Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

William C. Nierman; Arnab Pain; Michael J. Anderson; Jennifer R. Wortman; H. Stanley Kim; Javier Arroyo; Matthew Berriman; Keietsu Abe; David B. Archer; Clara Bermejo; Joan Bennett; Paul Bowyer; Dan Chen; Matthew Collins; Richard Coulsen; Robert Davies; Paul S. Dyer; Mark Farman; Nadia Fedorova; Natalie Fedorova; Tamara V. Feldblyum; Reinhard Fischer; Nigel Fosker; Audrey Fraser; Jose L. García; Maria J. García; Ariette Goble; Gustavo H. Goldman; Katsuya Gomi; Sam Griffith-Jones; Ryan Gwilliam; Brian Haas; Hubertus Haas; David Harris; H. Horiuchi; Jiaqi Huang; Sean Humphray; Javier Jiménez; Nancy Keller; Hoda Khouri; Katsuhiko Kitamoto; Tetsuo Kobayashi; Sven Konzack; Resham Kulkarni; Toshitaka Kumagai; Anne Lafton; Jean Paul Latgé; Weixi Li; Angela Lord; Charles Lu; William H. Majoros; Gregory S. May; Bruce L. Miller; Yasmin Mohamoud; Maria Molina; Michel Monod; Isabelle Mouyna; Stephanie Mulligan; Lee Murphy; Susan O'Neil; Ian Paulsen; Miguel A. Peñalva; Mihaela Pertea; Claire Price; Bethan L. Pritchard; Michael A. Quail; Ester Rabbinowitsch; Neil Rawlins; Marie Adele Rajandream; Utz Reichard; Hubert Renauld; Geoffrey D. Robson; Santiago Rodriguez De Cordoba; Jose M. Rodríguez-Peña; Catherine M. Ronning; Simon Rutter; Steven L. Salzberg; Miguel Sanchez; Juan C. Sánchez-Ferrero; David Saunders; Kathy Seeger; Rob Squares; Steven Squares; Michio Takeuchi; Fredj Tekaia; Geoffrey Turner; Carlos R. Vazquez De Aldana; Janice Weidman; Owen White; John Woodward; Jae Hyuk Yu; Claire Fraser; James E. Galagan; Kiyoshi Asai; Masayuki Machida; Neil Hall; Bart Barrell; David W. Denning

doi:10.1038/nature04332

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

William C. Nierman, Arnab Pain, Michael J. Anderson, Jennifer R. Wortman, H. Stanley Kim, Javier Arroyo, Matthew Berriman, Keietsu Abe, David B. Archer, Clara Bermejo, Joan Bennett, Paul Bowyer, Dan Chen, Matthew Collins, Richard Coulsen, Robert Davies, Paul S. Dyer, Mark Farman, Nadia Fedorova, Natalie FedorovaTamara V. Feldblyum, Reinhard Fischer, Nigel Fosker, Audrey Fraser, Jose L. García, Maria J. García, Ariette Goble, Gustavo H. Goldman, Katsuya Gomi, Sam Griffith-Jones, Ryan Gwilliam, Brian Haas, Hubertus Haas, David Harris, H. Horiuchi, Jiaqi Huang, Sean Humphray, Javier Jiménez, Nancy Keller, Hoda Khouri, Katsuhiko Kitamoto, Tetsuo Kobayashi, Sven Konzack, Resham Kulkarni, Toshitaka Kumagai, Anne Lafton, Jean Paul Latgé, Weixi Li, Angela Lord, Charles Lu, William H. Majoros, Gregory S. May, Bruce L. Miller, Yasmin Mohamoud, Maria Molina, Michel Monod, Isabelle Mouyna, Stephanie Mulligan, Lee Murphy, Susan O'Neil, Ian Paulsen, Miguel A. Peñalva, Mihaela Pertea, Claire Price, Bethan L. Pritchard, Michael A. Quail, Ester Rabbinowitsch, Neil Rawlins, Marie Adele Rajandream, Utz Reichard, Hubert Renauld, Geoffrey D. Robson, Santiago Rodriguez De Cordoba, Jose M. Rodríguez-Peña, Catherine M. Ronning, Simon Rutter, Steven L. Salzberg, Miguel Sanchez, Juan C. Sánchez-Ferrero, David Saunders, Kathy Seeger, Rob Squares, Steven Squares, Michio Takeuchi, Fredj Tekaia, Geoffrey Turner, Carlos R. Vazquez De Aldana, Janice Weidman, Owen White, John Woodward, Jae Hyuk Yu, Claire Fraser, James E. Galagan, Kiyoshi Asai, Masayuki Machida, Neil Hall, Bart Barrell, David W. Denning

Laboratory Medicine

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

1146 Scopus citations

Abstract

Aspergillus fumigatus is exceptional among microorganisms in being both a primary and opportunistic pathogen as well as a major allergen^1-3. Its conidia production is prolific, and so human respiratory tract exposure is almost constant⁴. A. fumigatus is isolated from human habitats ⁵ and vegetable compost heaps^6,7. In immunocompromised individuals, the incidence of invasive infection can be as high as 50% and the mortality rate is often about 50% (ref. 2). The interaction of A. fumigatus and other airborne fungi with the immune system is increasingly linked to severe asthma and sinusitis⁸. Although the burden of invasive disease caused by A. fumigatus is substantial, the basic biology of the organism is mostly obscure. Here we show the complete 29.4-megabase genome sequence of the clinical isolate Af293, which consists of eight chromosomes containing 9,926 predicted genes. Microarray analysis revealed temperature-dependent expression of distinct sets of genes, as well as 700 A. fumigatus genes not present or significantly diverged in the closely related sexual species Neosartorya fischeri, many of which may have roles in the pathogenicity phenotype. The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus.

Original language	English (US)
Pages (from-to)	1151-1156
Number of pages	6
Journal	Nature
Volume	438
Issue number	7071
DOIs	https://doi.org/10.1038/nature04332
State	Published - Dec 22 2005

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Nierman, W. C., Pain, A., Anderson, M. J., Wortman, J. R., Kim, H. S., Arroyo, J., Berriman, M., Abe, K., Archer, D. B., Bermejo, C., Bennett, J., Bowyer, P., Chen, D., Collins, M., Coulsen, R., Davies, R., Dyer, P. S., Farman, M., Fedorova, N., ... Denning, D. W. (2005). Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature, 438(7071), 1151-1156. https://doi.org/10.1038/nature04332

Nierman, WC, Pain, A, Anderson, MJ, Wortman, JR, Kim, HS, Arroyo, J, Berriman, M, Abe, K, Archer, DB, Bermejo, C, Bennett, J, Bowyer, P, Chen, D, Collins, M, Coulsen, R, Davies, R, Dyer, PS, Farman, M, Fedorova, N, Fedorova, N, Feldblyum, TV, Fischer, R, Fosker, N, Fraser, A, García, JL, García, MJ, Goble, A, Goldman, GH, Gomi, K, Griffith-Jones, S, Gwilliam, R, Haas, B, Haas, H, Harris, D, Horiuchi, H, Huang, J, Humphray, S, Jiménez, J, Keller, N, Khouri, H, Kitamoto, K, Kobayashi, T, Konzack, S, Kulkarni, R, Kumagai, T, Lafton, A, Latgé, JP, Li, W, Lord, A, Lu, C, Majoros, WH, May, GS, Miller, BL, Mohamoud, Y, Molina, M, Monod, M, Mouyna, I, Mulligan, S, Murphy, L, O'Neil, S, Paulsen, I, Peñalva, MA, Pertea, M, Price, C, Pritchard, BL, Quail, MA, Rabbinowitsch, E, Rawlins, N, Rajandream, MA, Reichard, U, Renauld, H, Robson, GD, Rodriguez De Cordoba, S, Rodríguez-Peña, JM, Ronning, CM, Rutter, S, Salzberg, SL, Sanchez, M, Sánchez-Ferrero, JC, Saunders, D, Seeger, K, Squares, R, Squares, S, Takeuchi, M, Tekaia, F, Turner, G, Vazquez De Aldana, CR, Weidman, J, White, O, Woodward, J, Yu, JH, Fraser, C, Galagan, JE, Asai, K, Machida, M, Hall, N, Barrell, B & Denning, DW 2005, 'Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus', Nature, vol. 438, no. 7071, pp. 1151-1156. https://doi.org/10.1038/nature04332

@article{2fd08b4e9f2d47ce987dd835ec1bf868,

title = "Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus",

abstract = "Aspergillus fumigatus is exceptional among microorganisms in being both a primary and opportunistic pathogen as well as a major allergen1-3. Its conidia production is prolific, and so human respiratory tract exposure is almost constant4. A. fumigatus is isolated from human habitats 5 and vegetable compost heaps6,7. In immunocompromised individuals, the incidence of invasive infection can be as high as 50% and the mortality rate is often about 50% (ref. 2). The interaction of A. fumigatus and other airborne fungi with the immune system is increasingly linked to severe asthma and sinusitis8. Although the burden of invasive disease caused by A. fumigatus is substantial, the basic biology of the organism is mostly obscure. Here we show the complete 29.4-megabase genome sequence of the clinical isolate Af293, which consists of eight chromosomes containing 9,926 predicted genes. Microarray analysis revealed temperature-dependent expression of distinct sets of genes, as well as 700 A. fumigatus genes not present or significantly diverged in the closely related sexual species Neosartorya fischeri, many of which may have roles in the pathogenicity phenotype. The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus.",

author = "Nierman, {William C.} and Arnab Pain and Anderson, {Michael J.} and Wortman, {Jennifer R.} and Kim, {H. Stanley} and Javier Arroyo and Matthew Berriman and Keietsu Abe and Archer, {David B.} and Clara Bermejo and Joan Bennett and Paul Bowyer and Dan Chen and Matthew Collins and Richard Coulsen and Robert Davies and Dyer, {Paul S.} and Mark Farman and Nadia Fedorova and Natalie Fedorova and Feldblyum, {Tamara V.} and Reinhard Fischer and Nigel Fosker and Audrey Fraser and Garc{\'i}a, {Jose L.} and Garc{\'i}a, {Maria J.} and Ariette Goble and Goldman, {Gustavo H.} and Katsuya Gomi and Sam Griffith-Jones and Ryan Gwilliam and Brian Haas and Hubertus Haas and David Harris and H. Horiuchi and Jiaqi Huang and Sean Humphray and Javier Jim{\'e}nez and Nancy Keller and Hoda Khouri and Katsuhiko Kitamoto and Tetsuo Kobayashi and Sven Konzack and Resham Kulkarni and Toshitaka Kumagai and Anne Lafton and Latg{\'e}, {Jean Paul} and Weixi Li and Angela Lord and Charles Lu and Majoros, {William H.} and May, {Gregory S.} and Miller, {Bruce L.} and Yasmin Mohamoud and Maria Molina and Michel Monod and Isabelle Mouyna and Stephanie Mulligan and Lee Murphy and Susan O'Neil and Ian Paulsen and Pe{\~n}alva, {Miguel A.} and Mihaela Pertea and Claire Price and Pritchard, {Bethan L.} and Quail, {Michael A.} and Ester Rabbinowitsch and Neil Rawlins and Rajandream, {Marie Adele} and Utz Reichard and Hubert Renauld and Robson, {Geoffrey D.} and {Rodriguez De Cordoba}, Santiago and Rodr{\'i}guez-Pe{\~n}a, {Jose M.} and Ronning, {Catherine M.} and Simon Rutter and Salzberg, {Steven L.} and Miguel Sanchez and S{\'a}nchez-Ferrero, {Juan C.} and David Saunders and Kathy Seeger and Rob Squares and Steven Squares and Michio Takeuchi and Fredj Tekaia and Geoffrey Turner and {Vazquez De Aldana}, {Carlos R.} and Janice Weidman and Owen White and John Woodward and Yu, {Jae Hyuk} and Claire Fraser and Galagan, {James E.} and Kiyoshi Asai and Masayuki Machida and Neil Hall and Bart Barrell and Denning, {David W.}",

note = "Funding Information: Acknowledgements Initial work was funded by the Fungal Research Trust and Burroughs Wellcome Fund. Major funding came from the National Institute of Allergy and Infectious Diseases (NIAID), the Wellcome Trust and the Fondo de Investigaciones Sanitarias. Construction of the Af293 microarray was funded by NIAID. Additional BAC end sequencing was funded internally by the Institut Pasteur. We thank D. Dixon, C. Caulcott, V. McGovern, P. Goodwin and J.-L. Rodriguez-Tudela for their support and encouragement during this project. We also thank C. Staben of the University of Kentucky for intellectual assistance and script development.",

year = "2005",

month = dec,

day = "22",

doi = "10.1038/nature04332",

language = "English (US)",

volume = "438",

pages = "1151--1156",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

number = "7071",

}

TY - JOUR

T1 - Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

AU - Nierman, William C.

AU - Pain, Arnab

AU - Anderson, Michael J.

AU - Wortman, Jennifer R.

AU - Kim, H. Stanley

AU - Arroyo, Javier

AU - Berriman, Matthew

AU - Abe, Keietsu

AU - Archer, David B.

AU - Bermejo, Clara

AU - Bennett, Joan

AU - Bowyer, Paul

AU - Chen, Dan

AU - Collins, Matthew

AU - Coulsen, Richard

AU - Davies, Robert

AU - Dyer, Paul S.

AU - Farman, Mark

AU - Fedorova, Nadia

AU - Fedorova, Natalie

AU - Feldblyum, Tamara V.

AU - Fischer, Reinhard

AU - Fosker, Nigel

AU - Fraser, Audrey

AU - García, Jose L.

AU - García, Maria J.

AU - Goble, Ariette

AU - Goldman, Gustavo H.

AU - Gomi, Katsuya

AU - Griffith-Jones, Sam

AU - Gwilliam, Ryan

AU - Haas, Brian

AU - Haas, Hubertus

AU - Harris, David

AU - Horiuchi, H.

AU - Huang, Jiaqi

AU - Humphray, Sean

AU - Jiménez, Javier

AU - Keller, Nancy

AU - Khouri, Hoda

AU - Kitamoto, Katsuhiko

AU - Kobayashi, Tetsuo

AU - Konzack, Sven

AU - Kulkarni, Resham

AU - Kumagai, Toshitaka

AU - Lafton, Anne

AU - Latgé, Jean Paul

AU - Li, Weixi

AU - Lord, Angela

AU - Lu, Charles

AU - Majoros, William H.

AU - May, Gregory S.

AU - Miller, Bruce L.

AU - Mohamoud, Yasmin

AU - Molina, Maria

AU - Monod, Michel

AU - Mouyna, Isabelle

AU - Mulligan, Stephanie

AU - Murphy, Lee

AU - O'Neil, Susan

AU - Paulsen, Ian

AU - Peñalva, Miguel A.

AU - Pertea, Mihaela

AU - Price, Claire

AU - Pritchard, Bethan L.

AU - Quail, Michael A.

AU - Rabbinowitsch, Ester

AU - Rawlins, Neil

AU - Rajandream, Marie Adele

AU - Reichard, Utz

AU - Renauld, Hubert

AU - Robson, Geoffrey D.

AU - Rodriguez De Cordoba, Santiago

AU - Rodríguez-Peña, Jose M.

AU - Ronning, Catherine M.

AU - Rutter, Simon

AU - Salzberg, Steven L.

AU - Sanchez, Miguel

AU - Sánchez-Ferrero, Juan C.

AU - Saunders, David

AU - Seeger, Kathy

AU - Squares, Rob

AU - Squares, Steven

AU - Takeuchi, Michio

AU - Tekaia, Fredj

AU - Turner, Geoffrey

AU - Vazquez De Aldana, Carlos R.

AU - Weidman, Janice

AU - White, Owen

AU - Woodward, John

AU - Yu, Jae Hyuk

AU - Fraser, Claire

AU - Galagan, James E.

AU - Asai, Kiyoshi

AU - Machida, Masayuki

AU - Hall, Neil

AU - Barrell, Bart

AU - Denning, David W.

N1 - Funding Information: Acknowledgements Initial work was funded by the Fungal Research Trust and Burroughs Wellcome Fund. Major funding came from the National Institute of Allergy and Infectious Diseases (NIAID), the Wellcome Trust and the Fondo de Investigaciones Sanitarias. Construction of the Af293 microarray was funded by NIAID. Additional BAC end sequencing was funded internally by the Institut Pasteur. We thank D. Dixon, C. Caulcott, V. McGovern, P. Goodwin and J.-L. Rodriguez-Tudela for their support and encouragement during this project. We also thank C. Staben of the University of Kentucky for intellectual assistance and script development.

PY - 2005/12/22

Y1 - 2005/12/22

N2 - Aspergillus fumigatus is exceptional among microorganisms in being both a primary and opportunistic pathogen as well as a major allergen1-3. Its conidia production is prolific, and so human respiratory tract exposure is almost constant4. A. fumigatus is isolated from human habitats 5 and vegetable compost heaps6,7. In immunocompromised individuals, the incidence of invasive infection can be as high as 50% and the mortality rate is often about 50% (ref. 2). The interaction of A. fumigatus and other airborne fungi with the immune system is increasingly linked to severe asthma and sinusitis8. Although the burden of invasive disease caused by A. fumigatus is substantial, the basic biology of the organism is mostly obscure. Here we show the complete 29.4-megabase genome sequence of the clinical isolate Af293, which consists of eight chromosomes containing 9,926 predicted genes. Microarray analysis revealed temperature-dependent expression of distinct sets of genes, as well as 700 A. fumigatus genes not present or significantly diverged in the closely related sexual species Neosartorya fischeri, many of which may have roles in the pathogenicity phenotype. The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus.

AB - Aspergillus fumigatus is exceptional among microorganisms in being both a primary and opportunistic pathogen as well as a major allergen1-3. Its conidia production is prolific, and so human respiratory tract exposure is almost constant4. A. fumigatus is isolated from human habitats 5 and vegetable compost heaps6,7. In immunocompromised individuals, the incidence of invasive infection can be as high as 50% and the mortality rate is often about 50% (ref. 2). The interaction of A. fumigatus and other airborne fungi with the immune system is increasingly linked to severe asthma and sinusitis8. Although the burden of invasive disease caused by A. fumigatus is substantial, the basic biology of the organism is mostly obscure. Here we show the complete 29.4-megabase genome sequence of the clinical isolate Af293, which consists of eight chromosomes containing 9,926 predicted genes. Microarray analysis revealed temperature-dependent expression of distinct sets of genes, as well as 700 A. fumigatus genes not present or significantly diverged in the closely related sexual species Neosartorya fischeri, many of which may have roles in the pathogenicity phenotype. The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus.

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UR - http://www.scopus.com/inward/citedby.url?scp=28644434509&partnerID=8YFLogxK

U2 - 10.1038/nature04332

DO - 10.1038/nature04332

M3 - Article

C2 - 16372009

AN - SCOPUS:28644434509

SN - 0028-0836

VL - 438

SP - 1151

EP - 1156

JO - Nature

JF - Nature

IS - 7071

ER -

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

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