Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

James E. Galagan; Sarah E. Calvo; Christina Cuomo; Li Jun Ma; Jennifer R. Wortman; Serafim Batzoglou; Su In Lee; Meray Baştürkmen; Christina C. Spevak; John Clutterbuck; Vladimir Kapitonov; Jerzy Jurka; Claudio Scazzocchio; Mark Farman; Jonathan Butler; Seth Purcell; Steve Harris; Gerhard H. Braus; Oliver Draht; Silke Busch; Christophe D'Enfert; Christiane Bouchier; Gustavo H. Goldman; Deborah Bell-Pedersen; Sam Griffiths-Jones; John H. Doonan; Jaehyuk Yu; Kay Vienken; Arnab Pain; Michael Freitag; Eric U. Selker; David B. Archer; Miguel Á Peñalva; Berl R. Oakley; Michelle Momany; Toshihiro Tanaka; Toshitaka Kumagai; Kiyoshi Asai; Masayuki Machida; William C. Nierman; David W. Denning; Mark Caddick; Michael Hynes; Mathieu Paoletti; Reinhard Fischer; Bruce Miller; Paul Dyer; Matthew S. Sachs; Stephen A. Osmani; Bruce W. Birren

doi:10.1038/nature04341

Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

James E. Galagan^*, Sarah E. Calvo, Christina Cuomo, Li Jun Ma, Jennifer R. Wortman, Serafim Batzoglou, Su In Lee, Meray Baştürkmen, Christina C. Spevak, John Clutterbuck, Vladimir Kapitonov, Jerzy Jurka, Claudio Scazzocchio, Mark Farman, Jonathan Butler, Seth Purcell, Steve Harris, Gerhard H. Braus, Oliver Draht, Silke BuschChristophe D'Enfert, Christiane Bouchier, Gustavo H. Goldman, Deborah Bell-Pedersen, Sam Griffiths-Jones, John H. Doonan, Jaehyuk Yu, Kay Vienken, Arnab Pain, Michael Freitag, Eric U. Selker, David B. Archer, Miguel Á Peñalva, Berl R. Oakley, Michelle Momany, Toshihiro Tanaka, Toshitaka Kumagai, Kiyoshi Asai, Masayuki Machida, William C. Nierman, David W. Denning, Mark Caddick, Michael Hynes, Mathieu Paoletti, Reinhard Fischer, Bruce Miller, Paul Dyer, Matthew S. Sachs, Stephen A. Osmani, Bruce W. Birren

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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Abstract

The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a comparative study with Aspergillus fumigatus, a serious humaloven pathogen, and Aspergillus oryzae, used in the production of sake, miso and soy sauce. Our analysis of genome structure provided a quantitative evaluation of forces driving long-term eukaryotic genome evolution. It also led to an experimentally validated model of mating-type locus evolution, suggesting the potential for sexual reproduction in A. fumigatus and A. oryzae. Our analysis of sequence conservation revealed over 5,000 non-coding regions actively conserved across all three species. Within these regions, we identified potential functional elements including a previously uncharacterized TPP riboswitch and motifs suggesting regulation in filamentous fungi by Puf family genes. We further obtained comparative and experimental evidence indicating widespread translational regulation by upstream open reading frames. These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation.

Original language	English (US)
Pages (from-to)	1105-1115
Number of pages	11
Journal	NATURE
Volume	438
Issue number	7071
DOIs	https://doi.org/10.1038/nature04341
State	Published - Dec 22 2005
Externally published	Yes

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Galagan, J. E., Calvo, S. E., Cuomo, C., Ma, L. J., Wortman, J. R., Batzoglou, S., Lee, S. I., Baştürkmen, M., Spevak, C. C., Clutterbuck, J., Kapitonov, V., Jurka, J., Scazzocchio, C., Farman, M., Butler, J., Purcell, S., Harris, S., Braus, G. H., Draht, O., ... Birren, B. W. (2005). Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. NATURE, 438(7071), 1105-1115. https://doi.org/10.1038/nature04341

@article{e0bd4c40331f4df9a5d367541b322509,

title = "Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae",

abstract = "The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a comparative study with Aspergillus fumigatus, a serious humaloven pathogen, and Aspergillus oryzae, used in the production of sake, miso and soy sauce. Our analysis of genome structure provided a quantitative evaluation of forces driving long-term eukaryotic genome evolution. It also led to an experimentally validated model of mating-type locus evolution, suggesting the potential for sexual reproduction in A. fumigatus and A. oryzae. Our analysis of sequence conservation revealed over 5,000 non-coding regions actively conserved across all three species. Within these regions, we identified potential functional elements including a previously uncharacterized TPP riboswitch and motifs suggesting regulation in filamentous fungi by Puf family genes. We further obtained comparative and experimental evidence indicating widespread translational regulation by upstream open reading frames. These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation.",

author = "Galagan, {James E.} and Calvo, {Sarah E.} and Christina Cuomo and Ma, {Li Jun} and Wortman, {Jennifer R.} and Serafim Batzoglou and Lee, {Su In} and Meray Ba{\c s}t{\"u}rkmen and Spevak, {Christina C.} and John Clutterbuck and Vladimir Kapitonov and Jerzy Jurka and Claudio Scazzocchio and Mark Farman and Jonathan Butler and Seth Purcell and Steve Harris and Braus, {Gerhard H.} and Oliver Draht and Silke Busch and Christophe D'Enfert and Christiane Bouchier and Goldman, {Gustavo H.} and Deborah Bell-Pedersen and Sam Griffiths-Jones and Doonan, {John H.} and Jaehyuk Yu and Kay Vienken and Arnab Pain and Michael Freitag and Selker, {Eric U.} and Archer, {David B.} and Pe{\~n}alva, {Miguel {\'A}} and Oakley, {Berl R.} and Michelle Momany and Toshihiro Tanaka and Toshitaka Kumagai and Kiyoshi Asai and Masayuki Machida and Nierman, {William C.} and Denning, {David W.} and Mark Caddick and Michael Hynes and Mathieu Paoletti and Reinhard Fischer and Bruce Miller and Paul Dyer and Sachs, {Matthew S.} and Osmani, {Stephen A.} and Birren, {Bruce W.}",

note = "Funding Information: Acknowledgements The authors would like to thank M. Zody, X. Xie, M. Kellis, M. Kamal, J. Taylor, G. Turgeon and E. Lander for numerous helpful conversations, comments and critical readings of the paper. We also thank all members of the sequencing platform at the Broad Institute. We thank R. Dean for providing the BAC library used in sequencing. We especially thank M. Brudno for his help in using Mlagan to align the three genomes, and R. Morris for his many contributions to the A. nidulans sequencing project and subsequent analyses. This work was supported in part by grants from the NIH, as well as the NIH Research Supplement for Underrepresented Minorities, the DFG, the CMPB and the BBSRC.",

year = "2005",

month = dec,

day = "22",

doi = "10.1038/nature04341",

language = "English (US)",

volume = "438",

pages = "1105--1115",

journal = "NATURE",

issn = "0028-0836",

publisher = "Nature Research",

number = "7071",

}

Galagan, JE, Calvo, SE, Cuomo, C, Ma, LJ, Wortman, JR, Batzoglou, S, Lee, SI, Baştürkmen, M, Spevak, CC, Clutterbuck, J, Kapitonov, V, Jurka, J, Scazzocchio, C, Farman, M, Butler, J, Purcell, S, Harris, S, Braus, GH, Draht, O, Busch, S, D'Enfert, C, Bouchier, C, Goldman, GH, Bell-Pedersen, D, Griffiths-Jones, S, Doonan, JH, Yu, J, Vienken, K, Pain, A, Freitag, M, Selker, EU, Archer, DB, Peñalva, MÁ, Oakley, BR, Momany, M, Tanaka, T, Kumagai, T, Asai, K, Machida, M, Nierman, WC, Denning, DW, Caddick, M, Hynes, M, Paoletti, M, Fischer, R, Miller, B, Dyer, P, Sachs, MS, Osmani, SA & Birren, BW 2005, 'Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae', NATURE, vol. 438, no. 7071, pp. 1105-1115. https://doi.org/10.1038/nature04341

TY - JOUR

T1 - Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

AU - Galagan, James E.

AU - Calvo, Sarah E.

AU - Cuomo, Christina

AU - Ma, Li Jun

AU - Wortman, Jennifer R.

AU - Batzoglou, Serafim

AU - Lee, Su In

AU - Baştürkmen, Meray

AU - Spevak, Christina C.

AU - Clutterbuck, John

AU - Kapitonov, Vladimir

AU - Jurka, Jerzy

AU - Scazzocchio, Claudio

AU - Farman, Mark

AU - Butler, Jonathan

AU - Purcell, Seth

AU - Harris, Steve

AU - Braus, Gerhard H.

AU - Draht, Oliver

AU - Busch, Silke

AU - D'Enfert, Christophe

AU - Bouchier, Christiane

AU - Goldman, Gustavo H.

AU - Bell-Pedersen, Deborah

AU - Griffiths-Jones, Sam

AU - Doonan, John H.

AU - Yu, Jaehyuk

AU - Vienken, Kay

AU - Pain, Arnab

AU - Freitag, Michael

AU - Selker, Eric U.

AU - Archer, David B.

AU - Peñalva, Miguel Á

AU - Oakley, Berl R.

AU - Momany, Michelle

AU - Tanaka, Toshihiro

AU - Kumagai, Toshitaka

AU - Asai, Kiyoshi

AU - Machida, Masayuki

AU - Nierman, William C.

AU - Denning, David W.

AU - Caddick, Mark

AU - Hynes, Michael

AU - Paoletti, Mathieu

AU - Fischer, Reinhard

AU - Miller, Bruce

AU - Dyer, Paul

AU - Sachs, Matthew S.

AU - Osmani, Stephen A.

AU - Birren, Bruce W.

N1 - Funding Information: Acknowledgements The authors would like to thank M. Zody, X. Xie, M. Kellis, M. Kamal, J. Taylor, G. Turgeon and E. Lander for numerous helpful conversations, comments and critical readings of the paper. We also thank all members of the sequencing platform at the Broad Institute. We thank R. Dean for providing the BAC library used in sequencing. We especially thank M. Brudno for his help in using Mlagan to align the three genomes, and R. Morris for his many contributions to the A. nidulans sequencing project and subsequent analyses. This work was supported in part by grants from the NIH, as well as the NIH Research Supplement for Underrepresented Minorities, the DFG, the CMPB and the BBSRC.

PY - 2005/12/22

Y1 - 2005/12/22

N2 - The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a comparative study with Aspergillus fumigatus, a serious humaloven pathogen, and Aspergillus oryzae, used in the production of sake, miso and soy sauce. Our analysis of genome structure provided a quantitative evaluation of forces driving long-term eukaryotic genome evolution. It also led to an experimentally validated model of mating-type locus evolution, suggesting the potential for sexual reproduction in A. fumigatus and A. oryzae. Our analysis of sequence conservation revealed over 5,000 non-coding regions actively conserved across all three species. Within these regions, we identified potential functional elements including a previously uncharacterized TPP riboswitch and motifs suggesting regulation in filamentous fungi by Puf family genes. We further obtained comparative and experimental evidence indicating widespread translational regulation by upstream open reading frames. These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation.

AB - The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a comparative study with Aspergillus fumigatus, a serious humaloven pathogen, and Aspergillus oryzae, used in the production of sake, miso and soy sauce. Our analysis of genome structure provided a quantitative evaluation of forces driving long-term eukaryotic genome evolution. It also led to an experimentally validated model of mating-type locus evolution, suggesting the potential for sexual reproduction in A. fumigatus and A. oryzae. Our analysis of sequence conservation revealed over 5,000 non-coding regions actively conserved across all three species. Within these regions, we identified potential functional elements including a previously uncharacterized TPP riboswitch and motifs suggesting regulation in filamentous fungi by Puf family genes. We further obtained comparative and experimental evidence indicating widespread translational regulation by upstream open reading frames. These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation.

UR - http://www.scopus.com/inward/record.url?scp=28844461287&partnerID=8YFLogxK

U2 - 10.1038/nature04341

DO - 10.1038/nature04341

M3 - Article

C2 - 16372000

AN - SCOPUS:28844461287

SN - 0028-0836

VL - 438

SP - 1105

EP - 1115

JO - NATURE

JF - NATURE

IS - 7071

ER -

Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

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