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Title: The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

Abstract

We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70percent of gene content in both genomes are homologs), but differ significantly in size (Cfu >61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2percent in Cfu versus 3.2percent in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxinmore » dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation.« less

Authors:
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Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1165996
Report Number(s):
LBNL-6843E
Journal ID: ISSN 1553-7404
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
PLoS Genetics
Additional Journal Information:
Journal Volume: 8; Journal Issue: 11; Journal ID: ISSN 1553-7404
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

de Wit, Pierre J. G. M., van der Burgt, Ate, Okmen, Bilal, Stergiopoulos, Ioannis, Abd-Elsalam, Kamel A., Aerts, Andrea L., Bahkali, Ali H., Beenen, Henriek G., Chettri, Oranav, Cos, Murray P., Datema, Erwin, de Vries, Ronald P., DHillon, Braham, Ganley, Austen R., Griffiths, Scott A., Guo, Yanan, Gamelin, Richard C., Henrissat, Bernard, Kabir, M. Shahjahan, Jashni, Mansoor Karimi, Kema, Gert, Klaubauf, Sylvia, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Mehrabi, Rahim, Ohm, Robin A., Owen, Timothy J., Salamov, Asaf, Schwelm, Arne, Schijlen, Elio, Sun, Hui, van den Burg, Harrold A., van Burg, Roeland C. H. J., Zhang, Shuguang, Goodwin, Stephen B., Grigoriev, Igor V., Collemare, Jerome, and Bradshaw, Rosie E. The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry. United States: N. p., 2012. Web. doi:10.1371/journal.pgen.1003088.
de Wit, Pierre J. G. M., van der Burgt, Ate, Okmen, Bilal, Stergiopoulos, Ioannis, Abd-Elsalam, Kamel A., Aerts, Andrea L., Bahkali, Ali H., Beenen, Henriek G., Chettri, Oranav, Cos, Murray P., Datema, Erwin, de Vries, Ronald P., DHillon, Braham, Ganley, Austen R., Griffiths, Scott A., Guo, Yanan, Gamelin, Richard C., Henrissat, Bernard, Kabir, M. Shahjahan, Jashni, Mansoor Karimi, Kema, Gert, Klaubauf, Sylvia, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Mehrabi, Rahim, Ohm, Robin A., Owen, Timothy J., Salamov, Asaf, Schwelm, Arne, Schijlen, Elio, Sun, Hui, van den Burg, Harrold A., van Burg, Roeland C. H. J., Zhang, Shuguang, Goodwin, Stephen B., Grigoriev, Igor V., Collemare, Jerome, & Bradshaw, Rosie E. The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry. United States. https://doi.org/10.1371/journal.pgen.1003088
de Wit, Pierre J. G. M., van der Burgt, Ate, Okmen, Bilal, Stergiopoulos, Ioannis, Abd-Elsalam, Kamel A., Aerts, Andrea L., Bahkali, Ali H., Beenen, Henriek G., Chettri, Oranav, Cos, Murray P., Datema, Erwin, de Vries, Ronald P., DHillon, Braham, Ganley, Austen R., Griffiths, Scott A., Guo, Yanan, Gamelin, Richard C., Henrissat, Bernard, Kabir, M. Shahjahan, Jashni, Mansoor Karimi, Kema, Gert, Klaubauf, Sylvia, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Mehrabi, Rahim, Ohm, Robin A., Owen, Timothy J., Salamov, Asaf, Schwelm, Arne, Schijlen, Elio, Sun, Hui, van den Burg, Harrold A., van Burg, Roeland C. H. J., Zhang, Shuguang, Goodwin, Stephen B., Grigoriev, Igor V., Collemare, Jerome, and Bradshaw, Rosie E. Fri . "The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry". United States. https://doi.org/10.1371/journal.pgen.1003088. https://www.osti.gov/servlets/purl/1165996.
@article{osti_1165996,
title = {The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry},
author = {de Wit, Pierre J. G. M. and van der Burgt, Ate and Okmen, Bilal and Stergiopoulos, Ioannis and Abd-Elsalam, Kamel A. and Aerts, Andrea L. and Bahkali, Ali H. and Beenen, Henriek G. and Chettri, Oranav and Cos, Murray P. and Datema, Erwin and de Vries, Ronald P. and DHillon, Braham and Ganley, Austen R. and Griffiths, Scott A. and Guo, Yanan and Gamelin, Richard C. and Henrissat, Bernard and Kabir, M. Shahjahan and Jashni, Mansoor Karimi and Kema, Gert and Klaubauf, Sylvia and Lapidus, Alla and Levasseur, Anthony and Lindquist, Erika and Mehrabi, Rahim and Ohm, Robin A. and Owen, Timothy J. and Salamov, Asaf and Schwelm, Arne and Schijlen, Elio and Sun, Hui and van den Burg, Harrold A. and van Burg, Roeland C. H. J. and Zhang, Shuguang and Goodwin, Stephen B. and Grigoriev, Igor V. and Collemare, Jerome and Bradshaw, Rosie E.},
abstractNote = {We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70percent of gene content in both genomes are homologs), but differ significantly in size (Cfu >61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2percent in Cfu versus 3.2percent in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation.},
doi = {10.1371/journal.pgen.1003088},
url = {https://www.osti.gov/biblio/1165996}, journal = {PLoS Genetics},
issn = {1553-7404},
number = 11,
volume = 8,
place = {United States},
year = {2012},
month = {5}
}