Order of Species in Fungi Phylogeny Species date for genome download link to genome download proteins.fasta? transcripts/CDS? genome? protein_filename processing protein FASTA processing transcripts FASTA (gave systematic names to all) processing genome FASTA 1 S. cerevisiae S288C 3/2/2011 http://www.broadinstitute.org/regev/orthogroups/ yes yes "October, 2008 > downloaded from SGD" S.cerevisiae.fa BROAD named only nothing 2 S. cerevisiae RM11-1a 3/2/2011 http://www.broadinstitute.org/annotation/genome/saccharomyces_cerevisiae.3/MultiDownloads.html yes yes supercontigs S.cerevisiaeRM11-1a.fa BROAD named only nothing 3 S. paradoxus 3/2/2011 http://www.broadinstitute.org/regev/orthogroups/ yes yes "October, 2008 > downloaded from SGD, used MIT" S.paradoxus.fa BROAD named only nothing 4 S. mikatae 3/2/2011 http://www.broadinstitute.org/regev/orthogroups/ yes yes "October, 2008 > downloaded from SGD, used MIT" S.mikatae.fa BROAD named only nothing 5 S. kudriavzevii 3/2/2011 ftp://genome-ftp.stanford.edu/pub/yeast/sequence/fungal_genomes/S_kudriavzevii/WashU/orf_protein/ yes yes contigs S.kudriavzevii.fa "split on WS and comma, combine 2nd element, 4th, 5th" named only nothing 6 S. bayanus 3/2/2011 http://www.broadinstitute.org/regev/orthogroups/ yes yes "contigs from http://fungalgenomes.org/data/NT/, OLD: October, 2008 > downloaded from SGD, used MIT" S.bayanus.fa BROAD named only nothing 7 C. glabrata 3/2/2011 http://fungalgenomes.org/data/PEP/ yes yes - fungalgenomes.org via NCBI yes - fungalgenomes.org via NCBI C.glabrata.fa "split on WS is fine, 1st element" named only nothing 8 S. castellii 3/2/2011 http://www.broadinstitute.org/regev/orthogroups/ yes yes "October, 2008 > downloaded from SGD, used WashU" S.castellii.fa BROAD named only nothing 9 K. waltii 3/2/2011 http://www.broadinstitute.org/regev/orthogroups/ yes yes "June, 2004 > downloaded from http://www.nature.com/nature/journal/v428/n6983/extref/nature02424-s1.htm" K.waltii.fa BROAD named only nothing 10 S. kluyveri 3/2/2011 http://www.broadinstitute.org/regev/orthogroups/ yes yes "chromsomes from http://www.genolevures.org/download.html#, OLD genome was October, 2008 > downloaded from SGD, used WashU (but gave poor BLAT results)" S.kluyveri.fa BROAD named only nothing 11 K. lactis 3/2/2011 http://fungalgenomes.org/data/PEP/ yes yes - fungalgenomes.org via NCBI yes - fungalgenomes.org via NCBI K.lactis.fa "split on WS is fine, 1st element" named only nothing 12 E. gossypii 3/2/2011 http://fungalgenomes.org/data/PEP/ yes yes - fungalgenomes.org via NCBI yes - fungalgenomes.org via NCBI E.gossypii.fa "split on WS is fine, 1st element" named only nothing 13 C. albicans WO1 3/2/2011 http://www.broadinstitute.org/annotation/genome/candida_albicans/MultiDownloads.html yes yes supercontigs C.albicansWO1.fa BROAD named only nothing 14 C. albicans sc5314 v21 3/2/2011 http://www.broadinstitute.org/annotation/genome/candida_albicans/MultiDownloads.html yes yes contigs C.albicansSC5314.fa BROAD named only nothing 15 C. dubliniensis 3/2/2011 ftp://ftp.sanger.ac.uk/pub/pathogens/Candida/dubliniensis/ yes yes - genes chromosomes from http://candidagenome.org/download/sequence/C_dubliniensis_CD36/current/ C.dubliniensis.fa BROAD-LIKE named only nothing 16 C. tropicalis 3/2/2011 http://www.broadinstitute.org/annotation/genome/candida_albicans/MultiDownloads.html yes yes supercontigs C.tropicalis.fa BROAD named only nothing 17 L. elongisporus 3/2/2011 http://www.broadinstitute.org/annotation/genome/candida_albicans/MultiDownloads.html yes yes supercontigs L.elongisporus.fa BROAD named only nothing 18 C. parapsilosis 3/2/2011 http://www.broadinstitute.org/annotation/genome/candida_albicans/MultiDownloads.html yes yes contigs C.parapsilosis.fa BROAD named only nothing 19 P. stipitis 3/2/2011 http://genome.jgi-psf.org/Picst3/Picst3.download.ftp.html yes transcripts - frozen masked scaffolds P.stipitis.fa "split on |, take 3rd element (unique number)" named only nothing 20 D. hansenii 3/2/2011 http://www.broadinstitute.org/annotation/genome/candida_albicans/MultiDownloads.html yes yes contigs D.hansenii.fa BROAD named only nothing 21 C. lusitaniae 3/2/2011 http://www.broadinstitute.org/annotation/genome/candida_albicans/MultiDownloads.html yes yes supercontigs C.lusitaniae.fa BROAD named only nothing 22 C. guilliermondii 3/2/2011 http://www.broadinstitute.org/annotation/genome/candida_albicans/MultiDownloads.html yes yes supercontigs C.guilliermondii.fa BROAD named only nothing 23 Y. lipolytica 3/2/2011 http://fungalgenomes.org/data/PEP/ yes yes - fungalgenomes.org via NCBI yes - fungalgenomes.org via NCBI Y.lipolytica.fa "split on WS is fine, 1st element" named only nothing 24 A. oligospora 1/8/2013 http://www.ncbi.nlm.nih.gov/bioproject?db=bioproject&cmd=Retrieve&dopt=Overview&list_uids=41495 yes NO unmasked scaffold A.oligospora.fa "split on WS is fine, 4th element" N/A nothing 25 T. melanosporum 1/6/2013 http://mycor.nancy.inra.fr/IMGC/TuberGenome/download.php?select=fast yes NO unmasked Sept 2007 assembly T.melanosporum.fa "split on WS is fine, 1st element" N/A nothing 26 T. tonsurans 2/26/2011 http://www.broadinstitute.org/annotation/genome/dermatophyte_comparative/MultiDownloads.html yes yes supercontigs T.tonsurans.fa BROAD named only nothing 27 T. equinum CBS127.97 2/26/2011 http://www.broadinstitute.org/annotation/genome/dermatophyte_comparative/MultiDownloads.html yes yes supercontigs T.equinum.fa BROAD named only nothing 28 T. rubrum CBS 118892 2/26/2011 http://www.broadinstitute.org/annotation/genome/dermatophyte_comparative/MultiDownloads.html yes yes supercontigs T.rubrum.fa BROAD named only nothing 29 A. benhamiae CBS 112371 2/26/2011 http://www.broadinstitute.org/annotation/genome/dermatophyte_comparative/MultiDownloads.html yes yes supercontigs A.benhamiae.fa BROAD cut 2nd line of sequence names nothing 30 T. verrucosum HKI 0517 2/26/2011 http://www.broadinstitute.org/annotation/genome/dermatophyte_comparative/MultiDownloads.html yes yes supercontigs T.verrucosum.fa BROAD cut 2nd line of sequence names nothing 31 M. gypseum CBS 118893 2/26/2011 http://www.broadinstitute.org/annotation/genome/dermatophyte_comparative/MultiDownloads.html yes yes supercontigs M.gypseum.fa BROAD named only nothing 32 M. canis CBS 113480 2/26/2011 http://www.broadinstitute.org/annotation/genome/dermatophyte_comparative/MultiDownloads.html yes yes supercontigs M.canis.fa BROAD named only nothing 33 C. immitis RS (finished) 2/26/2011 http://www.broadinstitute.org/annotation/genome/coccidioides_group/MultiDownloads.html yes yes supercontigs C.immitis.fa BROAD named only nothing 34 C. posadasii RMSCC 3488 2/26/2011 http://www.broadinstitute.org/annotation/genome/coccidioides_group/MultiDownloads.html yes yes supercontigs C.posadasii.fa BROAD named only nothing 35 U. reesii 2/26/2011 http://www.broadinstitute.org/annotation/genome/uncinocarpus_reesii.3/MultiDownloads.html yes yes supercontigs U.reesii.fa BROAD named only nothing 36 H. capsulatum NAm1 2/26/2011 http://www.broadinstitute.org/annotation/genome/histoplasma_capsulatum/MultiDownloads.html yes yes supercontigs H.capsulatum.fa BROAD named only nothing 37 B. dermatitidis SLH14081 2/26/2011 http://www.broadinstitute.org/annotation/genome/blastomyces_dermatitidis/MultiDownloads.html yes yes supercontigs B.dermatitidis.fa BROAD named only nothing 38 P. brasiliensis Pb01 2/26/2011 http://www.broadinstitute.org/annotation/genome/paracoccidioides_brasiliensis/MultiDownloads.html yes yes supercontigs P.brasiliensis.fa BROAD named only nothing 39 A. fumigatus 2/26/2011 http://www.broadinstitute.org/annotation/genome/aspergillus_group/MultiDownloads.html yes yes supercontigs A.fumigatus.fa BROAD named only nothing 40 N. fischeri 2/26/2011 http://www.broadinstitute.org/annotation/genome/aspergillus_group/MultiDownloads.html yes yes supercontigs N.fischeri.fa BROAD named only nothing 41 A. clavatus 2/26/2011 http://www.broadinstitute.org/annotation/genome/aspergillus_group/MultiDownloads.html yes yes supercontigs A.clavatus.fa BROAD named only nothing 42 A. niger 2/26/2011 http://www.broadinstitute.org/annotation/genome/aspergillus_group/MultiDownloads.html yes yes supercontigs A.niger.fa BROAD named only nothing 43 A. nidulans 2/26/2011 http://www.broadinstitute.org/annotation/genome/aspergillus_group/MultiDownloads.html yes yes supercontigs A.nidulans.fa BROAD named only nothing 44 A. terreus 2/26/2011 http://www.broadinstitute.org/annotation/genome/aspergillus_group/MultiDownloads.html yes yes supercontigs A.terreus.fa BROAD named only nothing 45 A. flavus 2/26/2011 http://www.broadinstitute.org/annotation/genome/aspergillus_group/MultiDownloads.html yes yes supercontigs A.flavus.fa BROAD named only nothing 46 A. oryzae 2/26/2011 http://www.broadinstitute.org/annotation/genome/aspergillus_group/MultiDownloads.html yes yes supercontigs A.oryzae.fa BROAD named only nothing 47 M. fijiensis 3/2/2011 http://genome.jgi-psf.org/Mycfi2/Mycfi2.download.ftp.html yes CDS -frozen masked scaffolds M.fijiensis.fa "split on |, take 3rd element (unique number)" named only nothing 48 M. graminicola 3/2/2011 http://genome.jgi-psf.org/Mycgr3/Mycgr3.download.ftp.html yes transcripts - frozen unmasked scaffolds M.graminicola.fa "split on |, take 3rd element (unique number)" named only nothing 49 P. tritici-repentis 2/26/2011 http://www.broadinstitute.org/annotation/genome/pyrenophora_tritici_repentis.3/MultiDownloads.html yes yes supercontigs P.tritici-repentis.fa BROAD named only nothing 50 S. nodorum 2/26/2011 http://www.broadinstitute.org/annotation/genome/stagonospora_nodorum.2/MultiDownloads.html yes yes supercontigs S.nodorum.fa BROAD named only nothing 51 B. cinerea 2/26/2011 http://www.broadinstitute.org/annotation/genome/botrytis_cinerea.2/MultiDownloads.html yes yes supercontigs B.cinerea.fa BROAD named only nothing 52 S. sclerotiorum 2/26/2011 http://www.broadinstitute.org/annotation/genome/sclerotinia_sclerotiorum/MultiDownloads.html yes yes supercontigs S.sclerotiorum.fa BROAD named only nothing 53 C. globosum 2/26/2011 http://www.broadinstitute.org/annotation/genome/chaetomium_globosum.2/MultiDownloads.html yes yes supercontigs C.globosum.fa BROAD named only nothing 54 P. anserina 3/2/2011 http://fungalgenomes.org/data/PEP/ yes yes - fungalgenomes.org via NCBI yes - fungalgenomes.org via NCBI P.anserina.fa "split on WS is fine, 1st element" named only nothing 55 N. crassa OR74A (NC10) 2/26/2011 http://www.broadinstitute.org/annotation/genome/neurospora/MultiDownloads.html yes yes supercontigs N.crassa.fa BROAD named only nothing 56 N. tetrasperma 3/2/2011 http://genome.jgi-psf.org/Neute_matA2/Neute_matA2.download.html yes CDS - filtered unmasked scaffolds N.tetrasperma.fa "split on |, take 3rd element (unique number)" named only nothing 57 N. discreta 3/2/2011 http://genome.jgi-psf.org/Neudi1/Neudi1.download.ftp.html yes CDS - filtered "masked ""assembly""" N.discreta.fa "split on |, take 3rd element (unique number)" named only nothing 58 M. oryzae 70-15 (MG6) 2/26/2011 http://www.broadinstitute.org/annotation/genome/magnaporthe_comparative/MultiDownloads.html yes yes supercontigs M.oryzae.fa BROAD named only nothing 59 V. albo-atrum VaMs.102 3/2/2011 http://www.broadinstitute.org/annotation/genome/verticillium_dahliae/MultiDownloads.html yes yes supercontigs V.albo-atrum.fa BROAD named only nothing 60 V. dahliae VdLs.17 2/26/2011 http://www.broadinstitute.org/annotation/genome/verticillium_dahliae/MultiDownloads.html yes yes supercontigs V.dahliae.fa BROAD named only nothing 61 T. reesei 3/2/2011 http://genome.jgi-psf.org/Trire2/Trire2.download.ftp.html yes transcripts - frozen masked scaffolds T.reesei.fa "split on |, take 3rd element (unique number)" named only nothing 62 T. virens 3/2/2011 http://genome.jgi-psf.org/TriviGv29_8_2/TriviGv29_8_2.download.ftp.html yes yes supercontigs T.virens.fa "split on |, take 3rd element (unique number)" nothing 63 T. atroviride 3/2/2011 http://genome.jgi-psf.org/Triat2/Triat2.download.ftp.html yes yes - frozen unmasked scaffolds T.atroviride.fa "split on |, take 3rd element (unique number)" named only nothing 64 N. haematococca 3/2/2011 http://genome.jgi-psf.org/Necha2/Necha2.download.ftp.html yes transcripts - best unmasked scaffolds N.haematococca.fa "split on |, take 3rd element (unique number)" named only nothing 65 F. graminearum PH-1 2/26/2011 http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiDownloads.html yes yes supercontigs F.graminearum.fa BROAD named only nothing 66 F. oxysporum 4287 2/26/2011 http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiDownloads.html yes yes supercontigs F.oxysporum.fa BROAD named only nothing 67 F. verticillioides 7600 2/26/2011 http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiDownloads.html yes yes supercontigs F.verticillioides.fa BROAD named only nothing 68 S. japonicus (SJ4) 3/2/2011 http://www.broadinstitute.org/annotation/genome/schizosaccharomyces_group/MultiDownloads.html yes yes supercontigs S.japonicus.fa BROAD named only nothing 69 S. cryophilus (SCY3) 3/2/2011 http://www.broadinstitute.org/annotation/genome/schizosaccharomyces_group/MultiDownloads.html yes yes supercontigs S.cryophilus.fa BROAD named only nothing 70 S. octosporus (SO5) 3/2/2011 http://www.broadinstitute.org/annotation/genome/schizosaccharomyces_group/MultiDownloads.html yes yes supercontigs S.octosporus.fa BROAD named only nothing 71 S. pombe 3/2/2011 http://www.broadinstitute.org/annotation/genome/schizosaccharomyces_group/MultiDownloads.html yes yes supercontigs S.pombe.fa BROAD named only nothing 72 C. neoformans H99 3/30/2011 http://www.broadinstitute.org/annotation/genome/cryptococcus_neoformans/MultiDownloads.html yes yes supercontigs C.neoformans.fa BROAD named only nothing 73 C. cinerea okayama7#130 3/30/2011 http://www.broadinstitute.org/annotation/genome/coprinus_cinereus/MultiDownloads.html yes yes supercontigs C.cinerea.fa BROAD named only nothing 74 L. bicolor S238N-H82 3/30/2011 http://www.broadinstitute.org/annotation/genome/coprinus_cinereus/MultiDownloads.html yes yes supercontigs L.bicolor.fa BROAD named only gave unique names to contigs 75 U. maydis 3/30/2011 http://www.broadinstitute.org/annotation/genome/ustilago_maydis.2/MultiDownloads.html yes yes contigs U.maydis.fa BROAD named only nothing 76 P. graminis tritici 3/30/2011 http://www.broadinstitute.org/annotation/genome/puccinia_group/MultiDownloads.html yes yes supercontigs P.graminis.fa BROAD named only nothing 77 R. oryzae RA 99-880 3/30/2011 http://www.broadinstitute.org/annotation/genome/rhizopus_oryzae/MultiDownloads.html yes yes supercontigs R.oryzae.fa BROAD named only nothing 78 A. macrogynus ATCC 38327 3/30/2011 http://www.broadinstitute.org/annotation/genome/multicellularity_project/MultiDownloads.html yes yes supercontigs A.macrogynus.fa BROAD named only nothing 79 B. dendrobatidis 3/30/2011 http://www.broadinstitute.org/annotation/genome/batrachochytrium_dendrobatidis/MultiDownloads.html yes yes supercontigs B.dendrobatidis.fa BROAD named only nothing 80 S. punctatus DAOM BR117 3/30/2011 http://www.broadinstitute.org/annotation/genome/multicellularity_project/MultiDownloads.html yes yes supercontigs S.punctatus.fa BROAD named only nothing Extra L. starkeyi 1/5/2013 http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Lipst1_1 yes yes - filtered unmasked scaffolds L.starkeyi.fa "split on |, take 3rd element (unique number)" N/A nothing Extra C. caseinolytica 1/5/2013 http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Canca1 yes yes - filtered unmasked scaffolds C.caseinolytica.fa "split on |, take 3rd element (unique number)" N/A nothing Extra W. anomalus 1/5/2013 http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Wican1 yes yes - filtered unmasked scaffolds W.anomalus.fa "split on |, take 3rd element (unique number)" N/A nothing Extra S. complicata 1/6/2013 http://genome.jgi-psf.org/pages/dynamicOrganismDownload.jsf?organism=Saico1 yes yes - filtered unmasked scaffolds S.complicata.fa "split on |, take 3rd element (unique number)" N/A nothing Extra M. verticillata 1/6/2013 http://www.broadinstitute.org/annotation/genome/multicellularity_project/MultiDownloads.html yes yes supercontigs M.verticillata.fa BROAD N/A nothing