Supplementary Table 1. Background Information for Fungal Species

Supplementary Table 1. Background information for fungal species.

Genus, Species / 5S rRNA
Linkage to rDNA Unit / Method of Data Collection / References
(GenBank Accession Number, Journal Article, URL)
Absidia glauca / non-coding strand / Journal Article / Wostemeyer J, Burmester A (1994) Dimorphism of rDNA organization in mating types of the zygomycete Absidia glauca. Microbiol Res 150:63-70
Agaricus arvensis / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Agaricus augustus / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Agaricus bernardii / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Agaricus bisporus / coding strand / Journal Article / Cassidy JR, Pukkila PJ (1987) Inversion of 5S ribosomal RNA genes within the genus Coprinus. Curr Genet 12:33-39
Agaricus bitorquis / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Agaricus campestris / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Agaricus caroli / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Agaricus chionodermis / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Agaricus edulis / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Agaricus excellans / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Agaricus fissuratus / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Agaricus hortensis / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Agaricus langei / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Agaricus macrocarpus / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Agaricus nivescens / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Agaricus placomyces / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Agaricus rodmanii / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Agaricus silvaticus
(synonym: Agaricus sylvaticus) / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Agaricus silvicola / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Agaricus subfloccosus / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Agaricus subrufescens / coding strand / Journal Article / Bunyad BA, Nicholson MS, Royse DJ (1996) Phylogeny of the genus Agaricus inferred from restriction analysis of enzymatically amplified ribosomal DNA. Fungal Genet Biol 20:243–253
Antrodia vailantii / coding strand / GenBank and Journal Article / AM286436; Moreth U, Schmidt O (2005) Investigations on ribosomal DNA of indoor wood decay fungi for their characterization and identification. Holzforschung 59(1):90-93
Armilliaria borealis / coding strand / Journal Article / Duchesne LC, Anderson JB (1990) Location and direction of transcription of the 5S rRNA gene in Armillaria. Mycol Res 94(2):266-269
Armillaria cepistipes / coding strand / GenBank and Journal Article / D89919; Terashima K, Cha JY, Yajima T, Igarashi T, Miura K (1998) Phylogenetic analysis of Japanese Armillaria based on the intergenic spacer (IGS) sequences of their ribosomal DNA. Eur J Forest Pathol 28:11-19
Armillaria fumosa / coding strand / Journal Article / Duchesne LC, Anderson JB. 1990. Location and direction of transcription of the 5S rRNA gene in Armillaria. Mycol Res 94(2):266-269
Armillaria gallica / coding strand / GenBank and Journal Article / D89920; Terashima K, Cha JY, Yajima T, Igarashi T, Miura K (1998) Phylogenetic analysis of Japanese Armillaria based on the intergenic spacer (IGS) sequences of their ribosomal DNA. Eur J Forest Pathol 28:11-19
Armillaria hinnulea / coding strand / Journal Article / Duchesne LC, Anderson JB. 1990. Location and direction of transcription of the 5S rRNA gene in Armillaria. Mycol Res 94(2):266-269
Armillaria jezoensis / coding strand / GenBank and Journal Article / D89921; Terashima K, Cha JY, Yajima T, Igarashi T, Miura K (1998) Phylogenetic analysis of Japanese Armillaria based on the intergenic spacer (IGS) sequences of their ribosomal DNA. Eur J Forest Pathol 28:11-19
Armillaria limonea / coding strand / Journal Article / Duchesne LC, Anderson JB (1990) Location and direction of transcription of the 5S rRNA gene in Armillaria. Mycol Res 94(2):266-269
Armillaria lutea / coding strand / Journal Article / Duchesne LC, Anderson JB (1990) Location and direction of transcription of the 5S rRNA gene in Armillaria. Mycol Res 94(2):266-269
Armillaria mellea / coding strand / GenBank and Journal Article / D89922; Terashima K, Cha JY, Yajima T, Igarashi T, Miura K (1998) Phylogenetic analysis of Japanese Armillaria based on the intergenic spacer (IGS) sequences of their ribosomal DNA. Eur J Forest Pathol 28:11-19
Armillaria novae-zelandiae / coding strand / Journal Article / Duchesne LC, Anderson JB (1990) Location and direction of transcription of the 5S rRNA gene in Armillaria. Mycol Res 94(2):266-269
Armillaria ostoyae / coding strand / GenBank and Journal Article / D89923, D89924; Terashima K, Cha JY, Yajima T, Igarashi T, Miura K (1998) Phylogenetic analysis of Japanese Armillaria based on the intergenic spacer (IGS) sequences of their ribosomal DNA. Eur J Forest Pathol 28:11-19
Armillaria sinapina / coding strand / GenBank and Journal Article / D89925; Terashima K, Cha JY, Yajima T, Igarashi T, Miura K (1998) Phylogenetic analysis of Japanese Armillaria based on the intergenic spacer (IGS) sequences of their ribosomal DNA. Eur J Forest Pathol 28:11-19
Armillaria singula / coding strand / GenBank and Journal Article / D89926; Terashima K, Cha JY, Yajima T, Igarashi T, Miura K (1998) Phylogenetic analysis of Japanese Armillaria based on the intergenic spacer (IGS) sequences of their ribosomal DNA. Eur J Forest Pathol 28:11-19
Armillaria tabascens / coding strand / Journal Article / Duchesne LC, Anderson JB (1990) Location and direction of transcription of the 5S rRNA gene in Armillaria. Mycol Res 94(2):266-269
Ashbya gossypii (synonym: Eremothecium gossypii) / non-coding strand / GenBank and Journal Article / NC_005788, Wendland J, Pohlmann R, Dietrich F, Steiner S, Mohr C, Philippsen P (1999) Compact organization of rRNA genes in the filamentous fungus Ashbya gossypii. Curr Genet 35: 618-625
Aspergillus clavatus / none / Broad Institute Rfam / http://www.broad.mit.edu/annotation/genome/aspergillus_group/Rfam.html
Aspergillus fischerianus (teleomorph: Neosartoya fischeri) / none / Blastall / AY924883 (A. unguis 5S rRNA query), AB185254 (N. fischeri rDNA query); ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/n_fischeri/annotation_dbs/
(A. fischerianus genome)
Aspergillus fumigatus (synonym: Aspergillus phialiseptus) / none / Broad Institute Rfam / http://www.broad.mit.edu/annotation/genome/aspergillus_group/Rfam.html
Aspergillus nidulans (teleomorph: Emericella nidulans) / none / Journal Article / Lockington RA, Taylor GG, Winther M, Scazzocchio C, Davies RW (1982) A physical map of the ribosomal DNA repeat unit of Aspergillus nidulans. Gene 20:135-137
Aspergillus niger / none / NCBI BLAST 2 Sequences / NT_166520 (A. niger genome), EF105366 (A. niger rDNA query), X00691 (A. niger 5S rRNA query)
Aspergillus oryzae / none / Broad Institute Rfam / http://www.broad.mit.edu/annotation/genome/aspergillus_group/Rfam.html
Aspergillus terreus / none / Broad Institute Rfam / http://www.broad.mit.edu/annotation/genome/aspergillus_group/Rfam.html
Batrachochytrium dendrobatidis / none / Broad Institute Rfam / http://www.broad.mit.edu/annotation/genome/batrachochytrium_dendrobatidis/Rfam.html
Botrytis cinerea (teleomorph: Botryotinia fuckeliana) / none / Blastall / AY544695 (B. fuckeliana 18S rRNA query), AY924895 (F. cerealis 5S rRNA query),
<http://www.broad.mit.edu/annotation/genome/botrytis_cinerea/Downloads.html> (B. cinerea genome)
Candida albicans / non-coding strand / GenBank / NW_139715
Candida dubliniensis / non-coding strand / Blastall / X00868 (C. albicans 5S rRNA query), X99399 (C. dubliniensis 18S rRNA query)
ftp://ftp.sanger.ac.uk/pub/pathogens/Candida/dubliniensis> (C. dubliniensis genome)
Candida glabrata (synonyms: Cryptococcus glabratus, Torulopsis glabrata, Torulopsis stercoralis) / non-coding strand (x2) / Journal Article / Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuvéglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisramé A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wésolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL (2004) Genome evolution in yeasts. Nature 430:35-44
Candida lipolityca (teleomorph: Yarrowia lipolityca) / none / Journal Article / Clare JJ, Davidow LS, Gardner DCJ, Oliver SG (1986) Cloning and characterisation of the ribosomal RNA genes of the dimorphic yeast, Yarrowia lipolytica. Curr Genet 10:449-45
Candida lusitaniae
(synonym: Candida parapsilosis var. obtuse, telomorph: Clavispora lusitaniae) / coding or non-coding strand / Blastall / DQ249209 (C. lusitaniae 18S rRNA query), YSA1785 (C. parapsilosis 5S rRNA query)
<http://www.broad.mit.edu/annotation/genome/candida_lusitaniae/Downloads.html> (C. lusitaniae genome)
Candida parapsilosis / non-coding strand / Blastall / AY055855 (C. parapsilosis 18S rRNA query), YSA1785 (C. parapsilosis 5S rRNA query),
ftp://ftp.sanger.ac.uk/pub/pathogens/Candida/parapsilosis> (C. parapsilosis genome)
Candida tropicalis / non-coding strand / Broad Institute Rfam / http://www.broad.mit.edu/annotation/genome/candida_tropicalis/Rfam.html
Clavispora opuntiae / non-coding strand / Journal Article / Lachance MA, Starmer WT, Bowles JM, Phaff HJ, Rosa CA (1999) Ribosomal DNA, species structure, and biogeography of the cactophilic yeast Clavispora opuntiae. Can J Microbiol 46:195–210
Coccidioides immitis / none / Broad Institute Rfam / http://www.broad.mit.edu/annotation/genome/coccidioides_group/Rfam.html
Coccidioides posadasii / none / Broad Institute Rfam / http://www.broad.mit.edu/annotation/genome/coccidioides_group/Rfam.html
Cochliobolus heterostrophus (anamorph: Bipolaris maydis, synonym: Helminthosporium maydis) / none / Journal Article / Garber RC, Turgeon BG, Selker EU, Yoder OC (1988) Organization of the ribosomal RNA genes in the fungus Cochliobolus heterostrophus. Curr Genet 14:573-582
Coprinus atramentarius (synonym: Coprinopsis atramentaria) / coding strand / Journal Article / Cassidy JR, Pukkila PJ (1987) Inversion of 5S ribosomal RNA genes within the genus Coprinus. Curr Genet 12:33-39
Coprinus cinereus / coding strand / Journal Article / Cassidy JR, Pukkila PJ (1987) Inversion of 5S ribosomal RNA genes within the genus Coprinus. Curr Genet 12:33-39
Coprinus comatus (synonym: Agaricus comatus, Coprinopsis comatus) / non-coding strand / Journal Article / Cassidy JR, Pukkila PJ (1987) Inversion of 5S ribosomal RNA genes within the genus Coprinus. Curr Genet 12:33-39
Coprinus micaceus / coding strand / Journal Article / Cassidy JR, Pukkila PJ (1987) Inversion of 5S ribosomal RNA genes within the genus Coprinus. Curr Genet 12:33-39
Cryptococcus gattii / coding strand / GenBank and Journal Article / DQ007967; Diaz MR, Boekhout T, Kiesling T, Fell JW (2005) Comparative analysis of the intergenic spacer regions and population structure of the species complex of the pathogenic yeast Cryptococcus neoformans. FEMS Yeast Res 5:1129-1140
Debaryomyces hanseni (anamorph: Candida famata, synonym: Torulaspora hansenii) / non-coding strand (x2) / Journal Article / Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuvéglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisramé A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wésolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL (2004) Genome evolution in yeasts. Nature 430:35-44
Encephalitozoon cuniculi / none / GenBank / NC_003231, NC_003232, NC_003234, NC_003238, NC_003242
Filobasidiella depauperata / none / Journal Article / Kwon-Chung KJ, Chang YC, Penoyer L (1997) Species of the genus Filobasidiella differ in the organization of their 5S rRNA genes. Mycologia 89:244-249
Filobasidiella neoformans (anamorph: Cryptococcus neoformans) / coding strand / GenBank and Journal Article / BR000310; Kwon-Chung KJ, Chang YC, Penoyer L (1997) Species of the genus Filobasidiella differ in the organization of their 5S rRNA genes. Mycologia 89:244-249