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Title: Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

Abstract

To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.

Authors:
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Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Genomics Division
Sponsoring Org.:
USDOE Office of Science (SC). Joint Genome Inst.; USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1242700
Report Number(s):
LBNL-177846
Journal ID: ISSN 1061-4036; ir:177846
Grant/Contract Number:
AC02-05CH11231; AC05-00OR22725
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Nature Genetics
Additional Journal Information:
Journal Volume: 47; Journal Issue: 4; Journal ID: ISSN 1061-4036
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Kohler, Annegret, Kuo, Alan, Nagy, Laszlo G., Morin, Emmanuelle, Barry, Kerrie W., Buscot, Francois, Canbäck, Björn, Choi, Cindy, Cichocki, Nicolas, Clum, Alicia, Colpaert, Jan, Copeland, Alex, Costa, Mauricio D., Doré, Jeanne, Floudas, Dimitrios, Gay, Gilles, Girlanda, Mariangela, Henrissat, Bernard, Herrmann, Sylvie, Hess, Jaqueline, Högberg, Nils, Johansson, Tomas, Khouja, Hassine-Radhouane, LaButti, Kurt, Lahrmann, Urs, Levasseur, Anthony, Lindquist, Erika A., Lipzen, Anna, Marmeisse, Roland, Martino, Elena, Murat, Claude, Ngan, Chew Y., Nehls, Uwe, Plett, Jonathan M., Pringle, Anne, Ohm, Robin A., Perotto, Silvia, Peter, Martina, Riley, Robert, Rineau, Francois, Ruytinx, Joske, Salamov, Asaf, Shah, Firoz, Sun, Hui, Tarkka, Mika, Tritt, Andrew, Veneault-Fourrey, Claire, Zuccaro, Alga, Tunlid, Anders, Grigoriev, Igor V., Hibbett, David S., and Martin, Francis. Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. United States: N. p., 2015. Web. doi:10.1038/ng.3223.
Kohler, Annegret, Kuo, Alan, Nagy, Laszlo G., Morin, Emmanuelle, Barry, Kerrie W., Buscot, Francois, Canbäck, Björn, Choi, Cindy, Cichocki, Nicolas, Clum, Alicia, Colpaert, Jan, Copeland, Alex, Costa, Mauricio D., Doré, Jeanne, Floudas, Dimitrios, Gay, Gilles, Girlanda, Mariangela, Henrissat, Bernard, Herrmann, Sylvie, Hess, Jaqueline, Högberg, Nils, Johansson, Tomas, Khouja, Hassine-Radhouane, LaButti, Kurt, Lahrmann, Urs, Levasseur, Anthony, Lindquist, Erika A., Lipzen, Anna, Marmeisse, Roland, Martino, Elena, Murat, Claude, Ngan, Chew Y., Nehls, Uwe, Plett, Jonathan M., Pringle, Anne, Ohm, Robin A., Perotto, Silvia, Peter, Martina, Riley, Robert, Rineau, Francois, Ruytinx, Joske, Salamov, Asaf, Shah, Firoz, Sun, Hui, Tarkka, Mika, Tritt, Andrew, Veneault-Fourrey, Claire, Zuccaro, Alga, Tunlid, Anders, Grigoriev, Igor V., Hibbett, David S., & Martin, Francis. Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. United States. doi:10.1038/ng.3223.
Kohler, Annegret, Kuo, Alan, Nagy, Laszlo G., Morin, Emmanuelle, Barry, Kerrie W., Buscot, Francois, Canbäck, Björn, Choi, Cindy, Cichocki, Nicolas, Clum, Alicia, Colpaert, Jan, Copeland, Alex, Costa, Mauricio D., Doré, Jeanne, Floudas, Dimitrios, Gay, Gilles, Girlanda, Mariangela, Henrissat, Bernard, Herrmann, Sylvie, Hess, Jaqueline, Högberg, Nils, Johansson, Tomas, Khouja, Hassine-Radhouane, LaButti, Kurt, Lahrmann, Urs, Levasseur, Anthony, Lindquist, Erika A., Lipzen, Anna, Marmeisse, Roland, Martino, Elena, Murat, Claude, Ngan, Chew Y., Nehls, Uwe, Plett, Jonathan M., Pringle, Anne, Ohm, Robin A., Perotto, Silvia, Peter, Martina, Riley, Robert, Rineau, Francois, Ruytinx, Joske, Salamov, Asaf, Shah, Firoz, Sun, Hui, Tarkka, Mika, Tritt, Andrew, Veneault-Fourrey, Claire, Zuccaro, Alga, Tunlid, Anders, Grigoriev, Igor V., Hibbett, David S., and Martin, Francis. Mon . "Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists". United States. doi:10.1038/ng.3223. https://www.osti.gov/servlets/purl/1242700.
@article{osti_1242700,
title = {Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists},
author = {Kohler, Annegret and Kuo, Alan and Nagy, Laszlo G. and Morin, Emmanuelle and Barry, Kerrie W. and Buscot, Francois and Canbäck, Björn and Choi, Cindy and Cichocki, Nicolas and Clum, Alicia and Colpaert, Jan and Copeland, Alex and Costa, Mauricio D. and Doré, Jeanne and Floudas, Dimitrios and Gay, Gilles and Girlanda, Mariangela and Henrissat, Bernard and Herrmann, Sylvie and Hess, Jaqueline and Högberg, Nils and Johansson, Tomas and Khouja, Hassine-Radhouane and LaButti, Kurt and Lahrmann, Urs and Levasseur, Anthony and Lindquist, Erika A. and Lipzen, Anna and Marmeisse, Roland and Martino, Elena and Murat, Claude and Ngan, Chew Y. and Nehls, Uwe and Plett, Jonathan M. and Pringle, Anne and Ohm, Robin A. and Perotto, Silvia and Peter, Martina and Riley, Robert and Rineau, Francois and Ruytinx, Joske and Salamov, Asaf and Shah, Firoz and Sun, Hui and Tarkka, Mika and Tritt, Andrew and Veneault-Fourrey, Claire and Zuccaro, Alga and Tunlid, Anders and Grigoriev, Igor V. and Hibbett, David S. and Martin, Francis},
abstractNote = {To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.},
doi = {10.1038/ng.3223},
journal = {Nature Genetics},
number = 4,
volume = 47,
place = {United States},
year = {Mon Feb 23 00:00:00 EST 2015},
month = {Mon Feb 23 00:00:00 EST 2015}
}

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