The genome sequence of the filamentous fungus Neurospora crassa

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

doi:10.1038/nature01554

Cited by 1,499 publications

(1,271 citation statements)

References 66 publications

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“…EC38 v3.0 (Wu et al 2017), Hypoxylon sp. CO27-5 v1.0 (Wu et al 2017), Neurospora crassa OR74A v2.0 (Galagan et al 2003), Lecythophora sp. AK0013 v1.0 (Damm et al 2010; U’Ren et al 2012), Botryosphaeria dothidea (Slippers et al 2004; Desprez-Loustau et al 2006; Schoch et al 2006; Slippers and Wingfield 2007; Piškur et al 2011), Fusarium oxysporum sp.…”

Section: Methodsmentioning

confidence: 99%

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

2017

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We have conducted a genome-level comparative study of basidiomycetes wood-rotting fungi (white, brown and soft rot) to understand the total plant biomass (lignin, cellulose, hemicellulose and pectin) -degrading abilities. We have retrieved the genome-level annotations of well-known 14 white rot fungi, 15 brown rot fungi and 13 soft rot fungi. Based on the previous literature and the annotations obtained from CAZy (carbohydrate-active enzyme) database, we have separated the genome-wide CAZymes of the selected fungi into lignin-, cellulose-, hemicellulose- and pectin-degrading enzymes. Results obtained in our study reveal that white rot fungi, especially Pleurotus eryngii and Pleurotus ostreatus potentially possess high ligninolytic ability, and soft rot fungi, especially Botryosphaeria dothidea and Fusarium oxysporum sp., potentially possess high cellulolytic, hemicellulolytic and pectinolytic abilities. The total number of genes encoding for cytochrome P450 monooxygenases and metabolic processes were high in soft and white rot fungi. We have tentatively calculated the overall lignocellulolytic abilities among the selected wood-rotting fungi which suggests that white rot fungi possess higher lignin and soft rot fungi potentially possess higher cellulolytic, hemicellulolytic and pectinolytic abilities. This approach can be applied industrially to efficiently find lignocellulolytic and aromatic compound-degrading fungi based on their genomic abilities.

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Section: Methodsmentioning

confidence: 99%

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

2017

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“…Orthologues of these genes from five other ascomycotan fungi, Aspergillus nidulans (http://www.broad.mit.edu/annotation/fungi/aspergil lus/), Schizosaccharomyces pombe (Wood et al 2002), Candida albicans (d'Enfert et al 2005, Neurospora crassa (Galagan et al 2003), and Saccharomyces mikatae (Cliften et al 2003;Kellis et al 2003), and two metazoans, Caenorhabditis elegans (C. elegans Sequencing Consortium 1998) and Drosophila melanogaster (Adams et al 2000), were also obtained.…”

Section: Introductionmentioning

confidence: 99%

Accelerated Evolutionary Rate May Be Responsible for the Emergence of Lineage-Specific Genes in Ascomycota

et al. 2006

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Abstract. The evolutionary origin of ''orphan'' genes, genes that lack sequence similarity to any known gene, remains a mystery. One suggestion has been that most orphan genes evolve rapidly so that similarity to other genes cannot be traced after a certain evolutionary distance. This can be tested by examining the divergence rates of genes with different degrees of lineage specificity. Here the lineage specificity (LS) of a gene describes the phylogenetic distribution of that gene's orthologues in related species. Highly lineagespecific genes will be distributed in fewer species in a phylogeny. In this study, we have used the complete genomes of seven ascomycotan fungi and two animals to define several levels of LS, such as Eukaryotes-core, Ascomycota-core, Euascomycetes-specific, Hemiascomycetes-specific, Aspergillus-specific, and Saccharomyces-specific. We compare the rates of gene evolution in groups of higher LS to those in groups with lower LS. Molecular evolutionary analyses indicate an increase in nonsynonymous nucleotide substitution rates in genes with higher LS. Several analyses suggest that LS is correlated with the evolutionary rate of the gene. This correlation is stronger than those of a number of other factors that have been proposed as predictors of a gene's evolutionary rate, including the expression level of genes, gene essentiality or dispensability, and the number of protein-protein interactions. The accelerated evolutionary rates of genes with higher LS may reflect the influence of selection and adaptive divergence during the emergence of orphan genes. These analyses suggest that accelerated rates of gene evolution may be responsible for the emergence of apparently orphan genes.

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“…Among these, the seminal demonstration of the one-gene, one-enzyme hypothesis (Beadle & Tatum 1941) led the way to the construction of a densely populated genetic map (Perkins et al 1962b; Nelson & Perkins 2000) including over 1000 phenotypic markers and more molecular, chromosomal, and cytogentic markers (Perkins et al 2001). As a leading model for the development of technologies important to industrial biology (Kato & Stuart 1998), plant pathology (Pandey et al 2004), and even human physiology (Dunlap 1999), Neurospora was first among filamentous fungi to have a fully sequenced and annotated genome (Galagan et al 2003). Going from 1500 genetic markers and the associated data to a fully annotated genome sequence represented a 10-fold increase in data about genes, and six orders of magnitude increase in the data describing the reference genome strain.…”

Section: Introductionmentioning

confidence: 99%

“…After the publication of the Neurospora genome (Galagan et al 2003), there was rapid development of genome-enabled technologies including a robust single-nucleotide-polymorphism-based map (Lambreghts et al 2009), DNA oligonucleotide micro-arrays (Kasuga et al 2005) supported by shared RNA expression data, and now the availability of targeted gene-deletion mutants at almost every locus (Colot et al 2006) which effectively provides a drug-resistance marker suitable for genetic mapping (Hammond et al 2012) across the genome. Currently Neurospora has nearly 2000 genome and transcriptome projects published in the National Center for Biotechnology Information Short Read Archive and over 600 strains in the FGSC collection have been subject to transcriptome or genome sequence analysis including wild-type (Ellison et al 2011a) and classical mutant strains (McCluskey et al 2011).…”

Section: Introductionmentioning

confidence: 99%

Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era

McCluskey

Baker

2017

Mycology

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Filamentous fungi have been important as model organisms since the beginning of modern biological inquiry and have benefitted from open data since the earliest genetic maps were shared. From early origins in simple Mendelian genetics of mating types, parasexual genetics of colony colour, and the foundational demonstration of the segregation of a nutritional requirement, the contribution of research systems utilising filamentous fungi has spanned the biochemical genetics era, through the molecular genetics era, and now are at the very foundation of diverse omics approaches to research and development. Fungal model organisms have come from most major taxonomic groups although Ascomycete filamentous fungi have seen the most major sustained effort. In addition to the published material about filamentous fungi, shared molecular tools have found application in every area of fungal biology. Similarly, shared data has contributed to the success of model systems. The scale of data supporting research with filamentous fungi has grown by 10 to 12 orders of magnitude. From genetic to molecular maps, expression databases, and finally genome resources, the open and collaborative nature of the research communities has assured that the rising tide of data has lifted all of the research systems together.

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The genome sequence of the filamentous fungus Neurospora crassa

Cited by 1,499 publications

References 66 publications

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

Accelerated Evolutionary Rate May Be Responsible for the Emergence of Lineage-Specific Genes in Ascomycota

Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era

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