De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis

Nowrousian, Minou; Stajich, Jason E.; Chu, Meiling; Engh, Ines; Espagne, Eric; Halliday, Karen; Kamerewerd, Jens; Kempken, Frank; Knab, Birgit; Kuo, Hsiao-Che; Osiewacz, Heinz D.; Pöggeler, Stefanie; Read, Nick D.; Seiler, Stephan; Smith, Kristina M.; Zickler, Denise; Kück, Ulrich; Freitag, Michael

doi:10.1371/journal.pgen.1000891

De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis

Journal Article · Thu Apr 08 00:00:00 EDT 2010 · PLoS Genetics

DOI:https://doi.org/10.1371/journal.pgen.1000891· OSTI ID:1627282

Nowrousian, Minou ^[1]; Stajich, Jason E. ^[2]; Chu, Meiling ^[3]; Engh, Ines ^[4]; Espagne, Eric ^[5]; Halliday, Karen ^[6]; Kamerewerd, Jens ^[4]; Kempken, Frank ^[7]; Knab, Birgit ^[8]; Kuo, Hsiao-Che ^[3]; Osiewacz, Heinz D. ^[8]; Pöggeler, Stefanie ^[9]; Read, Nick D. ^[3]; Seiler, Stephan ^[10]; Smith, Kristina M. ^[11]; Zickler, Denise ^[5]; Kück, Ulrich ^[4]; Freitag, Michael ^[11]

Ruhr Univ., Bochum (Germany). Lehrstuhl fur Allgemeine und Molekulare Botanik; DOE/OSTI
Univ. of California, Riverside, CA (United States). Dept. of Plant Pathology and Microbiology
Univ. of Edinburgh, Scotland (United Kingdom). Inst. of Cell Biology. Fungal Cell Biology Group
Ruhr Univ., Bochum (Germany). Lehrstuhl fur Allgemeine und Molekulare Botanik
Univ. Paris-Sud, Orsay (France). Inst. de Genetique et Microbiologie
Univ. of Edinburgh, Scotland (United Kingdom). Biological Sciences. Inst. of Molecular Plant Sciences
Christian-Albrechts-Universitat zu Kiel (Germany). Botanisches Institut und Botanischer Garten. Abteilung Botanische Genetik und Molekularbiologie
Johann Wolfgang Goethe Univ., Frankfurt (Germany). Faculty for Biosciences and Cluster of Excellence Macromolecular Complexes. Inst. of Molecular Biosciences
Georg-August Univ., Gottingen (Germany). Dept. of Genetics of Eukaryotic Microorganisms. Inst. of Microbiology and Genetics
Georg-August Univ., Gottingen (Germany). DFG Research Center Molecular Physiology of the Brain (CMPB). Dept. of Molecular Microbiology and Genetics. Inst. of Microbiology and Genetics
Oregon State Univ., Corvallis, OR (United States). Dept. of Biochemistry and Biophysics. Center for Genome Research and Biocomputing

Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While nextgeneration sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30–90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/ Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in ~4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb) with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed that S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data can be used for comparative studies to address basic questions of fungal biology.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; German Research Foundation (DFG); American Cancer Society; Biotechnological and Biological Sciences Research Council (BBSRC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1627282

Journal Information:: PLoS Genetics, Journal Name: PLoS Genetics Journal Issue: 4 Vol. 6; ISSN 1553-7404

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

References (155)

Molecular and Functional Analyses of Incompatibility Genes at het-6 in a Population of Neurospora crassa Mir-Rashed, N.; Jacobson, D. J.; Dehghany, M. R. Fungal Genetics and Biology, Vol. 30, Issue 3 https://doi.org/10.1006/fgbi.2000.1218	journal	August 2000
Transposons in filamentous fungi-facts and perspectives Kempken, Frank; Kück, Ulrich BioEssays, Vol. 20, Issue 8 https://doi.org/10.1002/(SICI)1521-1878(199808)20:8<652::AID-BIES8>3.0.CO;2-K	journal	August 1998
Natural Products of Filamentous Fungi: Enzymes, Genes, and Their Regulation Hoffmeister, Dirk; Keller, Nancy P. ChemInform, Vol. 38, Issue 30 https://doi.org/10.1002/chin.200730266	journal	July 2007
White collar-1, a central regulator of blue light responses in Neurospora, is a zinc finger protein. Ballario, P.; Vittorioso, P.; Magrelli, A. The EMBO Journal, Vol. 15, Issue 7 https://doi.org/10.1002/j.1460-2075.1996.tb00510.x	journal	April 1996
Metabolic Pathway Gene Clusters in Filamentous Fungi Keller, Nancy P.; Hohn, Thomas M. Fungal Genetics and Biology, Vol. 21, Issue 1 https://doi.org/10.1006/fgbi.1997.0970	journal	February 1997
Microscopic and Ultrastructural Examination of Vegetative Incompatibility in Partial Diploids Heterozygous athetLoci inNeurospora crassa Jacobson, D. J.; Beurkens, K.; Klomparens, K. L. Fungal Genetics and Biology, Vol. 23, Issue 1 https://doi.org/10.1006/fgbi.1997.1020	journal	February 1998
Principles governing amino acid composition of integral membrane proteins: application to topology prediction 1 1Edited by J. Thornton Tusnády, Gábor E.; Simon, István Journal of Molecular Biology, Vol. 283, Issue 2 https://doi.org/10.1006/jmbi.1998.2107	journal	October 1998
Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen Krogh, Anders; Larsson, Björn; von Heijne, Gunnar Journal of Molecular Biology, Vol. 305, Issue 3 https://doi.org/10.1006/jmbi.2000.4315	journal	January 2001
Observing Meiosis in Filamentous Fungi: Sordaria and Neurospora Zickler, Denise Meiosis, Vol. 2, 91–114 https://doi.org/10.1007/978-1-60761-103-5_7	book	January 2009
Fot1, a new family of fungal transposable elements Daboussi, Marie-Josée; Langin, Thierry; Brygoo, Yves Molecular and General Genetics MGG, Vol. 232, Issue 1 https://doi.org/10.1007/BF00299131	journal	March 1992
Transformation of Sordaria macrospora to hygromycin B resistance: characterization of transformants by electrophoretic karyotyping and tetrad analysis Walz, Markus; K�ck, Ulrich Current Genetics, Vol. 29, Issue 1 https://doi.org/10.1007/BF00313198	journal	December 1995
Vegetative incompatibility in Neurospora: its effect on horizontal transfer of mitochondrial plasmids and senescence in natural populations Debets, Fons; Yang, Xiao; Griffiths, Anthony J. F. Current Genetics, Vol. 26, Issue 2 https://doi.org/10.1007/BF00313797	journal	August 1994
Genomic evidence for mating abilities in the asexual pathogen Aspergillus fumigatus Pöggeler, Stefanie Current Genetics, Vol. 42, Issue 3 https://doi.org/10.1007/s00294-002-0338-3	journal	December 2002
Versatile EGFP reporter plasmids for cellular localization of recombinant gene products in filamentous fungi Pöggeler, Stefanie; Masloff, Sandra; Hoff, Birgit Current Genetics, Vol. 43, Issue 1 https://doi.org/10.1007/s00294-003-0370-y	journal	January 2003
Detection of hyphal fusion in filamentous fungi using differently fluorescence-labeled histones Rech, Christine; Engh, Ines; Kück, Ulrich Current Genetics, Vol. 52, Issue 5-6 https://doi.org/10.1007/s00294-007-0158-6	journal	October 2007
A novel polyketide biosynthesis gene cluster is involved in fruiting body morphogenesis in the filamentous fungi Sordaria macrospora and Neurospora crassa Nowrousian, Minou Current Genetics, Vol. 55, Issue 2 https://doi.org/10.1007/s00294-009-0236-z	journal	March 2009
Heterokaryon incompatibility blocks virus transfer among natural isolates of black Aspergilli van Diepeningen, A. D.; Debets, Alfons J. M.; Hoekstra, Rolf F. Current Genetics, Vol. 32, Issue 3 https://doi.org/10.1007/s002940050268	journal	September 1997
Identification and characterization of PaMTH1, a putative O -methyltransferase accumulating during senescence of Podospora anserina cultures Averbeck, N. B.; Jensen, O. N.; Mann, M. Current Genetics, Vol. 37, Issue 3 https://doi.org/10.1007/s002940050520	journal	March 2000
From early homologue recognition to synaptonemal complex formation Zickler, Denise Chromosoma, Vol. 115, Issue 3 https://doi.org/10.1007/s00412-006-0048-6	journal	March 2006
The hAT family: a versatile transposon group common to plants, fungi, animals, and man Kempken, Frank; Windhofer, Frank Chromosoma, Vol. 110, Issue 1 https://doi.org/10.1007/s004120000118	journal	April 2001
A Sordaria macrospora mutant lacking the leu1 gene shows a developmental arrest during fruiting body formation Kück, Ulrich Molecular Genetics and Genomics, Vol. 274, Issue 3 https://doi.org/10.1007/s00438-005-0021-8	journal	August 2005
Cross-species microarray hybridization to identify developmentally regulated genes in the filamentous fungus Sordaria macrospora Nowrousian, Minou; Ringelberg, Carol; Dunlap, Jay C. Molecular Genetics and Genomics, Vol. 273, Issue 2 https://doi.org/10.1007/s00438-005-1118-9	journal	March 2005
Strain-specific retrotransposon-mediated recombination in commercially used Aspergillus niger strain Braumann, Ilka; van den Berg, Marco A.; Kempken, Frank Molecular Genetics and Genomics, Vol. 280, Issue 4 https://doi.org/10.1007/s00438-008-0367-9	journal	August 2008
The degenerate DNA transposon Pat and repeat-induced point mutation (RIP) in Podospora anserina Hamann, A.; Feller, F.; Osiewacz, H. D. Molecular and General Genetics MGG, Vol. 263, Issue 6 https://doi.org/10.1007/s004380050035	journal	August 2000
Absence of differences in polysomal RNAs from vegetative monokaryotic and dikaryotic cells of the fungus Schizophyllum commune Hoge, J. Harry C.; Springer, Jan; Bert, Zantinge Experimental Mycology, Vol. 6, Issue 3 https://doi.org/10.1016/0147-5975(82)90114-1	journal	September 1982
Molecular analysis of aging processes in fungi Osiewacz, Heinz D. Mutation Research/DNAging, Vol. 237, Issue 1 https://doi.org/10.1016/0921-8734(90)90026-N	journal	January 1990
Seeing the Light: News in Neurospora Blue Light Signal Transduction Linden, H.; Ballario, P.; Arpaia, G. Advances in Genetics https://doi.org/10.1016/S0065-2660(08)60150-9	book	January 1999
A Gene Essential for De Novo Methylation and Development in Ascobolus Reveals a Novel Type of Eukaryotic DNA Methyltransferase Structure Malagnac, Fabienne; Wendel, Birgit; Goyon, Christophe Cell, Vol. 91, Issue 2 https://doi.org/10.1016/S0092-8674(00)80410-9	journal	October 1997
Spo76p Is a Conserved Chromosome Morphogenesis Protein that Links the Mitotic and Meiotic Programs van Heemst, Diana; James, Françoise; Pöggeler, Stefanie Cell, Vol. 98, Issue 2 https://doi.org/10.1016/S0092-8674(00)81020-X	journal	July 1999
Meiotic Silencing by Unpaired DNA Shiu, Patrick K. T.; Raju, Namboori B.; Zickler, Denise Cell, Vol. 107, Issue 7 https://doi.org/10.1016/S0092-8674(01)00609-2	journal	December 2001
An efficient procedure to isolate fungal genes from an indexed cosmid library Pöggeler, Stefanie; Nowrousian, Minou; Jacobsen, Sabine Journal of Microbiological Methods, Vol. 29, Issue 1 https://doi.org/10.1016/S0167-7012(97)00018-3	journal	April 1997
Repeats in genomic DNA: mining and meaning Jurka, Jerzy Current Opinion in Structural Biology, Vol. 8, Issue 3 https://doi.org/10.1016/S0959-440X(98)80067-5	journal	June 1998
Analysis of loss of pathogenicity mutants reveals that repeat-induced point mutations can occur in the Dothideomycete Leptosphaeria maculans Idnurm, Alexander; Howlett, Barbara J. Fungal Genetics and Biology, Vol. 39, Issue 1 https://doi.org/10.1016/S1087-1845(02)00588-1	journal	June 2003
The Aspergillus nidulans Phytochrome FphA Represses Sexual Development in Red Light Blumenstein, Anne; Vienken, Kay; Tasler, Ronja Current Biology, Vol. 15, Issue 20 https://doi.org/10.1016/j.cub.2005.08.061	journal	October 2005
Functional and Physical Interaction of Blue- and Red-Light Sensors in Aspergillus nidulans Purschwitz, Janina; Müller, Sylvia; Kastner, Christian Current Biology, Vol. 18, Issue 4 https://doi.org/10.1016/j.cub.2008.01.061	journal	February 2008
The Fungi Stajich, Jason E.; Berbee, Mary L.; Blackwell, Meredith Current Biology, Vol. 19, Issue 18 https://doi.org/10.1016/j.cub.2009.07.004	journal	September 2009
Differential proteomic profiling of mitochondria from Podospora anserina, rat and human reveals distinct patterns of age-related oxidative changes Groebe, Karlfried; Krause, Frank; Kunstmann, Birgit Experimental Gerontology, Vol. 42, Issue 9 https://doi.org/10.1016/j.exger.2007.07.001	journal	September 2007
Guest, a transposable element belonging to the Tc1/mariner superfamily is an ancient invader of Neurospora genomes Ramussen, J. P.; Taylor, A. H.; Ma, L. -J Fungal Genetics and Biology, Vol. 41, Issue 1 https://doi.org/10.1016/j.fgb.2003.09.001	journal	January 2004
Comparative sequence analysis of Sordaria macrospora and Neurospora crassa as a means to improve genome annotation Nowrousian, Minou; Würtz, Christian; Pöggeler, Stefanie Fungal Genetics and Biology, Vol. 41, Issue 3 https://doi.org/10.1016/j.fgb.2003.10.005	journal	March 2004
Multiple layers of temporal and spatial control regulate accumulation of the fruiting body-specific protein APP in Sordaria macrospora and Neurospora crassa Nowrousian, Minou; Piotrowski, Markus; Kück, Ulrich Fungal Genetics and Biology, Vol. 44, Issue 7 https://doi.org/10.1016/j.fgb.2006.09.009	journal	July 2007
Ancestral polymorphism and linkage disequilibrium at the het-6 region in pseudohomothallic Neurospora tetrasperma Powell, Amy J.; Jacobson, David J.; Natvig, Donald O. Fungal Genetics and Biology, Vol. 44, Issue 9 https://doi.org/10.1016/j.fgb.2007.04.010	journal	September 2007
Transposons in biotechnologically relevant strains of Aspergillus niger and Penicillium chrysogenum Braumann, Ilka; van den Berg, Marco; Kempken, Frank Fungal Genetics and Biology, Vol. 44, Issue 12 https://doi.org/10.1016/j.fgb.2007.07.010	journal	December 2007
Highly efficient generation of signal transduction knockout mutants using a fungal strain deficient in the mammalian ku70 ortholog Pöggeler, Stefanie; Kück, Ulrich Gene, Vol. 378 https://doi.org/10.1016/j.gene.2006.03.020	journal	August 2006
Improved Prediction of Signal Peptides: SignalP 3.0 Dyrløv Bendtsen, Jannick; Nielsen, Henrik; von Heijne, Gunnar Journal of Molecular Biology, Vol. 340, Issue 4, p. 783-795 https://doi.org/10.1016/j.jmb.2004.05.028	journal	July 2004
Quelling: post-transcriptional gene silencing guided by small RNAs in Neurospora crassa Fulci, Valerio; Macino, Giuseppe Current Opinion in Microbiology, Vol. 10, Issue 2 https://doi.org/10.1016/j.mib.2007.03.016	journal	April 2007
RIP: the evolutionary cost of genome defense Galagan, James E.; Selker, Eric U. Trends in Genetics, Vol. 20, Issue 9 https://doi.org/10.1016/j.tig.2004.07.007	journal	September 2004
Genome-wide high throughput analysis of DNA methylation in eukaryotes Pomraning, Kyle R.; Smith, Kristina M.; Freitag, Michael Methods, Vol. 47, Issue 3 https://doi.org/10.1016/j.ymeth.2008.09.022	journal	March 2009
The magnitude of fungal diversity: the 1.5 million species estimate revisited Hawksworth, David L. Mycological Research, Vol. 105, Issue 12 https://doi.org/10.1017/S0953756201004725	journal	December 2001
Polymorphism of het-genes prevents resource plundering in Neurospora crassa Debets, Alfons J. M.; Griffiths, Anthony J. F. Mycological Research, Vol. 102, Issue 11 https://doi.org/10.1017/S095375629800639X	journal	November 1998
A Eukaryotic Protein, NOP-1, Binds Retinal To Form an Archaeal Rhodopsin-like Photochemically Reactive Pigment ^† Bieszke, Jennifer A.; Spudich, Elena N.; Scott, Kenneth L. Biochemistry, Vol. 38, Issue 43 https://doi.org/10.1021/bi9916170	journal	October 1999
The genome sequence of the filamentous fungus Neurospora crassa Galagan, James E.; Calvo, Sarah E.; Borkovich, Katherine A. Nature, Vol. 422, Issue 6934 https://doi.org/10.1038/nature01554	journal	April 2003
The genome sequence of the rice blast fungus Magnaporthe grisea Dean, Ralph A.; Talbot, Nicholas J.; Ebbole, Daniel J. Nature, Vol. 434, Issue 7036 https://doi.org/10.1038/nature03449	journal	April 2005
Genome sequencing in microfabricated high-density picolitre reactors Margulies, Marcel; Egholm, Michael; Altman, William E. Nature, Vol. 437, Issue 7057, p. 376-380 https://doi.org/10.1038/nature03959	journal	July 2005
Discovery of a sexual cycle in the opportunistic fungal pathogen Aspergillus fumigatus O’Gorman, Céline M.; Fuller, Hubert T.; Dyer, Paul S. Nature, Vol. 457, Issue 7228 https://doi.org/10.1038/nature07528	journal	January 2009
Next-generation DNA sequencing Shendure, Jay; Ji, Hanlee Nature Biotechnology, Vol. 26, Issue 10 https://doi.org/10.1038/nbt1486	journal	October 2008
Emergence of a new disease as a result of interspecific virulence gene transfer Friesen, Timothy L.; Stukenbrock, Eva H.; Liu, Zhaohui Nature Genetics, Vol. 38, Issue 8 https://doi.org/10.1038/ng1839	journal	July 2006
The transcriptional program of meiosis and sporulation in fission yeast Mata, Juan; Lyne, Rachel; Burns, Gavin Nature Genetics, Vol. 32, Issue 1 https://doi.org/10.1038/ng951	journal	August 2002
A universal classification of eukaryotic transposable elements implemented in Repbase Kapitonov, Vladimir V.; Jurka, Jerzy Nature Reviews Genetics, Vol. 9, Issue 5 https://doi.org/10.1038/nrg2165-c1	journal	May 2008
Natural products of filamentous fungi: enzymes, genes, and their regulation Hoffmeister, Dirk; Keller, Nancy P. Nat. Prod. Rep., Vol. 24, Issue 2 https://doi.org/10.1039/B603084J	journal	January 2007
Polyketides, proteins and genes in fungi: programmed nano-machines begin to reveal their secrets Cox, Russell J. Organic & Biomolecular Chemistry, Vol. 5, Issue 13 https://doi.org/10.1039/b704420h	journal	January 2007
Genome quality control: RIP (repeat-induced point mutation) comes to Podospora: RIP (repeat-induced point mutation ) in Podospora Graïa, Fatima; Lespinet, Olivier; Rimbault, Blandine Molecular Microbiology, Vol. 40, Issue 3 https://doi.org/10.1046/j.1365-2958.2001.02367.x	journal	May 2001
Repeat-induced point mutation (RIP) in Magnaporthe grisea: implications for its sexual cycle in the natural field context: Repeat-induced point mutation in Magnaporthe grisea Ikeda, Ken-ichi; Nakayashiki, Hitoshi; Kataoka, Tomomori Molecular Microbiology, Vol. 45, Issue 5 https://doi.org/10.1046/j.1365-2958.2002.03101.x	journal	September 2002
Karyotype polymorphism correlates with intraspecific infertility in the homothallic ascomycete Sordaria macrospora No authors listed Journal of Evolutionary Biology, Vol. 13, Issue 2, p. 281-289 https://doi.org/10.1046/j.1420-9101.2000.00174.x	journal	March 2000
Body plan evolution of ascomycetes, as inferred from an RNA polymerase II phylogeny Liu, Y. J.; Hall, B. D. Proceedings of the National Academy of Sciences, Vol. 101, Issue 13 https://doi.org/10.1073/pnas.0400938101	journal	March 2004
A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassa Freitag, M.; Williams, R. L.; Kothe, G. O. Proceedings of the National Academy of Sciences, Vol. 99, Issue 13 https://doi.org/10.1073/pnas.132212899	journal	June 2002
Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes Kroken, S.; Glass, N. L.; Taylor, J. W. Proceedings of the National Academy of Sciences, Vol. 100, Issue 26 https://doi.org/10.1073/pnas.2532165100	journal	December 2003
Isolation of a transposable element from Neurospora crassa. Kinsey, J. A.; Helber, J. Proceedings of the National Academy of Sciences, Vol. 86, Issue 6 https://doi.org/10.1073/pnas.86.6.1929	journal	March 1989
AMID, an Apoptosis-inducing Factor-homologous Mitochondrion-associated Protein, Induces Caspase-independent Apoptosis Wu, Min; Xu, Liang-Guo; Li, Xiaoyan Journal of Biological Chemistry, Vol. 277, Issue 28 https://doi.org/10.1074/jbc.M202285200	journal	April 2002
New findings of Neurospora in Europe and comparisons of diversity in temperate climates on continental scales Jacobson, David J.; Dettman, Jeremy R.; Adams, Rachel I. Mycologia, Vol. 98, Issue 4 https://doi.org/10.1080/15572536.2006.11832658	journal	July 2006
Profile hidden Markov models Eddy, S. R. Bioinformatics, Vol. 14, Issue 9 https://doi.org/10.1093/bioinformatics/14.9.755	journal	October 1998
MRBAYES: Bayesian inference of phylogenetic trees Huelsenbeck, J. P.; Ronquist, F. Bioinformatics, Vol. 17, Issue 8 https://doi.org/10.1093/bioinformatics/17.8.754	journal	August 2001
InterProScan - an integration platform for the signature-recognition methods in InterPro Zdobnov, E. M.; Apweiler, R. Bioinformatics, Vol. 17, Issue 9, p. 847-848 https://doi.org/10.1093/bioinformatics/17.9.847	journal	September 2001
Gene prediction with a hidden Markov model and a new intron submodel Stanke, M.; Waack, S. Bioinformatics, Vol. 19, Issue Suppl 2 https://doi.org/10.1093/bioinformatics/btg1080	journal	September 2003
MrBayes 3: Bayesian phylogenetic inference under mixed models Ronquist, Fredrik; Huelsenbeck, John P. Bioinformatics, Vol. 19, Issue 12, p. 1572-1574 https://doi.org/10.1093/bioinformatics/btg180	journal	August 2003
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research Conesa, A.; Gotz, S.; Garcia-Gomez, J. M. Bioinformatics, Vol. 21, Issue 18 https://doi.org/10.1093/bioinformatics/bti610	journal	August 2005
Combo: a whole genome comparative browser Engels, R.; Yu, T.; Burge, C. Bioinformatics, Vol. 22, Issue 14 https://doi.org/10.1093/bioinformatics/btl193	journal	May 2006
Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction Liu, Qian; Mackey, Aaron J.; Roos, David S. Bioinformatics, Vol. 24, Issue 5 https://doi.org/10.1093/bioinformatics/btn004	journal	January 2008
Jalview Version 2--a multiple sequence alignment editor and analysis workbench Waterhouse, A. M.; Procter, J. B.; Martin, D. M. A. Bioinformatics, Vol. 25, Issue 9 https://doi.org/10.1093/bioinformatics/btp033	journal	January 2009
Infernal 1.0: inference of RNA alignments Nawrocki, E. P.; Kolbe, D. L.; Eddy, S. R. Bioinformatics, Vol. 25, Issue 10 https://doi.org/10.1093/bioinformatics/btp157	journal	March 2009
Nonself recognition is mediated by HET-C heterocomplex formation during vegetative incompatibility Sarkar, S. The EMBO Journal, Vol. 21, Issue 18 https://doi.org/10.1093/emboj/cdf479	journal	September 2002
Neurospora: the organism behind the molecular revolution. Perkins, D. D. Genetics, Vol. 130, Issue 4 https://doi.org/10.1093/genetics/130.4.687	journal	April 1992
Mating-Type Genes From the Homothallic Fungus Sordaria macrospora Are Functionally Expressed in a Heterothallic Ascomycete Pöggeler, Stefanie; Risch, Siegfried; Kück, Ulrich Genetics, Vol. 147, Issue 2 https://doi.org/10.1093/genetics/147.2.567	journal	October 1997
A Methylated Neurospora 5S rRNA Pseudogene Contains a Transposable Element Inactivated by Repeat-Induced Point Mutation Margolin, Brian S.; Garrett-Engele, Phillip W.; Stevens, Judith N. Genetics, Vol. 149, Issue 4 https://doi.org/10.1093/genetics/149.4.1787	journal	August 1998
Molecular Characterization of tol, a Mediator of Mating-Type-Associated Vegetative Incompatibility in Neurospora crassa Shiu, Patrick Ka Tai; Glass, N. Louise Genetics, Vol. 151, Issue 2 https://doi.org/10.1093/genetics/151.2.545	journal	February 1999
The pro1+ Gene From Sordaria macrospora Encodes a C6 Zinc Finger Transcription Factor Required for Fruiting Body Development Masloff, Sandra; Pöggeler, Stefanie; Kück, Ulrich Genetics, Vol. 152, Issue 1 https://doi.org/10.1093/genetics/152.1.191	journal	May 1999
Vegetative Incompatibility in the het-6 Region of Neurospora crassa Is Mediated by Two Linked Genes Smith, M. L.; Micali, O. C.; Hubbard, S. P. Genetics, Vol. 155, Issue 3 https://doi.org/10.1093/genetics/155.3.1095	journal	July 2000
Genetic Control of Horizontal Virus Transmission in the Chestnut Blight Fungus, Cryphonectria parasitica Cortesi, Paolo; McCulloch, Charles E.; Song, Haiyue Genetics, Vol. 159, Issue 1 https://doi.org/10.1093/genetics/159.1.107	journal	September 2001
HET-E and HET-D Belong to a New Subfamily of WD40 Proteins Involved in Vegetative Incompatibility Specificity in the Fungus Podospora anserina Espagne, Eric; Balhadère, Pascale; Penin, Marie-Louise Genetics, Vol. 161, Issue 1 https://doi.org/10.1093/genetics/161.1.71	journal	May 2002
Heterocaryosis in Neurospora Crassa Beadle, G. W.; Coonradt, Verna L. Genetics, Vol. 29, Issue 3 https://doi.org/10.1093/genetics/29.3.291	journal	May 1944
HETEROKARYON INCOMPATIBILITY GENES IN NEUROSPORA CRASSA DETECTED USING DUPLICATION-PRODUCING CHROMOSOME REARRANGEMENTS Mylyk, Orest M. Genetics, Vol. 80, Issue 1 https://doi.org/10.1093/genetics/80.1.107	journal	May 1975
The use of Duplication-Generating Rearrangements for Studying Heterokaryon Incompatibility Genes in Neurospora Perkins, David D. Genetics, Vol. 80, Issue 1 https://doi.org/10.1093/genetics/80.1.87	journal	May 1975
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A. Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402 https://doi.org/10.1093/nar/25.17.3389	journal	September 1997
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Thompson, J. Nucleic Acids Research, Vol. 25, Issue 24 https://doi.org/10.1093/nar/25.24.4876	journal	December 1997
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Lowe, Todd M.; Eddy, Sean R. Nucleic Acids Research, Vol. 25, Issue 5 https://doi.org/10.1093/nar/25.5.0955	journal	March 1997
GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses Besemer, J.; Borodovsky, M. Nucleic Acids Research, Vol. 33, Issue Web Server https://doi.org/10.1093/nar/gki487	journal	July 2005
TFAM 1.0: an online tRNA function classifier Taquist, H.; Cui, Y.; Ardell, D. H. Nucleic Acids Research, Vol. 35, Issue Web Server https://doi.org/10.1093/nar/gkm393	journal	May 2007
The Pfam protein families database Finn, R. D.; Tate, J.; Mistry, J. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm960	journal	December 2007
An analysis of the feasibility of short read sequencing Whiteford, N. Nucleic Acids Research, Vol. 33, Issue 19 https://doi.org/10.1093/nar/gni170	journal	October 2005
Horizontal Gene Transfer of Glycosyl Hydrolases of the Rumen Fungi Garcia-Vallvé, S.; Romeu, A.; Palau, J. Molecular Biology and Evolution, Vol. 17, Issue 3 https://doi.org/10.1093/oxfordjournals.molbev.a026315	journal	March 2000
Meiotic double-strand breaks at the interface of chromosome movement, chromosome remodeling, and reductional division Storlazzi, A. Genes & Development, Vol. 17, Issue 21 https://doi.org/10.1101/gad.275203	journal	October 2003
Coupling meiotic chromosome axis integrity to recombination Storlazzi, A.; Tesse, S.; Ruprich-Robert, G. Genes & Development, Vol. 22, Issue 6 https://doi.org/10.1101/gad.459308	journal	March 2008
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs Zerbino, D. R.; Birney, E. Genome Research, Vol. 18, Issue 5 https://doi.org/10.1101/gr.074492.107	journal	February 2008
De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae Reinhardt, J. A.; Baltrus, D. A.; Nishimura, M. T. Genome Research, Vol. 19, Issue 2 https://doi.org/10.1101/gr.083311.108	journal	December 2008
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes Li, L. Genome Research, Vol. 13, Issue 9 https://doi.org/10.1101/gr.1224503	journal	September 2003
GeneWise and Genomewise Birney, E. Genome Research, Vol. 14, Issue 5 https://doi.org/10.1101/gr.1865504	journal	May 2004
The Bioperl Toolkit: Perl Modules for the Life Sciences Stajich, J. E. Genome Research, Vol. 12, Issue 10 https://doi.org/10.1101/gr.361602	journal	October 2002
Genetic Analysis of Phototropism of Neurospora crassa Perithecial Beaks Using White Collar and Albino Mutants Harding, Roy W.; Melles, Sahle Plant Physiology, Vol. 72, Issue 4 https://doi.org/10.1104/pp.72.4.996	journal	August 1983
Dothideomycete–Plant Interactions Illuminated by Genome Sequencing and EST Analysis of the Wheat Pathogen Stagonospora nodorum Hane, James K.; Lowe, Rohan G. T.; Solomon, Peter S. The Plant Cell, Vol. 19, Issue 11 https://doi.org/10.1105/tpc.107.052829	journal	November 2007
The novel ER membrane protein PRO41 is essential for sexual development in the filamentous fungus Sordaria macrospora Nowrousian, Minou; Frank, Sandra; Koers, Sandra Molecular Microbiology, Vol. 64, Issue 4 https://doi.org/10.1111/j.1365-2958.2007.05694.x	journal	May 2007
Over-expression of an S-adenosylmethionine-dependent methyltransferase leads to an extended lifespan of Podospora anserina without impairments in vital functions Kunstmann, Birgit; Osiewacz, Heinz D. Aging Cell, Vol. 7, Issue 5 https://doi.org/10.1111/j.1474-9726.2008.00412.x	journal	October 2008
Comparative gene expression analysis of fruiting body development in two filamentous fungi Nowrousian, Minou; KÃ¼ck, Ulrich FEMS Microbiology Letters, Vol. 257, Issue 2 https://doi.org/10.1111/j.1574-6968.2006.00192.x	journal	April 2006
Regulation of melanin biosynthesis via the dihydroxynaphthalene pathway is dependent on sexual development in the ascomycete Sordaria macrospora Engh, Ines; Nowrousian, Minou; KÃ¼ck, Ulrich FEMS Microbiology Letters, Vol. 275, Issue 1 https://doi.org/10.1111/j.1574-6968.2007.00867.x	journal	October 2007
White Collar-1, a DNA Binding Transcription Factor and a Light Sensor He, Q. Science, Vol. 297, Issue 5582 https://doi.org/10.1126/science.1072795	journal	July 2002
White Collar-1, a Circadian Blue Light Photoreceptor, Binding to the frequency Promoter Froehlich, A. C. Science, Vol. 297, Issue 5582 https://doi.org/10.1126/science.1073681	journal	July 2002
Polyketide and Nonribosomal Peptide Antibiotics: Modularity and Versatility Walsh, C. T. Science, Vol. 303, Issue 5665 https://doi.org/10.1126/science.1094318	journal	March 2004
The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization Cuomo, C. A.; Guldener, U.; Xu, J. -R. Science, Vol. 317, Issue 5843 https://doi.org/10.1126/science.1143708	journal	September 2007
The B73 Maize Genome: Complexity, Diversity, and Dynamics Schnable, P. S.; Ware, D.; Fulton, R. S. Science, Vol. 326, Issue 5956, p. 1112-1115 https://doi.org/10.1126/science.1178534	journal	November 2009
Life with 6000 Genes Goffeau, A.; Barrell, B. G.; Bussey, H. Science, Vol. 274, Issue 5287 https://doi.org/10.1126/science.274.5287.546	journal	October 1996
VIB-1 Is Required for Expression of Genes Necessary for Programmed Cell Death in Neurospora crassa Dementhon, Karine; Iyer, Gopal; Glass, N. Louise Eukaryotic Cell, Vol. 5, Issue 12 https://doi.org/10.1128/EC.00253-06	journal	September 2006
The WW Domain Protein PRO40 Is Required for Fungal Fertility and Associates with Woronin Bodies Engh, Ines; Würtz, Christian; Witzel-Schlömp, Konstanze Eukaryotic Cell, Vol. 6, Issue 5 https://doi.org/10.1128/EC.00269-06	journal	March 2007
Fatal Attraction: Nonself Recognition and Heterokaryon Incompatibility in Filamentous Fungi Glass, N. Louise; Kaneko, Isao Eukaryotic Cell, Vol. 2, Issue 1 https://doi.org/10.1128/EC.2.1.1-8.2003	journal	February 2003
A WD40 Repeat Protein Regulates Fungal Cell Differentiation and Can Be Replaced Functionally by the Mammalian Homologue Striatin Pöggeler, Stefanie; Kück, Ulrich Eukaryotic Cell, Vol. 3, Issue 1 https://doi.org/10.1128/EC.3.1.232-240.2004	journal	February 2004
The Value of Complete Microbial Genome Sequencing (You Get What You Pay For) Fraser, C. M.; Eisen, J. A.; Nelson, K. E. Journal of Bacteriology, Vol. 184, Issue 23 https://doi.org/10.1128/JB.184.23.6403-6405.2002	journal	December 2002
On the High Value of Low Standards Branscomb, E.; Predki, P. Journal of Bacteriology, Vol. 184, Issue 23 https://doi.org/10.1128/JB.184.23.6406-6409.2002	journal	December 2002
Cell Differentiation during Sexual Development of the Fungus Sordaria macrospora Requires ATP Citrate Lyase Activity Nowrousian, Minou; Masloff, Sandra; Pöggeler, Stefanie Molecular and Cellular Biology, Vol. 19, Issue 1 https://doi.org/10.1128/MCB.19.1.450	journal	January 1999
Identification of Specificity Determinants and Generation of Alleles with Novel Specificity at the het-cHeterokaryon Incompatibility Locus of Neurospora crassa Wu, Jennifer; Glass, N. Louise Molecular and Cellular Biology, Vol. 21, Issue 4 https://doi.org/10.1128/MCB.21.4.1045-1057.2001	journal	February 2001
An electrophoretic karyotype of Neurospora crassa. Orbach, M. J.; Vollrath, D.; Davis, R. W. Molecular and Cellular Biology, Vol. 8, Issue 4 https://doi.org/10.1128/MCB.8.4.1469	journal	April 1988
Molecular Genetics of Heterokaryon Incompatibility in Filamentous Ascomycetes Saupe, S. J. Microbiology and Molecular Biology Reviews, Vol. 64, Issue 3 https://doi.org/10.1128/MMBR.64.3.489-502.2000	journal	September 2000
Lessons from the Genome Sequence of Neurospora crassa: Tracing the Path from Genomic Blueprint to Multicellular Organism Borkovich, K. A.; Alex, L. A.; Yarden, O. Microbiology and Molecular Biology Reviews, Vol. 68, Issue 1 https://doi.org/10.1128/MMBR.68.1.1-108.2004	journal	March 2004
A scanning electron microscopic study of the external features of perithecium development in Sordaria humana Read, N. D. Canadian Journal of Botany, Vol. 61, Issue 12 https://doi.org/10.1139/b83-359	journal	December 1983
Control of mating type heterokaryon incompatibility by the tol gene in Neurospora crassa and N . tetrasperma Jacobson, David J. Genome, Vol. 35, Issue 2 https://doi.org/10.1139/g92-053	journal	April 1992
The Genetics and Molecular Biology of the Synaptonemal Complex Page, Scott L.; Hawley, R. Scott Annual Review of Cell and Developmental Biology, Vol. 20, Issue 1 https://doi.org/10.1146/annurev.cellbio.19.111301.155141	journal	November 2004
Fungal Senescence Griffiths, Anthony J. F. Annual Review of Genetics, Vol. 26, Issue 1 https://doi.org/10.1146/annurev.ge.26.120192.002031	journal	December 1992
Role of Horizontal Gene Transfer in the Evolution of Fungi Rosewich, U. Liane; Kistler, H. Corby Annual Review of Phytopathology, Vol. 38, Issue 1 https://doi.org/10.1146/annurev.phyto.38.1.325	journal	September 2000
Gene finding in novel genomes Korf, Ian BMC Bioinformatics, Vol. 5, Issue 1 https://doi.org/10.1186/1471-2105-5-59	journal	May 2004
Dendroscope: An interactive viewer for large phylogenetic trees Huson, Daniel H.; Richter, Daniel C.; Rausch, Christian BMC Bioinformatics, Vol. 8, Issue 1 https://doi.org/10.1186/1471-2105-8-460	journal	November 2007
Origin and distribution of epipolythiodioxopiperazine (ETP) gene clusters in filamentous ascomycetes Patron, Nicola J.; Waller, Ross F.; Cozijnsen, Anton J. BMC Evolutionary Biology, Vol. 7, Issue 1 https://doi.org/10.1186/1471-2148-7-174	journal	January 2007
Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi Khaldi, Nora; Collemare, Jérôme; Lebrun, Marc-Henri Genome Biology, Vol. 9, Issue 1 https://doi.org/10.1186/gb-2008-9-1-r18	journal	January 2008
The genome sequence of the model ascomycete fungus Podospora anserina Espagne, Eric; Lespinet, Olivier; Malagnac, Fabienne Genome Biology, Vol. 9, Issue 5 https://doi.org/10.1186/gb-2008-9-5-r77	journal	January 2008
De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data DiGuistini, Scott; Liao, Nancy Y.; Platt, Darren Genome Biology, Vol. 10, Issue 9 https://doi.org/10.1186/gb-2009-10-9-r94	journal	January 2009
Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus Fedorova, Natalie D.; Khaldi, Nora; Joardar, Vinita S. PLoS Genetics, Vol. 4, Issue 4, Article No. e1000046 https://doi.org/10.1371/journal.pgen.1000046	journal	April 2008
The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion Coleman, Jeffrey J.; Rounsley, Steve D.; Rodriguez-Carres, Marianela PLoS Genetics, Vol. 5, Issue 8 https://doi.org/10.1371/journal.pgen.1000618	journal	August 2009
Genesis of a Fungal Non-Self Recognition Repertoire Paoletti, Mathieu; Saupe, Sven J.; Clavé, Corinne PLoS ONE, Vol. 2, Issue 3 https://doi.org/10.1371/journal.pone.0000283	journal	March 2007
A Cytosine Methyltransferase Homologue Is Essential for Sexual Development in Aspergillus nidulans Lee, Dong W.; Freitag, Michael; Selker, Eric U. PLoS ONE, Vol. 3, Issue 6 https://doi.org/10.1371/journal.pone.0002531	journal	June 2008
An Expanded Inventory of Conserved Meiotic Genes Provides Evidence for Sex in Trichomonas vaginalis Malik, Shehre-Banoo; Pightling, Arthur W.; Stefaniak, Lauren M. PLoS ONE, Vol. 3, Issue 8 https://doi.org/10.1371/journal.pone.0002879	journal	August 2008
Elusive Origins of the Extra Genes in Aspergillus oryzae Khaldi, Nora; Wolfe, Kenneth H. PLoS ONE, Vol. 3, Issue 8 https://doi.org/10.1371/journal.pone.0003036	journal	August 2008
Relationship between Phylogenetic Distribution and Genomic Features in Neurospora crassa Kasuga, Takao; Mannhaupt, Gertrud; Glass, N. Louise PLoS ONE, Vol. 4, Issue 4 https://doi.org/10.1371/journal.pone.0005286	journal	April 2009
De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data DiGuistini, Scott; Liao, Nancy Y.; Platt, Darren BioMed Central https://doi.org/10.14288/1.0167807	text	January 2009
Mining meiosis and gametogenesis with DNA microarrays Schlecht, U.; Primig, M. Reproduction https://doi.org/10.1530/rep.0.1250447	journal	April 2003
Nonallelic Interactions Between het-c and a Polymorphic Locus, pin-c , Are Essential for Nonself Recognition and Programmed Cell Death in Neurospora crassa Kaneko, Isao; Dementhon, Karine; Xiang, Qijun Genetics, Vol. 172, Issue 3 https://doi.org/10.1534/genetics.105.051490	journal	March 2006
A Nonself Recognition Gene Complex in Neurospora crassa Micali, Cristina O.; Smith, Myron L. Genetics, Vol. 173, Issue 4 https://doi.org/10.1534/genetics.106.057562	journal	June 2006
The S-adenosylmethionine dependent O-methyltransferase PaMTH1: a longevity assurance factor protecting Podospora anserina against oxidative stress Kunstmann, Birgit; Osiewacz, Heinz D. Aging, Vol. 1, Issue 3 https://doi.org/10.18632/aging.100029	journal	March 2009
Neurospora. I. Preliminary Observations of the Chromosomes of Neurospora crassa McClintock, Barbara American Journal of Botany, Vol. 32, Issue 10 https://doi.org/10.2307/2437624	journal	December 1945
Neurospora in Temperate Forests of Western North America Jacobson, David J.; Powell, Amy J.; Dettman, Jeremy R. Mycologia, Vol. 96, Issue 1 https://doi.org/10.2307/3761989	journal	January 2004
New findings of Neurospora in Europe and comparisons of diversity in temperate climates on continental scales Jacobson, D. J.; Dettman, J. R.; Adams, R. I. Mycologia, Vol. 98, Issue 4 https://doi.org/10.3852/mycologia.98.4.550	journal	July 2006

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