Difference between revisions of "Fungal genomics"

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list of sequenced fungi genome paper    
       

Ascomycota    

Ascomycetes  

  1. Neurospora crassa : 붉은빵곰팡이 류, model eukaryote,  2003, nature, The genome sequence of the filamentous fungus Neurospora crassa,  http://www.nature.com/nature/journal/v422/n6934/full/nature01554.html

Dothideomycetes       

  1. Leptosphaeria maculans :   plant pathogen, 2011, Nature, Communications Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations,  http://www.nature.com/ncomms/journal/v2/n2/full/ncomms1189.html

Eurotiomycetes  

  1. Aspergillus fumigatus :  human pathogen, 2008, PLoS Genetics,  Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus  
  2. Aspergillus fumigatus : human pathogen, 2005, nature, Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus,  http://www.nature.com/nature/journal/v438/n7071/full/nature04332.html
  3. Aspergillus niger : 흑국균, industrial use, 2007, Nature Biotechnology Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88,  http://www.nature.com/nbt/journal/v25/n2/full/nbt1282.html
  4. Aspergillus oryzae : 누룩곰팡이, industrial use, 2005, nature, Genome sequencing and analysis of Aspergillus oryzae,  http://www.nature.com/nature/journal/v438/n7071/full/nature04300.html
  5. Coccidioides immitis : human pathogen, 2009, Genome Res, Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives,  http://genome.cshlp.org/content/19/10/1722
  6. Coccidioides posadasii :  human pathogen, 2009, Genome Res, Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives,   http://genome.cshlp.org/content/19/10/1722
  7. Penicillium chrysogenum : 푸른곰팡이속, industrial use,  2008, Nature Biotechnology Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum,  http://www.nature.com/nbt/journal/v26/n10/full/nbt.1498.html
  8. Penicillium marneffei : human pathogen, 2011, Eukaryotic Cell Draft Genome Sequence of Penicillium marneffei Strain PM1,  http://ec.asm.org/content/10/12/1740       

Leotiomycetes       

  1. Botrytis cinerea : plant pathogen 2011 PLoS Genetics Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea  http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002230      

Pezizomycetes       

  1. Tuber melanosporum : 송로버섯 Périgord black truffle  2010 nature Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis  http://www.nature.com/nature/journal/v464/n7291/full/nature08867.html       

Saccharomycetes       

  1. Ashbya gossypii :  plant pathogen  2004 nature The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome  http://www.sciencemag.org/content/304/5668/304
  2. Candida albicans :  human pathogen  2004 PNAS The diploid genome sequence of Candida albicans  http://www.pnas.org/content/101/19/7329
  3. Candida albicans : human pathogen  2005 Genetics Sequence finishing and gene mapping for Candida albicans chromosome 7 and syntenic analysis against the Saccharomyces cerevisiae genome.  http://www.genetics.org/content/170/4/1525.long
  4. Candida albicans :  human pathogen  2009 nature(candida 8종 해독) Evolution of pathogenicity and sexual reproduction in eight Candida genomes  http://www.nature.com/nature/journal/v459/n7247/full/nature08064.html
  5. Candida glabrata : human pathogen  2009 nature(candida 8종 해독) Evolution of pathogenicity and sexual reproduction in eight Candida genomes  http://www.nature.com/nature/journal/v459/n7247/full/nature08064.html
  6. Candida tropicalis : human pathogen  2009 nature(candida 8종 해독) Evolution of pathogenicity and sexual reproduction in eight Candida genomes  http://www.nature.com/nature/journal/v459/n7247/full/nature08064.html
  7. Candida parapsilosis : human pathogen  2009 nature(candida 8종 해독) Evolution of pathogenicity and sexual reproduction in eight Candida genomes  http://www.nature.com/nature/journal/v459/n7247/full/nature08064.html
  8. Candida krusei : human pathogen  2009 nature(candida 8종 해독) Evolution of pathogenicity and sexual reproduction in eight Candida genomes  http://www.nature.com/nature/journal/v459/n7247/full/nature08064.html
  9. Candida lusitaniae : human pathogen  2009 nature(candida 8종 해독) Evolution of pathogenicity and sexual reproduction in eight Candida genomes  http://www.nature.com/nature/journal/v459/n7247/full/nature08064.html
  10. Candida guilliermondii : human pathogen  2009 nature(candida 8종 해독) Evolution of pathogenicity and sexual reproduction in eight Candida genomes  http://www.nature.com/nature/journal/v459/n7247/full/nature08064.html
  11. Candida lusitaniae : human pathogen  2009 nature(candida 8종 해독) Evolution of pathogenicity and sexual reproduction in eight Candida genomes  http://www.nature.com/nature/journal/v459/n7247/full/nature08064.html
  12. Debaryomyces hansenii : industrial use 2012 Eukaryotic Cell Draft Genome Sequence of Salt-Tolerant Yeast Debaryomyces hansenii var. hansenii MTCC 234   http://ec.asm.org/content/11/7/961.full
  13. Hansenula polymorpha :  industrial use  2003 FEMS Yeast Research The Hansenula polymorpha (strain CBS4732) genome sequencing and analysis  http://onlinelibrary.wiley.com/doi/10.1016/S1567-1356(03)00125-9/full
  14. Lachancea (Saccharomyces) kluyveri :   plant pathogen  2009 Genome Res. Unusual composition of a yeast chromosome arm is associated with its delayed replication  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765276/
  15. Saccharomyces cerevisiae : industrial/model 2007 Proc Natl Acad Sci U S A. Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789  http://www.pnas.org/content/104/31/12825.long
  16. Saccharomyces cerevisiae : industrial/model 2008 PLoS Genetics A Catalog of Neutral and Deleterious Polymorphism in Yeast  http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000183
  17. Saccharomyces cerevisiae : industrial/model 2008 FEMS Yeast Research Comparative genome analysis of a Saccharomyces cerevisiae wine strain  http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2008.00434.x/abstract;jsessionid=8A70BABAA07CBDF67AFAA1AE0275FD89.d04t04?systemMessage=Wiley+Online+Library+will+be+disrupted+on+7+July+from+10%3A00-12%3A00+BST+%2805%3A00-07%3A00+EDT%29+for+essential+maintenance
  18. Saccharomyces cerevisiae : industrial/model 2009 Genome Res. Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production  http://genome.cshlp.org/content/19/12/2258.long
  19. Pichia stipitis : lignin/xylose degrader  2007 Nature Biotechnology Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis  http://www.nature.com/nbt/journal/v25/n3/full/nbt1290.html
  20. Saccharomyces pastorianus : industrial, beer  2009 DNA Res Genome Sequence of the Lager Brewing Yeast, an Interspecies Hybrid  http://dnaresearch.oxfordjournals.org/content/16/2/115
  21. Saccharomyces cerevisiae : industrial/model 2003 nature Sequencing and comparison of yeast species to identify genes and regulatory elements  http://www.nature.com/nature/journal/v423/n6937/full/nature01644.html
  22. Saccharomyces paradoxus :  2003 nature Sequencing and comparison of yeast species to identify genes and regulatory elements  http://www.nature.com/nature/journal/v423/n6937/full/nature01644.html
  23. Saccharomyces mikatae :  2003 nature Sequencing and comparison of yeast species to identify genes and regulatory elements  http://www.nature.com/nature/journal/v423/n6937/full/nature01644.html
  24. Saccharomyces bayanus :  2003 nature Sequencing and comparison of yeast species to identify genes and regulatory elements  http://www.nature.com/nature/journal/v423/n6937/full/nature01644.html
  25. Yarrowia lipolytica : industrial use 2004 nature Genome evolution in yeasts  http://www.nature.com/nature/journal/v430/n6995/full/nature02579.html       

Schizosaccharomycetes       

  1. Schizosaccharomyces pombe :  model eukaryote  2002 nature The genome sequence of Schizosaccharomyces pombe V. Wood et al http://www.nature.com/nature/journal/v415/n6874/full/nature724.html       

Sordariomycetes       

  1. Fusarium oxysporum : human/plant pathogen 2010 nature(Fusarium 3종) Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium Li-Jun Ma et al http://www.nature.com/nature/journal/v464/n7287/full/nature08850.html
  2. Fusarium graminearum : human/plant pathogen 2010 nature(Fusarium 3종) Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium Li-Jun Ma et al http://www.nature.com/nature/journal/v464/n7287/full/nature08850.html
  3. Fusarium verticillioides :  human/plant pathogen 2010 nature(Fusarium 3종) Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium Li-Jun Ma et al http://www.nature.com/nature/journal/v464/n7287/full/nature08850.html
  4. Fusarium graminearum :  2007 Science The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization Cuomo CA et al http://www.sciencemag.org/content/317/5843/1400
  5. Grosmannia clavigera : plant pathogen  2011 PNAS Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen Scott DiGuistini et al http://www.pnas.org/content/early/2011/01/18/1011289108
  6. Magnaporthe grisea : plant pathogen 2005 nature The genome sequence of the rice blast fungus Magnaporthe grisea Ralph A. Dean et al http://www.nature.com/nature/journal/v434/n7036/full/nature03449.html
  7. Nectria haematococca : plastic/pest./lignin degrader  2009 PLoS Genetics The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion Jeffrey J. Coleman et al http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000618
  8. Podospora anserina :  2008 Genome Biology The genome sequence of the model ascomycete fungus Podospora anserina Eric Espagne et al http://genomebiology.com/content/9/5/R77
  9. Sporotrichum thermophile : thermophilic cellulose degrader      
  10. Myceliophthora thermophila :  2011 Nature Biotechnology Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris Randy M Berka et al http://www.nature.com/nbt/journal/v29/n10/full/nbt.1976.html
  11. Thielavia terrestris : model thermophile/industrial  2011 Nature Biotechnology Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris Randy M Berka et al http://www.nature.com/nbt/journal/v29/n10/full/nbt.1976.html    
  12. Trichoderma reesei : biomass-degrading 2008 Nature Biotechnology Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina) Diego Martinez et al http://www.nature.com/nbt/journal/v26/n5/full/nbt1403.html
           

Basidiomycota       

Agaricomycetes       


  1. Auricularia delicata  : 2012 science The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 funal genomes Floudas, et al. http://www.sciencemag.org/content/336/6089/1715.long
  2. Coprinopsis cinerea : model organism for multicellular fungi 2010 PNAS Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)  Jason E. Stajich et al http://www.pnas.org/content/107/26/11889
  3. Laccaria bicolor :  mycorrhiza  2007 nature The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis F. Martin et al http://www.nature.com/nature/journal/v452/n7183/full/nature06556.html
  4. Moniliophthora perniciosa :  2008 BMC Genomics  A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom Disease of cacao Jorge MC Mondego et al http://www.biomedcentral.com/1471-2164/9/548
  5. Phanerochaete chrysosporium :   mycoremediation(균류정화법) 2004 Nature Biotechnology Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78 Diego Martinez et al http://www.nature.com/nbt/journal/v22/n6/full/nbt967.html
  6. Postia placenta :  cellulose degrader  2009 PNAS Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion Diego Martinez et al http://www.pnas.org/content/106/6/1954
  7. Schizophyllum commune :  model mushroom 2010 Nature Biotechnology Genome sequence of the model mushroom Schizophyllum commune Robin A Ohm et al http://www.nature.com/nbt/journal/v28/n9/full/nbt.1643.html
  8. Serpula lacrymans : plant pathogen 2011 Science The Plant Cell Wall–Decomposing Machinery Underlies the Functional Diversity of Forest Fungi Daniel C. Eastwood et al http://www.sciencemag.org/content/333/6043/762       

Pucciniomycetes       

  1. Puccinia graminis f. sp. Tritici : plant pathogen  2011 PNAS Obligate biotrophy features unraveled by the genomic analysis of rust fungi Sébastien Duplessis et al http://www.pnas.org/content/108/22/9166
  2. Cryptococcus neoformans : human pathogen 2005 Science The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans Brendan J. Loftus et al http://www.sciencemag.org/content/307/5713/1321
           

Ustilaginomycetes       

  1. Malassezia globosa : human/plant pathogen 2007 PNAS Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens  Jun Xu et al http://www.pnas.org/content/104/47/18730
  2. Malassezia restricta : dandruff-associated  2007 PNAS Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens  Jun Xu et al http://www.pnas.org/content/104/47/18730
  3. Sporisorium rellianum : plant pathogen  2010 Science Pathogenicity Determinants in Smut Fungi Revealed by Genome Comparison Jan Schirawski et al http://www.sciencemag.org/content/330/6010/1546
  4. Ustilago maydis : plant pathogen  2006 nature Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis Jörg Kämper et al http://www.nature.com/nature/journal/v444/n7115/full/nature05248.html      

Microsporidia       

  1. Encephalitozoon cuniculi : human pathogen  2001 nature Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi Michaël D. Katinka et al http://www.nature.com/nature/journal/v414/n6862/full/414450a0.html
  2. Encephalitozoon intestinalis : human pathogen 2010 Nature Communications The complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis Nicolas Corradi et al http://www.nature.com/ncomms/journal/v1/n6/full/ncomms1082.html
  3. Enterocytozoon bieneusi : human pathogen particularly in the context of HIV infection  2009 PLoS Pathogens Genomic survey of the non-cultivatable opportunistic human pathogen, Enterocytozoon bieneusi Donna E. Akiyoshi et al http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1000261
  4. Nosema ceranae : honey bee pathogen  2009 PLoS Pathogens Genomic Analyses of the Microsporidian Nosema ceranae, an Emergent Pathogen of Honey Bees R. Scott Cornman et al http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1000466
  5. Octosporea bayeri : Daphnia pathogen  2009 Genome Biology Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions Nicolas Corradi et al http://genomebiology.com/2009/10/10/R106

Zygomycota       

  1. Rhizopus oryzae : human pathogen  2009 PLoS Genetics Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole genome duplication Li-Jun Ma et al http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000549
  2. Mortierella alpina : commercial source of arachidonic acid  2011 PLoS One Genome characterization of the oleaginous fungus Mortierella alpina Lei Wang et al http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0028319

 

 

 

 

 

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