Publication details
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
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[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Taphrinomycotina incertae sedis | Saitoella | Saitoella complicata ]
Picture Source
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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 |
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Go to NCBI Taxonomy (698492) |
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Encyclopedia of life |
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Wikipedia |
Publications: |
Riley R, Haridas S, Wolfe KH et. al.
( 2016)
Proc Natl Acad Sci U S A 113, 9882-9887.
Yamauchi K, Kondo S, Hamamoto M et. al.
( 2015)
Genome Announc 3, e00220-15.
Nishida H, Hamamoto M, Sugiyama J
(2011)
J Gen Appl Microbiol 57, 243-246.
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Pichia membranifaciens NRRL Y-2026
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[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Pichiaceae | Pichia | Pichia membranifaciens ]
Courtesy of Thomas Jeffries
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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 |
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Go to NCBI Taxonomy (763406) |
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Encyclopedia of life |
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Wikipedia |
Publication: |
Riley R, Haridas S, Wolfe KH et. al.
( 2016)
Proc Natl Acad Sci U S A 113, 9882-9887.
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Wickerhamomyces anomalus NRRL Y-366-8
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[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Phaffomycetaceae | Wickerhamomyces | Wickerhamomyces anomalus ]
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Taxonomy: | Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Phaffomycetaceae | Wickerhamomyces | Wickerhamomyces anomalus |
Synonym: | Pichia anomala NRRL Y-366-8 |
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Go to NCBI Taxonomy (683960) |
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Encyclopedia of life |
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Wikipedia |
Publication: |
Riley R, Haridas S, Wolfe KH et. al.
( 2016)
Proc Natl Acad Sci U S A 113, 9882-9887.
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Nadsonia fulvescens var. elongata DSM 6958
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[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Nadsonia | Nadsonia fulvescens | Nadsonia fulvescens var. elongata ]
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Taxonomy: | Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Saccharomycetales incertae sedis | Nadsonia | Nadsonia fulvescens | Nadsonia fulvescens var. elongata |
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Go to NCBI Taxonomy (857566) |
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Encyclopedia of life |
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Wikipedia |
Publication: |
Riley R, Haridas S, Wolfe KH et. al.
( 2016)
Proc Natl Acad Sci U S A 113, 9882-9887.
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Babjeviella inositovora NRRL Y-12698
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[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Debaryomycetaceae | Babjeviella | Babjeviella inositovora ]
Courtesy of Linda Barnett
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Taxonomy: | Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Debaryomycetaceae | Babjeviella | Babjeviella inositovora |
Synonym: | Pichia inositovora, Yamadazyma inositovora |
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Go to NCBI Taxonomy (984486) |
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Encyclopedia of life |
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Wikipedia |
Publication: |
Riley R, Haridas S, Wolfe KH et. al.
( 2016)
Proc Natl Acad Sci U S A 113, 9882-9887.
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Pachysolen tannophilus NRRL Y-2460
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[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Saccharomycetaceae | Pachysolen | Pachysolen tannophilus ]
Courtesy of Linda Barnett
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Publications: |
Riley R, Haridas S, Wolfe KH et. al.
( 2016)
Proc Natl Acad Sci U S A 113, 9882-9887.
Liu X, Kaas RS, Jensen PR et. al.
( 2012)
Eukaryot Cell 11, 827.
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Lipomyces starkeyi NRRL Y-11557
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[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Lipomycetaceae | Lipomyces | Lipomyces starkeyi ]
Hyphopichia burtonii NRRL Y-1933
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[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Debaryomycetaceae | Hyphopichia | Hyphopichia burtonii ]
Ascoidea rubescens DSM 1968
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[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Ascoideaceae | Ascoidea | Ascoidea rubescens ]
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Publication: |
Riley R, Haridas S, Wolfe KH et. al.
( 2016)
Proc Natl Acad Sci U S A 113, 9882-9887.
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Candida tanzawaensis NRRL Y-17324
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[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Debaryomycetaceae | Suhomyces | Suhomyces tanzawaensis ]
Tortispora caseinolytica NRRL Y-17796
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[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Trigonopsidaceae | Tortispora | Tortispora caseinolytica ]
Courtesy of Linda Barnett
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Taxonomy: | Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Trigonopsidaceae | Tortispora | Tortispora caseinolytica |
Synonym: | Candida caseinolytica NRRL Y-17796 |
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Go to NCBI Taxonomy (767744) |
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Encyclopedia of life |
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Wikipedia |
Publication: |
Riley R, Haridas S, Wolfe KH et. al.
( 2016)
Proc Natl Acad Sci U S A 113, 9882-9887.
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Cyberlindnera jadinii NRRL Y-1542
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[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Phaffomycetaceae | Cyberlindnera | Cyberlindnera jadinii ]
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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 |
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Go to NCBI Taxonomy (983966) |
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Encyclopedia of life |
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Wikipedia |
Publication: |
Riley R, Haridas S, Wolfe KH et. al.
( 2016)
Proc Natl Acad Sci U S A 113, 9882-9887.
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Candida arabinofermentans NRRL YB-2248
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[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Ogataea | Ogataea/Candida clade | [Candida] arabinofermentans ]
Ogataea angusta NCYC 495 leu1.1
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[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Pichiaceae | Ogataea | Ogataea polymorpha ]
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Taxonomy: | Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Pichiaceae | Ogataea | Ogataea polymorpha |
Synonym: | Pichia angusta NCYC 495 leu1.1, Pichia angusta ATCC MYA-335 |
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Go to NCBI Taxonomy (638633) |
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Encyclopedia of life |
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Wikipedia |
Publication: |
Riley R, Haridas S, Wolfe KH et. al.
( 2016)
Proc Natl Acad Sci U S A 113, 9882-9887.
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Metschnikowia bicuspidata var. bicuspidata NRRL YB-4993
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[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Metschnikowia | Metschnikowia bicuspidata | Metschnikowia bicuspidata var. bicuspidata ]
Courtesy of Andre Lachance
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Taxonomy: | Eukaryota | Opisthokonta | Fungi | Dikarya | Ascomycota | saccharomyceta | Saccharomycotina | Saccharomycetes | Saccharomycetales | Metschnikowiaceae | Metschnikowia | Metschnikowia bicuspidata | Metschnikowia bicuspidata var. bicuspidata |
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Go to NCBI Taxonomy (869754) |
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Encyclopedia of life |
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Wikipedia |
Publication: |
Riley R, Haridas S, Wolfe KH et. al.
( 2016)
Proc Natl Acad Sci U S A 113, 9882-9887.
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Hanseniaspora valbyensis NRRL Y-1626
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[ Opisthokonta | Fungi | Dikarya | . . .
. . . | Saccharomycodaceae | Hanseniaspora | Hanseniaspora valbyensis ]