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
Agaricus arvensis
coding strand
Journal Article
Agaricus augustus
coding strand
Journal Article
Agaricus bernardii
coding strand
Journal Article
Agaricus bisporus
coding strand
Journal Article
Agaricus bitorquis
coding strand
Journal Article
Agaricus campestris
coding strand
Journal Article
Agaricus caroli
coding strand
Journal Article
Agaricus chionodermis
coding strand
Journal Article
Agaricus edulis
coding strand
Journal Article
Agaricus excellans
coding strand
Journal Article
Agaricus fissuratus
coding strand
Journal Article
Agaricus hortensis
coding strand
Journal Article
Agaricus langei
coding strand
Journal Article
Agaricus macrocarpus
coding strand
Journal Article
Agaricus nivescens
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
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
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
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
Cassidy JR, Pukkila PJ (1987) Inversion of 5S ribosomal RNA genes within the genus Coprinus. Curr
Genet 12:33-39
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
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
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
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
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
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
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
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
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
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
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
Agaricus rodmanii
coding strand
Journal Article
Agaricus silvaticus
(synonym: Agaricus
sylvaticus)
Agaricus silvicola
coding strand
Journal Article
coding strand
Journal Article
Agaricus subfloccosus
coding strand
Journal Article
Agaricus subrufescens
coding strand
Journal Article
Antrodia vailantii
coding strand
GenBank and
Journal Article
Armilliaria borealis
coding strand
Journal Article
Armillaria cepistipes
coding strand
GenBank and
Journal Article
Armillaria fumosa
coding strand
Journal Article
Armillaria gallica
coding strand
GenBank and
Journal Article
Armillaria hinnulea
coding strand
Journal Article
Armillaria jezoensis
coding strand
GenBank and
Journal Article
Armillaria limonea
coding strand
Journal Article
Armillaria lutea
coding strand
Journal Article
Armillaria mellea
coding strand
GenBank and
Journal Article
Armillaria novaezelandiae
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
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
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
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
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
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
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
Duchesne LC, Anderson JB (1990) Location and direction of transcription of the 5S rRNA gene in
Armillaria. Mycol Res 94(2):266-269
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
Duchesne LC, Anderson JB. 1990. Location and direction of transcription of the 5S rRNA gene in
Armillaria. Mycol Res 94(2):266-269
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
Duchesne LC, Anderson JB. 1990. Location and direction of transcription of the 5S rRNA gene in
Armillaria. Mycol Res 94(2):266-269
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
Duchesne LC, Anderson JB (1990) Location and direction of transcription of the 5S rRNA gene in
Armillaria. Mycol Res 94(2):266-269
Duchesne LC, Anderson JB (1990) Location and direction of transcription of the 5S rRNA gene in
Armillaria. Mycol Res 94(2):266-269
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
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
Armillaria sinapina
coding strand
GenBank and
Journal Article
Armillaria singula
coding strand
GenBank and
Journal Article
Armillaria tabascens
coding strand
Journal Article
Ashbya gossypii
(synonym: Eremothecium
gossypii)
Aspergillus clavatus
non-coding strand
GenBank and
Journal Article
none
Aspergillus fischerianus
(teleomorph: Neosartoya
fischeri)
Aspergillus fumigatus
(synonym: Aspergillus
phialiseptus)
Aspergillus nidulans
(teleomorph: Emericella
nidulans)
Aspergillus niger
none
Broad Institute
Rfam
Blastall
Aspergillus oryzae
none
Aspergillus terreus
none
Batrachochytrium
dendrobatidis
Botrytis cinerea
(teleomorph: Botryotinia
fuckeliana)
Candida albicans
none
Candida dubliniensis
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
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
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
Duchesne LC, Anderson JB (1990) Location and direction of transcription of the 5S rRNA gene in
Armillaria. Mycol Res 94(2):266-269
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
<http://www.broad.mit.edu/annotation/genome/aspergillus_group/Rfam.html>
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)
<http://www.broad.mit.edu/annotation/genome/aspergillus_group/Rfam.html>
none
Broad Institute
Rfam
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
none
NT_166520 (A. niger genome), EF105366 (A. niger rDNA query), X00691 (A. niger 5S rRNA query)
none
NCBI BLAST 2
Sequences
Broad Institute
Rfam
Broad Institute
Rfam
Broad Institute
Rfam
Blastall
non-coding strand
GenBank
non-coding strand
Blastall
<http://www.broad.mit.edu/annotation/genome/aspergillus_group/Rfam.html>
<http://www.broad.mit.edu/annotation/genome/aspergillus_group/Rfam.html>
<http://www.broad.mit.edu/annotation/genome/batrachochytrium_dendrobatidis/Rfam.html>
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)
NW_139715
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
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 lipolityca
(teleomorph: Yarrowia
lipolityca)
Candida lusitaniae
(synonym: Candida
parapsilosis var. obtuse,
telomorph: Clavispora
lusitaniae)
Candida parapsilosis
none
Journal Article
coding or noncoding 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)
non-coding strand
Blastall
Candida tropicalis
non-coding strand
Clavispora opuntiae
non-coding strand
Broad Institute
Rfam
Journal Article
AY055855 (C. parapsilosis 18S rRNA query), YSA1785 (C. parapsilosis 5S rRNA query),
<ftp://ftp.sanger.ac.uk/pub/pathogens/Candida/parapsilosis> (C. parapsilosis genome)
<http://www.broad.mit.edu/annotation/genome/candida_tropicalis/Rfam.html>
Coccidioides immitis
none
Coccidioides posadasii
none
Cochliobolus
heterostrophus
(anamorph: Bipolaris
maydis, synonym:
Helminthosporium
maydis)
Coprinus atramentarius
(synonym: Coprinopsis
atramentaria)
Coprinus cinereus
none
Broad Institute
Rfam
Broad Institute
Rfam
Journal Article
coding strand
Journal Article
Cassidy JR, Pukkila PJ (1987) Inversion of 5S ribosomal RNA genes within the genus Coprinus. Curr
Genet 12:33-39
coding strand
Journal Article
Coprinus 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
Cassidy JR, Pukkila PJ (1987) Inversion of 5S ribosomal RNA genes within the genus Coprinus. Curr
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
<http://www.broad.mit.edu/annotation/genome/coccidioides_group/Rfam.html>
<http://www.broad.mit.edu/annotation/genome/coccidioides_group/Rfam.html>
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
(synonym: Agaricus
comatus, Coprinopsis
comatus)
Coprinus micaceus
Genet 12:33-39
coding strand
Journal Article
Cryptococcus gattii
coding strand
GenBank and
Journal Article
Debaryomyces hanseni
(anamorph: Candida
famata, synonym:
Torulaspora hansenii)
non-coding strand
(x2)
Journal Article
Encephalitozoon cuniculi
none
GenBank
Filobasidiella
depauperata
Filobasidiella neoformans
(anamorph: Cryptococcus
neoformans)
Flammulina velutipes
none
Journal Article
coding strand
GenBank and
Journal Article
coding strand
Fusarium graminearum
(anamorph: Gibberella
zeae)
Fusarium oxysporum
none
GenBank and
Journal Article
Broad Institute
Rfam
AB286985; Babasaki K, Neda H, Murata H (2007) megB1, a novel macroevolutionary genomic
marker of the fungal phylum Basidiomycota. Biosci Biotechnol Biochem 71:1927-1939
<http://www.broad.mit.edu/annotation/genome/fusarium_group/Rfam.html>
<http://www.broad.mit.edu/annotation/genome/fusarium_group/Rfam.html>
Fusarium solani
(teleomorph:
Haematonectria
haematococca, Nectria
haemotococca,)
Fusarium verticillioides
(anamorph: Gibberella
moniliformis, synonym:
Fusarium moniliforme)
non-coding strand
Broad Institute
Rfam
GenBank
Broad Institute
Rfam
<http://www.broad.mit.edu/annotation/genome/fusarium_group/Rfam.html>
none
none
Cassidy JR, Pukkila PJ (1987) Inversion of 5S ribosomal RNA genes within the genus Coprinus. Curr
Genet 12:33-39
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
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
NC_003231, NC_003232, NC_003234, NC_003238, NC_003242
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
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
AJ317959
Grifola frondosa
coding strand
GenBank
AB069683
Hebeloma cylindrosporum
coding strand
Journal Article
Histoplasma capsulatum
(teleomorph: Ajellomyces
capsulatus)
none
Blastall
Kluyveromyces lactis
non-coding strand
GenBank and
Journal Article
Kluyveromyces waltii
non-coding strand
Laccaria bicolor
coding strand
NCBI Genomic
BLAST
GenBank and
Journal Article
Lentinula boryana
coding strand
Lentinula edodes
coding strand
Lodderomyces
elongisporus
Magnaporthe grisea
non-coding strand
Guidot A, Lumina E, Debaud JC, Marmeisse R (1999) The nuclear ribosomal DNA intergenic spacer
as a target sequence to study intraspecific diversity of the ectomycorrhizal basidiomycete Hebeloma
cylindrosporum directly on Pinus root systems. Appl Environ Microbiol 65: 903-909
AB071831 (A. capsulatum rDNA query), AY924883 (A. unguis 5S rRNA query)
<http://genome.wustl.edu/pub/organism/Fungi/Histoplasma_capsulatum/> (H. capsulatum genome)
<http://www.broad.mit.edu/annotation/genome/histoplasma_capsulatum/Rfam.html > (Broad Insitute
Rfam)
DQ130100; Verbeet MP, van Heerikhuizen H, Klootwijk J, Fontijn RD, Planta RJ (1984) Evolution
of yeast ribosomal DNA: Molecular cloning of the rDNA units of Kluyveromyces lactis and
Hansenula wingei and their comparison with the rDNA units of other Saccharomycetoideae. Mol Gen
Genet 195:116-125
AF543841 (K. marxianus rDNA query), YSKRRA (K. lactis 5S rRNA query),
<http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi?organism=fungi&database=262981>
AF116534; Martin F, Selosse MA, Le Tacon F (1999) The nuclear rDNA intergenic spacer of the
ectomycorrhizal basidiomycete Laccaria bicolor: Structural analysis and allelic polymorphism.
Microbiology 145: 1605-1611
AB286978; Babasaki K, Neda H, Murata H (2007) megB1, a novel macroevolutionary genomic
marker of the fungal phylum Basidiomycota. Biosci Biotechnol Biochem 71:1927-1939
AB286982; Babasaki K, Neda H, Murata H (2007) megB1, a novel macroevolutionary genomic
marker of the fungal phylum Basidiomycota. Biosci Biotechnol Biochem 71:1927-1939
<http://www.broad.mit.edu/annotation/genome/lodderomyces_elongisporus/Rfam.html>
Malassezia globosa
coding or noncoding strand
Mrakia frigida (synonym:
Cryptococcus curiosus)
Mrakia gelida
coding strand
Mrakia nivalis
coding strand
Mrakia stokesii
coding strand
Mucor racemosus
coding or noncoding strand
none
Neurospora crassa
none
coding strand
GenBank and
Journal Article
GenBank and
Journal Article
Broad Institute
Rfam
Broad Institute
Rfam
Journal Article
GenBank and
Journal Article
GenBank and
Journal Article
GenBank and
Journal Article
GenBank and
Journal Article
Journal Article
Journal Article
<http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/Rfam.html>
Sugita T, Kodama M, Saito M, Ito T, Kato Y, Tsuboi R, Nishikawa A (2003) Sequence diversity of
the intergenic spacer region of the rRNA gene of Malassezia globosa colonizing the skin of patients
with atopic dermatitis and healthy individuals. J Clin Microbiol 41:3022-3027
AF144414; Diaz MR, Fell JW (2000) Molecular analyses of the IGS & ITS regions of rDNA of the
psychrophilic yeasts in the genus Mrakia. Antonie Van Leeuwenhoek 77: 7-12
AF144416; Diaz MR, Fell JW (2000) Molecular analyses of the IGS & ITS regions of rDNA of the
psychrophilic yeasts in the genus Mrakia. Antonie Van Leeuwenhoek 77: 7-12
AF144415; Diaz MR, Fell JW (2000) Molecular analyses of the IGS & ITS regions of rDNA of the
psychrophilic yeasts in the genus Mrakia. Antonie Van Leeuwenhoek 77: 7-12
AF144417; Diaz MR, Fell JW (2000) Molecular analyses of the IGS & ITS regions of rDNA of the
psychrophilic yeasts in the genus Mrakia. Antonie Van Leeuwenhoek 77: 7-12
Cihlar RL, Sypherd PY (1980) The organization of the ribosomal RNA genes in the fungus Mucor
racemosus. Nucleic Acids Res 8:793-804
Metzenberg RL, Stevens JN, Selker EU (1985) Identification and chromosomal distribution of 5S
rRNA genes in Neurospora crassa. PNAS 82:2067-2071
Nosema antheraeae
coding strand
Journal Article
Nosema bombycis
coding strand
Nosema ceranae
non-coding strand
GenBank and
Journal Article
GenBank and
Journal Article
Nosema spodopterae
coding strand
Journal Article
Paracoccidioides
brassiliensis
none
Blastall
Phaffia rhodozyma
coding or noncoding strand
Journal Article
Pholiota abstrusa
coding strand
Pholiota aurivella
coding strand
Pholiota nameko
coding strand
Pholiota spumosa
coding strand
Pichia angusta
(anamorph: Candida
pelliculosa, synonym:
Hansenula polymorpha)
Pichia anomala
(synonym: Candida
javanica, Hansenula
anomala)
Pichia canadensis
(synonym: Hansenula
wingei)
coding strand
GenBank and
Journal Article
GenBank and
Journal Article
GenBank and
Journal Article
GenBank and
Journal Article
GenBank and
Journal Article
Pichia jadinii (anamorph:
Candida utilis, synonym:
Torula utilis, Torulopsis
utilis)
Wang LL, Chen KP, Zhang Z, Yao Q, Gao GT, Zhao Y (2006) Phylogenetic analysis of Nosema
antheraeae (Microsporidia) isolated from Chinese oak silkworm, Antheraea pernyi. J Eukaryot
Microbiol 53:310–313
AY259631; Huang WF, Tsai SJ, Lo CF, Soichi Y, Wang CH (2004) The novel organization and
complete sequence of the ribosomal RNA gene of Nosema bombycis. Fungal Genet Biol 41: 473-481
EF091885; Huang WF, Bocquet M, Lee KC, Sung IH, Jiang JH, Chen YW, Wang CH (2008) The
comparison of rDNA spacer regions of Nosema ceranae isolates from different hosts and locations. J
Invertebr Pathol 97:9-13
Tsai SJ, Huang WF, Wang CH (2005) Complete sequence and gene organization of the Nosema
spodopterae rRNA gene. J Eukaryot Microbiol 52:52-54
AB035710 (P. brassiliensis rDNA query), AY924944 (N. crassa 5S rRNA query),
<http://www.broad.mit.edu/annotation/genome/paracoccidioides_brasiliensis/MultiDownloads.html>
(P. brassilensis genome)
Fell JW, Blatt GM (1999) Separation of strains of the yeasts Xanthophyllomyces dendrorhous and
Phaffia rhodozyma based on rDNA IGS and ITS sequence analysis. Journal of Industrial
Microbiology & Biotechnology 23: 677-681
AB286999; Babasaki K, Neda H, Murata H (2007) megB1, a novel macroevolutionary genomic
marker of the fungal phylum Basidiomycota. Biosci Biotechnol Biochem 71:1927-1939
AB286998; Babasaki K, Neda H, Murata H (2007) megB1, a novel macroevolutionary genomic
marker of the fungal phylum Basidiomycota. Biosci Biotechnol Biochem. 71:1927-1939
AB286997; Babasaki K, Neda H, Murata H (2007) megB1, a novel macroevolutionary genomic
marker of the fungal phylum Basidiomycota. Biosci Biotechnol Biochem 71:1927-1939
AB287000; Babasaki K, Neda H, Murata H. (2007) megB1, a novel macroevolutionary genomic
marker of the fungal phylum Basidiomycota. Biosci Biotechnol Biochem 71:1927-1939
AF467695; Klabunde J, Diesel A, Waschk D, Gellissen G, Hollenberg CP, Suckow M (2002) Singlestep co-integration of multiple expressible heterologous genes into the ribosomal DNA of the
methylotrophic yeast Hansenula polymorpha. Appl Microbiol Biotechnol 58(6): 797-805
coding strand
GenBank and
Journal Article
AY231605; Sutar R, David JK, Ganesan K, Ghosh AK, Singhi S, Chakrabarti A, Bachhawat AK
(2004) Comparison of ITS and IGS1 regions for strain typing of clinical and non-clinical isolates of
Pichia anomala. J Med Microbiol 53:119-123
non-coding strand
Journal Article
non-coding strand
Journal Article
Verbeet MP, van Heerikhuizen H, Klootwijk J, Fontijn RD, Planta RJ (1984) Evolution of yeast
ribosomal DNA: Molecular cloning of the rDNA units of Kluyveromyces lactis and Hansenula wingei
and their comparison with the rDNA units of other Saccharomycetoideae. Mol Gen Genet 195:116125
Tabata S (1980) Structure of the 5-S ribosomal RNA gene and its adjacent regions in Torulopsis
utilis. Eur J Biochem 110: 107-114
Pichia stipitis
non-coding strand
Blastall
Pleurotus eryngii
coding strand
Pleurotus fuscus
coding strand
Pleurotus nebrodensis
coding strand
Pleurotus ostreatus
coding strand
Pleurotus pulmonarius
coding strand
Pneumocystis carinii
none
GenBank and
Journal Article
GenBank and
Journal Article
GenBank and
Journal Article
GenBank and
Journal Article
GenBank and
Journal Article
Journal Article
Podospora anserina
none
Journal Article
Puccinia coronata
coding strand
Journal Article
Puccinia graminis
coding strand
Puccinia recondita
coding strand
Broad Institute
Rfam
Journal Article
Pyrenophora graminea
coding strand
Journal Article
Rhizoctonia solani
(teleomorph:
Thanatephorus praticola)
Rhizomucor miehei
coding or noncoding strand
Journal Article
non-coding strand
Rhizopus oryzae
coding strand
Saccharomyces bayanus
non-coding strand
GenBank and
Journal Article
Broad Institute
Rfam
GenBank
Saccharomyces castellii
(synonym: Naumovia
castellii)
Saccharomyces cerevisiae
(anamorph: Candida
robusta, synonym:
non-coding strand
Blastall
non-coding strand
Journal Article
AB054280 (P. stipitis 18S rRNA query), YSRRRA (P. membranifaciens 5S rRNA query)
<http://genome.jgi-psf.org/Picst3/Picst3.download.ftp.html> (P. stipitis genome)
AB234047; Babasaki K, Neda H, Murata H (2007) megB1, a novel macroevolutionary genomic
marker of the fungal phylum Basidiomycota. Biosci Biotechnol Biochem 71:1927-1939
AB234033; Babasaki K, Neda H, Murata H (2007) megB1, a novel macroevolutionary genomic
marker of the fungal phylum Basidiomycota. Biosci Biotechnol Biochem 71:1927-1939
AB286121; Babasaki K, Neda H, Murata H (2007) megB1, a novel macroevolutionary genomic
marker of the fungal phylum Basidiomycota. Biosci Biotechnol Biochem 71:1927-1939
AB234029; Babasaki K, Neda H, Murata H (2007) megB1, a novel macroevolutionary genomic
marker of the fungal phylum Basidiomycota. Biosci Biotechnol Biochem 71:1927-1939
AB234031; Babasaki K, Neda H, Murata H (2007) megB1, a novel macroevolutionary genomic
marker of the fungal phylum Basidiomycota. Biosci Biotechnol Biochem 71:1927-1939
Yoganathan T, Lin H, Buck GA (1989) An electrophoretic karyotype and assignment of ribosomal
genes to resolved chromosomes of Pneumocystis carinii. Mol Microbiol 3: 1473-1480
Labat N, Perrot M, Bégueret J (1985) Cloning and characterization of the rDNA repeat unit of
Podospora anserina. Mol Gen Genet 199:154-157
Kim WK, Zerucha T, Klassen GR (1992) A region of heterogeneity adjacent to the 5S ribosomal
RNA gene of cereal rusts. Curr Genet 22:101-105
<http://www.broad.mit.edu/annotation/genome/puccinia_graminis/Rfam.html>
Kim WK, Zerucha T, Klassen GR (1992) A region of heterogeneity adjacent to the 5S ribosomal
RNA gene of cereal rusts. Curr Genet 22:101-105
Amici A, Rollo F (1991) The nucleotide sequence of the 5S ribosomal RNA gene of Pyrenophora
graminea. Nucleic Acids Res 19:5073
Vigalys R, Gonzalez D (1990) Organization of ribosomal DNA in the basidiomycete Thanatephorus
praticola. Curr Genet 18:277-280
AF205941; Maicas S, Adam AC, Polaina J (2000) The ribosomal DNA of the Zygomycete Mucor
miehei. Curr Genet 37:412-419
<http://www.broad.mit.edu/annotation/genome/rhizopus_oryzae/Rfam.html>
DQ130079; Ganley ARD, Hayashi K, Horiuchi T, Kobayashi T (2005) Identifying gene-independent
noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting. Proc Natl
Acad Sci USA 102:11787-11792
AY198397 (C. glabrata 5S rRNA query), Z75577 (S. castellii 18S rRNA query),
<ftp://genome-ftp.stanford.edu/yeast/data_download/sequence/fungal_
genomes/S_castellii/WashU> (S. castellii genome)
Z73326; Kramer RA, Philippsen P, Davis RW (1978) Divergent transcription in the yeast ribosomal
RNA coding region as shown by hybridization to separated strands and sequence analysis of cloned
DNA. J Mol Biol 123:405-416
Hormiscium cerevisiae,
Mycotorula robusta,
Saccharomyces
carlsbergensis)
Saccharomyces
dairenensis
non-coding strand
GenBank and
Journal Article
DQ130085; Ganley ARD, Hayashi K, Horiuchi T, Kobayashi T (2005) Identifying gene-independent
noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting. Proc Natl
Acad Sci USA 102:11787-11792
Saccharomyces exiguus
non-coding strand
GenBank and
Journal Article
DQ130081; Ganley ARD, Hayashi K, Horiuchi T, Kobayashi T (2005) Identifying gene-independent
noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting. Proc Natl
Acad Sci USA 102:11787-11792
Saccharomyces kluyveri
(synonym: Lachancea
kluyveri)
non-coding strand
GenBank and
Journal Article
DQ130084; Ganley ARD, Hayashi K, Horiuchi T, Kobayashi T (2005) Identifying gene-independent
noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting. Proc Natl
Acad Sci USA 102:11787-11792
Saccharomyces
kudriavzevii
non-coding strand
GenBank and
Journal Article
Saccharomyces mikatae
non-coding strand
GenBank and
Journal Article
Saccharomyces paradoxus
non-coding strand
GenBank and
Journal Article
Saccharomyces
pastorianus
non-coding strand
GenBank and
Journal Article
Saccharomyces rosei
(synonym: Torulaspora
delbrueckii)
Saccharomyces servazzii
non-coding strand
Journal Article
non-coding strand
GenBank and
Journal Article
Saccharomyces unisporus
non-coding strand
GenBank
Schizophyllum commune
coding strand
Journal Article
Schizosaccharomyces
none
Broad Institute
DQ130076; Ganley ARD, Hayashi K, Horiuchi T, Kobayashi T (2005) Identifying gene-independent
noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting. Proc Natl
Acad Sci USA 102:11787-11792
DQ130080; Ganley ARD, Hayashi K, Horiuchi T, Kobayashi T (2005) Identifying gene-independent
noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting. Proc Natl
Acad Sci USA 102:11787-11792
BR000309; Ganley ARD, Hayashi K, Horiuchi T, Kobayashi T (2005) Identifying gene-independent
noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting. Proc Natl
Acad Sci USA 102:11787-11792
DQ130078; Ganley ARD, Hayashi K, Horiuchi T, Kobayashi T (2005) Identifying gene-independent
noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting. Proc Natl
Acad Sci USA 102:11787-11792
Verbeet MP, Klootwijk J, van Heerikhuizen H, Fontijn R, Vreugdenhil E, Planta RJ (1983) Molecular
cloning of the rDNA of Saccharomyces rosei and comparison of its transcription initiation region
with that of Saccharomyces carlsbergensis. Gene 23:53-63
DQ130082; Ganley ARD, Hayashi K, Horiuchi T, Kobayashi T (2005) Identifying gene-independent
noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting. Proc Natl
Acad Sci USA 102:11787-11792
DQ130083; Ganley ARD, Hayashi K, Horiuchi T, Kobayashi T (2005) Identifying gene-independent
noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting. Proc Natl
Acad Sci USA 102:11787-11792
Buckner B, Novotny CP, Ullrich RC (1988) Organization of the ribosomal RNA gene of
Schizophyllum commune. Curr Genet 12:33-36
<http://www.broad.mit.edu/annotation/genome/schizosaccharomyces_japonicus/Rfam.html>
japonicus
Rfam
Schizosaccharomyces
octosporus
Schizosaccharomyces
pombe
Sclerotinia sclerotiorum
none
Tilletia caries
coding strand
Broad Institute
Rfam
GenBank and
Journal Article
Broad Institute
Rfam
Journal Article
Tilletia controversa
coding strand
Journal Article
Tilletia laevis
coding strand
GenBank
Trichoderma reesei
(teleomorph: Hypocrea
jecorina)
Tricholoma
bakamotsutake
Tricholoma matsutake
none
Blastall
AF548103 (H. jecorina 18S rRNA query), D88368 (H. lutea 5S rRNA query),
<http://genome.jgi-psf.org/Trire2/Trire2.download.ftp.html> (H. jecorina genome)
coding strand
GenBank
DQ323057
coding strand
Trichosporon dermatis
(synonym: Cryptococcus
humicola)
Uncinocarpus reesei
coding strand
GenBank and
Journal Article
GenBank
DQ323062; Babasaki K, Neda H, Murata H (2007) megB1, a novel macroevolutionary genomic
marker of the fungal phylum Basidiomycota. Biosci Biotechnol Biochem 71:1927-1939
EU081842
<http://www.broad.mit.edu/annotation/genome/uncinocarpus_reesii/Rfam.html>
Ustilago maydis
(synonym: Ustilago zeae)
Vanderwaltozyma
polyspora (synonym:
Kluyveromyces
polysporus)
Xanthopyllomyces
dendrorhous
none
Broad Institute
Rfam
Journal Article
non-coding strand
GenBank
coding or noncoding strand
Journal Article
none
none
none
<http://www.broad.mit.edu/annotation/genome/schizosaccharomyces_japonicus/Rfam.html>
NC_003421; Tabata S (1981) Nucleotide sequences of the 5S ribosomal RNA genes and their
adjacent regions in Schizosaccharomyces pombe. Nucleic Acids Res 9:6429-6437
<http://www.broad.mit.edu/annotation/genome/sclerotinia_sclerotiorum/Rfam.html>
DQ354964; Zerucha T, Kim WK, Mauthe W, Klassen GR (1992) The location and nucleotide
sequence of the 5S rRNA gene of bunt wheat, Tilletia caries and Tilletia controversa. Nucleic Acids
Res 20:2600
DQ354962; Zerucha T, Kim WK, Mauthe W, Klassen GR (1992) The location and nucleotide
sequence of the 5S rRNA gene of bunt wheat, Tilletia caries and Tilletia controversa. Nucleic Acids
Res 20:2600
DQ354967
Kahmann R, Kämper J (2004) Ustilago maydis: How its biology relates to pathogenic development.
New Phytologist 164:31–42
NW_001834527
Fell JW, Blatt GM (1999) Separation of strains of the yeasts Xanthophyllomyces dendrorhous and
Phaffia rhodozyma based on rDNA IGS and ITS sequence analysis. Journal of Industrial
Microbiology & Biotechnology 23: 677-681