MycoCosm portal: gearing up for 1000 fungal genomes

MycoCosm is a fungal genomics portal (http://jgi.doe.gov/fungi), developed by the US Department of Energy Joint Genome Institute to support integration, analysis and dissemination of fungal genome sequences and other ‘omics’ data by providing interactive web-based tools. MycoCosm also promotes and facilitates user community participation through the nomination of new species of fungi for sequencing, and the annotation and analysis of resulting data. By efficiently filling gaps in the Fungal Tree of Life, MycoCosm will help address important problems associated with energy and the environment, taking advantage of growing fungal genomics resources.

[1]  María Martín,et al.  Activities at the Universal Protein Resource (UniProt) , 2013, Nucleic Acids Res..

[2]  M. Blackwell The fungi: 1, 2, 3 ... 5.1 million species? , 2011, American journal of botany.

[3]  Justin Powlowski,et al.  Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris , 2011, Nature Biotechnology.

[4]  F. Martin,et al.  The Ecological Genomics of Fungi , 2013 .

[5]  Anton J. Enright,et al.  An efficient algorithm for large-scale detection of protein families. , 2002, Nucleic acids research.

[6]  Peter Schattner,et al.  The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs , 2005, Nucleic Acids Res..

[7]  Vincent Lombard,et al.  Genome sequence of the model mushroom Schizophyllum commune , 2010, Nature Biotechnology.

[8]  R. Durbin,et al.  GeneWise and Genomewise. , 2004, Genome research.

[9]  Edith D. Wong,et al.  Saccharomyces Genome Database: the genomics resource of budding yeast , 2011, Nucleic Acids Res..

[10]  Lior Pachter,et al.  VISTA: computational tools for comparative genomics , 2004, Nucleic Acids Res..

[11]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[12]  I. Grigoriev A Changing Landscape of Fungal Genomics , 2013 .

[13]  M. Borodovsky,et al.  Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. , 2008, Genome research.

[14]  A. Salamov,et al.  Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi , 2012, PLoS pathogens.

[15]  A. Salamov,et al.  The Plant Cell Wall–Decomposing Machinery Underlies the Functional Diversity of Forest Fungi , 2011, Science.

[16]  Jodie J. Yin,et al.  A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes , 2004, Genome Biology.

[17]  Ni Li,et al.  Gene Ontology Annotations and Resources , 2012, Nucleic Acids Res..

[18]  Wendy S. Schackwitz,et al.  Rediscovery by Whole Genome Sequencing: Classical Mutations and Genome Polymorphisms in Neurospora crassa , 2011, G3: Genes | Genomes | Genetics.

[19]  David L. Hawksworth,et al.  The fungal dimension of biodiversity: magnitude, significance, and conservation , 1991 .

[20]  I-Min A. Chen,et al.  The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata , 2011, Nucleic Acids Res..

[21]  Paramvir S. Dehal,et al.  Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis , 2011, PLoS genetics.

[22]  Christina A. Cuomo,et al.  Obligate Biotrophy Features Unraveled by the Genomic Analysis of the Rust Fungi, Melampsora larici-populina and Puccinia graminis f. sp. tritici , 2011 .

[23]  D. Hibbett,et al.  Fueling the future with fungal genomics , 2011 .

[24]  S. Brunak,et al.  SignalP 4.0: discriminating signal peptides from transmembrane regions , 2011, Nature Methods.

[25]  Mary Goldman,et al.  The UCSC Genome Browser database: extensions and updates 2013 , 2012, Nucleic Acids Res..

[26]  V. Solovyev,et al.  Ab initio gene finding in Drosophila genomic DNA. , 2000, Genome research.

[27]  Inna Dubchak,et al.  The genome portal of the Department of Energy Joint Genome Institute: 2014 updates , 2013, Nucleic Acids Res..

[28]  Y. Van de Peer,et al.  The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis , 2008, Nature.

[29]  Katherine H. Huang,et al.  Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78 , 2004, Nature Biotechnology.

[30]  Jean-Michel Claverie,et al.  FusionDB: a database for in-depth analysis of prokaryotic gene fusion events , 2004, Nucleic Acids Res..

[31]  Susumu Goto,et al.  KEGG for integration and interpretation of large-scale molecular data sets , 2011, Nucleic Acids Res..

[32]  Christina A. Cuomo,et al.  Obligate biotrophy features unraveled by the genomic analysis of rust fungi , 2011, Proceedings of the National Academy of Sciences.

[33]  Marcus C. Chibucos,et al.  The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources , 2011, Nucleic Acids Res..

[34]  S E Baker,et al.  Sequencing the fungal tree of life. , 2011, The New phytologist.

[35]  The UniProt Consortium,et al.  Update on activities at the Universal Protein Resource (UniProt) in 2013 , 2012, Nucleic Acids Res..

[36]  Robert D. Finn,et al.  InterPro: the integrative protein signature database , 2008, Nucleic Acids Res..

[37]  Albee Y. Ling,et al.  The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes , 2012, Science.

[38]  Asaf Salamov,et al.  Fungal Genomic Annotation , 2006 .

[39]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[40]  I-Min A. Chen,et al.  The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata , 2007, Nucleic Acids Res..

[41]  Ning Ma,et al.  BLAST: a more efficient report with usability improvements , 2013, Nucleic Acids Res..