Species Publications

Publication details

Comparative genomics of biotechnologically important yeasts. (2016) Proc Natl Acad Sci U S A 113, 9882-9887.
Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Goker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, Deshpande S, Douglass AP, Hanson SJ, Klenk HP, LaButti KM, Lapidus A, Lindquist EA, Lipzen AM, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan JL, Peng Y, Rokas A, Rosa CA, Scheuner C, Sibirny AA, Slot JC, Stielow JB, Sun H, Kurtzman CP, Blackwell M, Grigoriev IV, Jeffries TW
Abstract: Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.

Saitoella complicata NRRL Y-17804

[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Taphrinomycotina incertae sedis | Saitoella | Saitoella complicata ]

Saitoella_complicata_NRRL_Y_17804 Picture Source
Taxonomy:Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | Taphrinomycotina | Taphrinomycotina incertae sedis | Saitoella | Saitoella complicata
Synonym:Saitoella complicata NBRC 10748, Saitoella complicata JCM 7358, Saitoella complicata IAM 12963, Saitoella complicata CCRC 22490, Saitoella complicata CBS 7301
Ncbi Go to NCBI Taxonomy (698492)
Eol Encyclopedia of life
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Publications:
et. al. Right (2016)
Proc Natl Acad Sci U S A 113, 9882-9887. Down
et. al. Right (2015)
Genome Announc 3, e00220-15. Down
(2011)
J Gen Appl Microbiol 57, 243-246.

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Pichia membranifaciens NRRL Y-2026

[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Pichiaceae | Pichia | Pichia membranifaciens ]

Pichia_membranifaciens_NRRL_Y_2026 Courtesy of Thomas Jeffries
Taxonomy:Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Pichiaceae | Pichia | Pichia membranifaciens
Anamorph:Candida valida
Synonym:Pichia membranifaciens (E.C.Hansen) E.C.Hansen, Pichia membranaefaciens
Ncbi Go to NCBI Taxonomy (763406)
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Publication:
et. al. Right (2016)
Proc Natl Acad Sci U S A 113, 9882-9887. Down

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Wickerhamomyces anomalus NRRL Y-366-8

[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Phaffomycetaceae | Wickerhamomyces | Wickerhamomyces anomalus ]

Wickerhamomyces_anomalus_NRRL_Y_366_8 Picture Source
Taxonomy:Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Phaffomycetaceae | Wickerhamomyces | Wickerhamomyces anomalus
Synonym:Pichia anomala NRRL Y-366-8
Ncbi Go to NCBI Taxonomy (683960)
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Publication:
et. al. Right (2016)
Proc Natl Acad Sci U S A 113, 9882-9887. Down

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Nadsonia fulvescens var. elongata DSM 6958

[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Nadsonia | Nadsonia fulvescens | Nadsonia fulvescens var. elongata ]

Nadsonia_fulvescens_var__elongata_DSM_6958 Picture Source
Taxonomy:Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Saccharomycetales incertae sedis | Nadsonia | Nadsonia fulvescens | Nadsonia fulvescens var. elongata
Ncbi Go to NCBI Taxonomy (857566)
Eol Encyclopedia of life
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Publication:
et. al. Right (2016)
Proc Natl Acad Sci U S A 113, 9882-9887. Down

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Babjeviella inositovora NRRL Y-12698

[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Debaryomycetaceae | Babjeviella | Babjeviella inositovora ]

Babjeviella_inositovora_NRRL_Y_12698 Courtesy of Linda Barnett
Taxonomy:Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Debaryomycetaceae | Babjeviella | Babjeviella inositovora
Synonym:Pichia inositovora, Yamadazyma inositovora
Ncbi Go to NCBI Taxonomy (984486)
Eol Encyclopedia of life
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Publication:
et. al. Right (2016)
Proc Natl Acad Sci U S A 113, 9882-9887. Down

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Pachysolen tannophilus NRRL Y-2460

[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Saccharomycetaceae | Pachysolen | Pachysolen tannophilus ]

Pachysolen_tannophilus_NRRL_Y_2460 Courtesy of Linda Barnett
Taxonomy:Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Saccharomycetaceae | Pachysolen | Pachysolen tannophilus
Ncbi Go to NCBI Taxonomy (669874)
Eol Encyclopedia of life
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Publications:
et. al. Right (2016)
Proc Natl Acad Sci U S A 113, 9882-9887. Down
et. al. Right (2012)
Eukaryot Cell 11, 827. Down

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Lipomyces starkeyi NRRL Y-11557

[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Lipomycetaceae | Lipomyces | Lipomyces starkeyi ]

Lipomyces_starkeyi_NRRL_Y_11557 Courtesy of Chris Calvey and Thomas Jeffries
Taxonomy:Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Lipomycetaceae | Lipomyces | Lipomyces starkeyi
Ncbi Go to NCBI Taxonomy (675824)
Eol Encyclopedia of life
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Publication:
et. al. Right (2016)
Proc Natl Acad Sci U S A 113, 9882-9887. Down

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Hyphopichia burtonii NRRL Y-1933

[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Debaryomycetaceae | Hyphopichia | Hyphopichia burtonii ]

Hyphopichia_burtonii_NRRL_Y_1933 Courtesy of Clete Kurtzman
Taxonomy:Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Debaryomycetaceae | Hyphopichia | Hyphopichia burtonii
Synonym:Endomycopsis burtonii
Ncbi Go to NCBI Taxonomy (984485)
Eol Encyclopedia of life
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Publication:
et. al. Right (2016)
Proc Natl Acad Sci U S A 113, 9882-9887. Down

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Ascoidea rubescens DSM 1968

[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Ascoideaceae | Ascoidea | Ascoidea rubescens ]

Ascoidea_rubescens_DSM_1968 Picture Source
Taxonomy:Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Ascoideaceae | Ascoidea | Ascoidea rubescens
Ncbi Go to NCBI Taxonomy (1344418)
Eol Encyclopedia of life
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Publication:
et. al. Right (2016)
Proc Natl Acad Sci U S A 113, 9882-9887. Down

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Candida tanzawaensis NRRL Y-17324

[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Debaryomycetaceae | Candida tanzawaensis clade | [Candida] tanzawaensis ]

Candida_tanzawaensis_NRRL_Y_17324 Courtesy of Linda Barnett
Taxonomy:Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Debaryomycetaceae | Candida tanzawaensis clade | [Candida] tanzawaensis
Ncbi Go to NCBI Taxonomy (984487)
Eol Encyclopedia of life
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Publication:
et. al. Right (2016)
Proc Natl Acad Sci U S A 113, 9882-9887. Down

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Tortispora caseinolytica NRRL Y-17796

[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Trigonopsidaceae | Tortispora | Tortispora caseinolytica ]

Tortispora_caseinolytica_NRRL_Y_17796 Courtesy of Linda Barnett
Taxonomy:Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Trigonopsidaceae | Tortispora | Tortispora caseinolytica
Synonym:Candida caseinolytica NRRL Y-17796
Ncbi Go to NCBI Taxonomy (767744)
Eol Encyclopedia of life
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Publication:
et. al. Right (2016)
Proc Natl Acad Sci U S A 113, 9882-9887. Down

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Cyberlindnera jadinii NRRL Y-1542

[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Phaffomycetaceae | Cyberlindnera | Cyberlindnera jadinii ]

Cyberlindnera_jadinii_NRRL_Y_1542 Picture Source
Taxonomy:Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Phaffomycetaceae | Cyberlindnera | Cyberlindnera jadinii
Anamorph:Candida utilis
Synonym:Pichia jadinii, Candida guilliermondii var. nitratophila, Hansenula jadinii, Torula utilis, Torulopsis utilis, Pichia jadinii (Candida utilis), Lindnera jadinii (misnomer)
Common:Torula yeast
Ncbi Go to NCBI Taxonomy (983966)
Eol Encyclopedia of life
Wiki Wikipedia
Publication:
et. al. Right (2016)
Proc Natl Acad Sci U S A 113, 9882-9887. Down

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Candida arabinofermentans NRRL YB-2248

[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Ogataea | Ogataea/Candida clade | [Candida] arabinofermentans ]

Candida_arabinofermentans_NRRL_YB_2248 Courtesy of Linda Barnett
Taxonomy:Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Pichiaceae | Ogataea | Ogataea/Candida clade | [Candida] arabinofermentans
Ncbi Go to NCBI Taxonomy (983967)
Eol Encyclopedia of life
Wiki Wikipedia
Publication:
et. al. Right (2016)
Proc Natl Acad Sci U S A 113, 9882-9887. Down

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Ogataea angusta NCYC 495 leu1.1

[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Pichiaceae | Ogataea | Ogataea angusta ]

Ogataea_angusta_NCYC_495_leu1_1 Picture Source
Taxonomy:Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Pichiaceae | Ogataea | Ogataea angusta
Synonym:Pichia angusta NCYC 495 leu1.1, Pichia angusta ATCC MYA-335
Ncbi Go to NCBI Taxonomy (638633)
Eol Encyclopedia of life
Wiki Wikipedia
Publication:
et. al. Right (2016)
Proc Natl Acad Sci U S A 113, 9882-9887. Down

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Metschnikowia bicuspidata var. bicuspidata NRRL YB-4993

[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Metschnikowia | Metschnikowia bicuspidata | Metschnikowia bicuspidata var. bicuspidata ]

Metschnikowia_bicuspidata_var__bicuspidata_NRRL_YB_4993 Courtesy of Andre Lachance
Taxonomy:Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Metschnikowiaceae | Metschnikowia | Metschnikowia bicuspidata | Metschnikowia bicuspidata var. bicuspidata
Ncbi Go to NCBI Taxonomy (869754)
Eol Encyclopedia of life
Wiki Wikipedia
Publication:
et. al. Right (2016)
Proc Natl Acad Sci U S A 113, 9882-9887. Down

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Hanseniaspora valbyensis NRRL Y-1626

[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Saccharomycodaceae | Hanseniaspora | Hanseniaspora valbyensis ]

Hanseniaspora_valbyensis_NRRL_Y_1626 Courtesy of Linda Barnett
Taxonomy:Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Saccharomycodaceae | Hanseniaspora | Hanseniaspora valbyensis
Ncbi Go to NCBI Taxonomy (766949)
Eol Encyclopedia of life
Wiki Wikipedia
Publication:
et. al. Right (2016)
Proc Natl Acad Sci U S A 113, 9882-9887. Down

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diArk 3.0 Content Info

Species:4998
References:153
Projects:7180
gen DNA Projects:3854
EST/cDNA Projects:849
Publications:1853
link to cymobase
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