The genome sequence of the filamentous fungus Neurospora crassa

James E. Galagan; Sarah E. Calvo; Katherine A. Borkovich; Eric U. Selker; Nick O. Read; David Jaffe; William FitzHugh; Li Jun Ma; Serge Smirnov; Seth Purcell; Bushra Rehman; Timothy Elkins; Reinhard Engels; Shunguang Wang; Cydney B. Nielsen; Jonathan Butler; Matthew Endrizzi; Dayong Qui; Peter Ianakiev; Deborah Bell-Pedersen; Mary Anne Nelson; Margaret Werner-Washburne; Claude P. Selitrennikoff; John A. Kinsey; Edward L. Braun; Alex Zelter; Ulrich Schulte; Gregory O. Kothe; Gregory Jedd; Werner Mewes; Chuck Staben; Edward Marcotte; David Greenberg; Alice Roy; Karen Foley; Jerome Naylor; Nicole Stange-Thomann; Robert Barrett; Sante Gnerre; Michael Kamal; Manolis Kamvysselis; Evan Mauceli; Cord Bielke; Stephen Rudd; Dmitrij Frishman; Svetlana Krystofova; Carolyn Rasmussen; Robert L. Metzenberg; David D. Perkins; Scott Kroken; Carlo Cogoni; Giuseppe Macino; David Catcheside; Weixi Li; Robert J. Pratt; Stephen A. Osmani; Colin P.C. DeSouza; Louise Glass; Marc J. Orbach; J. Andrew Berglund; Rodger Voelker; Oded Yarden; Michael Plamann; Stephan Seiler; Jay Dunlap; Alan Radford; Rodolfo Aramayo; Donald O. Natvig; Lisa A. Alex; Gertrud Mannhaupt; Daniel J. Ebbole; Michael Freitag; Ian Paulsen; Matthew S. Sachs; Eric S. Lander; Chad Nusbaum; Bruce Birren

doi:10.1038/nature01554

The genome sequence of the filamentous fungus Neurospora crassa

James E. Galagan^*, Sarah E. Calvo, Katherine A. Borkovich, Eric U. Selker, Nick O. Read, David Jaffe, William FitzHugh, Li Jun Ma, Serge Smirnov, Seth Purcell, Bushra Rehman, Timothy Elkins, Reinhard Engels, Shunguang Wang, Cydney B. Nielsen, Jonathan Butler, Matthew Endrizzi, Dayong Qui, Peter Ianakiev, Deborah Bell-PedersenMary Anne Nelson, Margaret Werner-Washburne, Claude P. Selitrennikoff, John A. Kinsey, Edward L. Braun, Alex Zelter, Ulrich Schulte, Gregory O. Kothe, Gregory Jedd, Werner Mewes, Chuck Staben, Edward Marcotte, David Greenberg, Alice Roy, Karen Foley, Jerome Naylor, Nicole Stange-Thomann, Robert Barrett, Sante Gnerre, Michael Kamal, Manolis Kamvysselis, Evan Mauceli, Cord Bielke, Stephen Rudd, Dmitrij Frishman, Svetlana Krystofova, Carolyn Rasmussen, Robert L. Metzenberg, David D. Perkins, Scott Kroken, Carlo Cogoni, Giuseppe Macino, David Catcheside, Weixi Li, Robert J. Pratt, Stephen A. Osmani, Colin P.C. DeSouza, Louise Glass, Marc J. Orbach, J. Andrew Berglund, Rodger Voelker, Oded Yarden, Michael Plamann, Stephan Seiler, Jay Dunlap, Alan Radford, Rodolfo Aramayo, Donald O. Natvig, Lisa A. Alex, Gertrud Mannhaupt, Daniel J. Ebbole, Michael Freitag, Ian Paulsen, Matthew S. Sachs, Eric S. Lander, Chad Nusbaum, Bruce Birren

^*Corresponding author for this work

Department of Plant Pathology and Microbiology

Research output: Contribution to journal › Article › peer-review

1319 Scopus citations

Abstract

Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report a high-quality draft sequence of the N. crassa genome. The approximately 40-megabase genome encodes about 10,000 protein-coding genes-more than twice as many as in the fission yeast Schizosaccharomyces pombe and only about 25% fewer than in the fruiffly Drosophila melanogaster. Analysis of the gene set yields insights into unexpected aspects of Neurospora biology including the identification of genes potentially associated with red light photobiology, genes implicated in secondary metabolism, and important differences in Ca²⁺ signalling as compared with plants and animals. Neurospora possesses the widest array of genome defence mechanisms known for any eukaryotic organism, including a process unique to fungi called repeat-induced point mutation (RIP). Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.

Original language	English
Pages (from-to)	859-868
Number of pages	10
Journal	Nature
Volume	422
Issue number	6934
DOIs	https://doi.org/10.1038/nature01554
State	Published - 24 Apr 2003

Bibliographical note

Funding Information:
Acknowledgements The authors would like to thank J. Arnold, H. Inoue, G. Turner, B. Bowman, P. Harriman and P. Youderian for their support. We also thank Lion Bioscience, V. Aign and J. Hoheisel for making available the BAC libraries used during sequencing; M. Karasz for developing the web pages hosting the Neurospora Interpro analysis at MIPS; the Torrey Mesa Research Institute/Syngenta for providing genome data for C. heterostrophus, B. fuckeliana, G. verticillioides and G. zeae; and all members of the Whitehead Institute/MIT Center for Genome Research sequencing group. Funding for the Neurospora genome project was provided by the National Science Foundation. Additional funding was provided by the Deutsche Forschungsgemeinschaft, The Israel Science Foundation and the National Institutes of Health.

Access to Document

10.1038/nature01554

Cite this

Galagan, J. E., Calvo, S. E., Borkovich, K. A., Selker, E. U., Read, N. O., Jaffe, D., FitzHugh, W., Ma, L. J., Smirnov, S., Purcell, S., Rehman, B., Elkins, T., Engels, R., Wang, S., Nielsen, C. B., Butler, J., Endrizzi, M., Qui, D., Ianakiev, P., ... Birren, B. (2003). The genome sequence of the filamentous fungus Neurospora crassa. Nature, 422(6934), 859-868. https://doi.org/10.1038/nature01554

@article{f827d1702cac4bfc805ef4319843d69f,

title = "The genome sequence of the filamentous fungus Neurospora crassa",

abstract = "Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report a high-quality draft sequence of the N. crassa genome. The approximately 40-megabase genome encodes about 10,000 protein-coding genes-more than twice as many as in the fission yeast Schizosaccharomyces pombe and only about 25% fewer than in the fruiffly Drosophila melanogaster. Analysis of the gene set yields insights into unexpected aspects of Neurospora biology including the identification of genes potentially associated with red light photobiology, genes implicated in secondary metabolism, and important differences in Ca2+ signalling as compared with plants and animals. Neurospora possesses the widest array of genome defence mechanisms known for any eukaryotic organism, including a process unique to fungi called repeat-induced point mutation (RIP). Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.",

author = "Galagan, {James E.} and Calvo, {Sarah E.} and Borkovich, {Katherine A.} and Selker, {Eric U.} and Read, {Nick O.} and David Jaffe and William FitzHugh and Ma, {Li Jun} and Serge Smirnov and Seth Purcell and Bushra Rehman and Timothy Elkins and Reinhard Engels and Shunguang Wang and Nielsen, {Cydney B.} and Jonathan Butler and Matthew Endrizzi and Dayong Qui and Peter Ianakiev and Deborah Bell-Pedersen and Nelson, {Mary Anne} and Margaret Werner-Washburne and Selitrennikoff, {Claude P.} and Kinsey, {John A.} and Braun, {Edward L.} and Alex Zelter and Ulrich Schulte and Kothe, {Gregory O.} and Gregory Jedd and Werner Mewes and Chuck Staben and Edward Marcotte and David Greenberg and Alice Roy and Karen Foley and Jerome Naylor and Nicole Stange-Thomann and Robert Barrett and Sante Gnerre and Michael Kamal and Manolis Kamvysselis and Evan Mauceli and Cord Bielke and Stephen Rudd and Dmitrij Frishman and Svetlana Krystofova and Carolyn Rasmussen and Metzenberg, {Robert L.} and Perkins, {David D.} and Scott Kroken and Carlo Cogoni and Giuseppe Macino and David Catcheside and Weixi Li and Pratt, {Robert J.} and Osmani, {Stephen A.} and DeSouza, {Colin P.C.} and Louise Glass and Orbach, {Marc J.} and Berglund, {J. Andrew} and Rodger Voelker and Oded Yarden and Michael Plamann and Stephan Seiler and Jay Dunlap and Alan Radford and Rodolfo Aramayo and Natvig, {Donald O.} and Alex, {Lisa A.} and Gertrud Mannhaupt and Ebbole, {Daniel J.} and Michael Freitag and Ian Paulsen and Sachs, {Matthew S.} and Lander, {Eric S.} and Chad Nusbaum and Bruce Birren",

note = "Funding Information: Acknowledgements The authors would like to thank J. Arnold, H. Inoue, G. Turner, B. Bowman, P. Harriman and P. Youderian for their support. We also thank Lion Bioscience, V. Aign and J. Hoheisel for making available the BAC libraries used during sequencing; M. Karasz for developing the web pages hosting the Neurospora Interpro analysis at MIPS; the Torrey Mesa Research Institute/Syngenta for providing genome data for C. heterostrophus, B. fuckeliana, G. verticillioides and G. zeae; and all members of the Whitehead Institute/MIT Center for Genome Research sequencing group. Funding for the Neurospora genome project was provided by the National Science Foundation. Additional funding was provided by the Deutsche Forschungsgemeinschaft, The Israel Science Foundation and the National Institutes of Health.",

year = "2003",

month = apr,

day = "24",

doi = "10.1038/nature01554",

language = "אנגלית",

volume = "422",

pages = "859--868",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "6934",

}

Galagan, JE, Calvo, SE, Borkovich, KA, Selker, EU, Read, NO, Jaffe, D, FitzHugh, W, Ma, LJ, Smirnov, S, Purcell, S, Rehman, B, Elkins, T, Engels, R, Wang, S, Nielsen, CB, Butler, J, Endrizzi, M, Qui, D, Ianakiev, P, Bell-Pedersen, D, Nelson, MA, Werner-Washburne, M, Selitrennikoff, CP, Kinsey, JA, Braun, EL, Zelter, A, Schulte, U, Kothe, GO, Jedd, G, Mewes, W, Staben, C, Marcotte, E, Greenberg, D, Roy, A, Foley, K, Naylor, J, Stange-Thomann, N, Barrett, R, Gnerre, S, Kamal, M, Kamvysselis, M, Mauceli, E, Bielke, C, Rudd, S, Frishman, D, Krystofova, S, Rasmussen, C, Metzenberg, RL, Perkins, DD, Kroken, S, Cogoni, C, Macino, G, Catcheside, D, Li, W, Pratt, RJ, Osmani, SA, DeSouza, CPC, Glass, L, Orbach, MJ, Berglund, JA, Voelker, R, Yarden, O, Plamann, M, Seiler, S, Dunlap, J, Radford, A, Aramayo, R, Natvig, DO, Alex, LA, Mannhaupt, G, Ebbole, DJ, Freitag, M, Paulsen, I, Sachs, MS, Lander, ES, Nusbaum, C & Birren, B 2003, 'The genome sequence of the filamentous fungus Neurospora crassa', Nature, vol. 422, no. 6934, pp. 859-868. https://doi.org/10.1038/nature01554

TY - JOUR

T1 - The genome sequence of the filamentous fungus Neurospora crassa

AU - Galagan, James E.

AU - Calvo, Sarah E.

AU - Borkovich, Katherine A.

AU - Selker, Eric U.

AU - Read, Nick O.

AU - Jaffe, David

AU - FitzHugh, William

AU - Ma, Li Jun

AU - Smirnov, Serge

AU - Purcell, Seth

AU - Rehman, Bushra

AU - Elkins, Timothy

AU - Engels, Reinhard

AU - Wang, Shunguang

AU - Nielsen, Cydney B.

AU - Butler, Jonathan

AU - Endrizzi, Matthew

AU - Qui, Dayong

AU - Ianakiev, Peter

AU - Bell-Pedersen, Deborah

AU - Nelson, Mary Anne

AU - Werner-Washburne, Margaret

AU - Selitrennikoff, Claude P.

AU - Kinsey, John A.

AU - Braun, Edward L.

AU - Zelter, Alex

AU - Schulte, Ulrich

AU - Kothe, Gregory O.

AU - Jedd, Gregory

AU - Mewes, Werner

AU - Staben, Chuck

AU - Marcotte, Edward

AU - Greenberg, David

AU - Roy, Alice

AU - Foley, Karen

AU - Naylor, Jerome

AU - Stange-Thomann, Nicole

AU - Barrett, Robert

AU - Gnerre, Sante

AU - Kamal, Michael

AU - Kamvysselis, Manolis

AU - Mauceli, Evan

AU - Bielke, Cord

AU - Rudd, Stephen

AU - Frishman, Dmitrij

AU - Krystofova, Svetlana

AU - Rasmussen, Carolyn

AU - Metzenberg, Robert L.

AU - Perkins, David D.

AU - Kroken, Scott

AU - Cogoni, Carlo

AU - Macino, Giuseppe

AU - Catcheside, David

AU - Li, Weixi

AU - Pratt, Robert J.

AU - Osmani, Stephen A.

AU - DeSouza, Colin P.C.

AU - Glass, Louise

AU - Orbach, Marc J.

AU - Berglund, J. Andrew

AU - Voelker, Rodger

AU - Yarden, Oded

AU - Plamann, Michael

AU - Seiler, Stephan

AU - Dunlap, Jay

AU - Radford, Alan

AU - Aramayo, Rodolfo

AU - Natvig, Donald O.

AU - Alex, Lisa A.

AU - Mannhaupt, Gertrud

AU - Ebbole, Daniel J.

AU - Freitag, Michael

AU - Paulsen, Ian

AU - Sachs, Matthew S.

AU - Lander, Eric S.

AU - Nusbaum, Chad

AU - Birren, Bruce

N1 - Funding Information: Acknowledgements The authors would like to thank J. Arnold, H. Inoue, G. Turner, B. Bowman, P. Harriman and P. Youderian for their support. We also thank Lion Bioscience, V. Aign and J. Hoheisel for making available the BAC libraries used during sequencing; M. Karasz for developing the web pages hosting the Neurospora Interpro analysis at MIPS; the Torrey Mesa Research Institute/Syngenta for providing genome data for C. heterostrophus, B. fuckeliana, G. verticillioides and G. zeae; and all members of the Whitehead Institute/MIT Center for Genome Research sequencing group. Funding for the Neurospora genome project was provided by the National Science Foundation. Additional funding was provided by the Deutsche Forschungsgemeinschaft, The Israel Science Foundation and the National Institutes of Health.

PY - 2003/4/24

Y1 - 2003/4/24

N2 - Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report a high-quality draft sequence of the N. crassa genome. The approximately 40-megabase genome encodes about 10,000 protein-coding genes-more than twice as many as in the fission yeast Schizosaccharomyces pombe and only about 25% fewer than in the fruiffly Drosophila melanogaster. Analysis of the gene set yields insights into unexpected aspects of Neurospora biology including the identification of genes potentially associated with red light photobiology, genes implicated in secondary metabolism, and important differences in Ca2+ signalling as compared with plants and animals. Neurospora possesses the widest array of genome defence mechanisms known for any eukaryotic organism, including a process unique to fungi called repeat-induced point mutation (RIP). Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.

AB - Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report a high-quality draft sequence of the N. crassa genome. The approximately 40-megabase genome encodes about 10,000 protein-coding genes-more than twice as many as in the fission yeast Schizosaccharomyces pombe and only about 25% fewer than in the fruiffly Drosophila melanogaster. Analysis of the gene set yields insights into unexpected aspects of Neurospora biology including the identification of genes potentially associated with red light photobiology, genes implicated in secondary metabolism, and important differences in Ca2+ signalling as compared with plants and animals. Neurospora possesses the widest array of genome defence mechanisms known for any eukaryotic organism, including a process unique to fungi called repeat-induced point mutation (RIP). Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.

UR - http://www.scopus.com/inward/record.url?scp=0037464589&partnerID=8YFLogxK

U2 - 10.1038/nature01554

DO - 10.1038/nature01554

M3 - ???researchoutput.researchoutputtypes.contributiontojournal.article???

C2 - 12712197

AN - SCOPUS:0037464589

SN - 0028-0836

VL - 422

SP - 859

EP - 868

JO - Nature

JF - Nature

IS - 6934

ER -

The genome sequence of the filamentous fungus Neurospora crassa

Abstract

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this