., Ballario P., Bolchi A., Brenna A., Brun A., Buée M., Cantarel B., Chevalier G., Couloux A., Da Silva C., Denoeud F., Duplessis S., Ghignone S., Hilselberger B., Iotti M., Mello M., Miranda M., Pacioni G., Quesneville H., Riccioni C., Ruotolo R., Splivallo R., Stocchi V., Tisserant E., Viscomi A.R., Zambonelli A., Zampieri E., Henrissat B., Lebrun M.H., Paolocci F., Bonfante P., Ottonello S., Wincker P., Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Università degli studi di Parma = University of Parma (UNIPR), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Università degli studi di Torino = University of Turin (UNITO), Università degli Studi dell'Aquila = University of L'Aquila (UNIVAQ), Georg-August-University = Georg-August-Universität Göttingen, Centre National de la Recherche Scientifique (CNRS)-Université de Provence - Aix-Marseille 1, University of Parma = Università degli studi di Parma [Parme, Italie], Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Università degli Studi dell'Aquila (UNIVAQ), University of Göttingen - Georg-August-Universität Göttingen, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, Tuber melanosporum, tuber, ectomycorrhizal fungi, TRUFFE NOIRE DU PERIGORD, [SDV]Life Sciences [q-bio], Genes, Fungal, Molecular Sequence Data, TRUFFE BLANCHE DU PIEMONT, Carbohydrates, Genomics, Haploidy, 01 natural sciences, Genome, Ectosymbiosis, Evolution, Molecular, 03 medical and health sciences, truffe, Symbiosis, Ascomycota, Tuber aestivum, champignon comestible, Fruiting Bodies, Fungal, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, Truffle, biology, génome, Fungal genetics, Sequence Analysis, DNA, biology.organism_classification, DNA Transposable Elements, fungal genoma, Genome, Fungal, europe, symbiose, Sulfur, 010606 plant biology & botany
Abstract

Letter; International audience; The Périgord black truffle ($Tuber\ melanosporum$ Vittad.) and the Piedmont white truffle dominate today's truffle market. The hypogeous fruiting body of $T.\ melanosporum$ is a gastronomic delicacy produced by an ectomycorrhizal symbiont endemic to calcareous soils in southern Europe. The worldwide demand for this truffle has fuelled intense efforts at cultivation. Identification of processes that condition and trigger fruit body and symbiosis formation, ultimately leading to efficient crop production, will be facilitated by a thorough analysis of truffle genomic traits. In the ectomycorrhizal $Laccaria\ bicolor$, the expansion of gene families may have acted as a 'symbiosis toolbox'. This feature may however reflect evolution of this particular taxon and not a general trait shared by all ectomycorrhizal species. To get a better understanding of the biology and evolution of the ectomycorrhizal symbiosis, we report here the sequence of the haploid genome of $T.\ melanosporum$, which at $\sim$125 megabases is the largest and most complex fungal genome sequenced so far. This expansion results from a proliferation of transposable elements accounting for $\sim$58% of the genome. In contrast, this genome only contains $\sim$7,500 protein-coding genes with very rare multigene families. It lacks large sets of carbohydrate cleaving enzymes, but a few of them involved in degradation of plant cell walls are induced in symbiotic tissues. The latter feature and the upregulation of genes encoding for lipases and multicopper oxidases suggest that $T.\ melanosporum$ degrades its host cell walls during colonization. Symbiosis induces an increased expression of carbohydrate and amino acid transporters in both $L.\ bicolor$ and $T.\ melanosporum$, but the comparison of genomic traits in the two ectomycorrhizal fungi showed that genetic predispositions for symbiosis $-$'the symbiosis toolbox'$-$ evolved along different ways in ascomycetes and basidiomycetes

Published
2010

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