Insight into the genome of Aspergillus fumigatus: Analysis of a 922 kb region encompassing the nitrate assimilation gene cluster

Arnab Pain; John Woodward; Michael A. Quail; Michael J. Anderson; Richard Clark; Matthew Collins; Nigel Fosker; Audrey Fraser; David Harris; Natasha Larke; Lee Murphy; Sean Humphray; Susan O'Neil; Mihaela Pertea; Claire Price; Ester Rabbinowitsch; Marie Adele Rajandream; Steven Salzberg; David Saunders; Kathy Seeger; Sarah Sharp; Tim Warren; David W. Denning; Bart Barrell; Neil Hall

doi:10.1016/j.fgb.2003.12.003

Insight into the genome of Aspergillus fumigatus: Analysis of a 922 kb region encompassing the nitrate assimilation gene cluster

Arnab Pain, John Woodward, Michael A. Quail, Michael J. Anderson, Richard Clark, Matthew Collins, Nigel Fosker, Audrey Fraser, David Harris, Natasha Larke, Lee Murphy, Sean Humphray, Susan O'Neil, Mihaela Pertea, Claire Price, Ester Rabbinowitsch, Marie Adele Rajandream, Steven Salzberg, David Saunders, Kathy SeegerSarah Sharp, Tim Warren, David W. Denning, Bart Barrell, Neil Hall^*

^*Corresponding author for this work

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

57 Scopus citations

Abstract

Aspergillus fumigatus is the most ubiquitous opportunistic filamentous fungal pathogen of human. As an initial step toward sequencing the entire genome of A. fumigatus, which is estimated to be ∼30Mb in size, we have sequenced a 922kb region, contained within 16 overlapping bacterial artificial chromosome (BAC) clones. Fifty-four percent of the DNA is predicted to be coding with 341 putative protein coding genes. Functional classification of the proteins showed the presence of a higher proportion of enzymes and membrane transporters when compared to those of Saccharomyces cerevisiae. In addition to the nitrate assimilation gene cluster, the quinate utilisation gene cluster is also present on this 922kb genomic sequence. We observed large scale synteny between A. fumigatus and Aspergillus nidulans by comparing this sequence to the A. nidulans genetic map of linkage group VIII.

Original language	English (US)
Pages (from-to)	443-453
Number of pages	11
Journal	Fungal Genetics and Biology
Volume	41
Issue number	4
DOIs	https://doi.org/10.1016/j.fgb.2003.12.003
State	Published - Apr 2004
Externally published	Yes

Bibliographical note

Funding Information:
We are indebted to Rod Warren for having the forethought to save the clinical isolate that was selected for sequencing and for providing extensive clinical details on this strain. Also thanks to Caroline Moore for susceptibility testing, to Stephan Bretagne for microsattelite typing, to David Geiser for his phylogenetic analysis, to Mike Bromley for providing the niaD gene sequence and to Jonathon Ross for performing the orthology analysis between A. fumigatus and A. nidulans. We are also indebted to the Wellcome Trust and the Fungal Research Trust for funding the work. We are grateful to Hubert Renauld for advice and corrections to the manuscript.

Keywords

Annotation
Aspergillus fumigatus
BAC-end sequencing
Comparative genomics
Gene-cluster
Genome
Synteny

ASJC Scopus subject areas

Microbiology
Genetics

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10.1016/j.fgb.2003.12.003

Cite this

Pain, A., Woodward, J., Quail, M. A., Anderson, M. J., Clark, R., Collins, M., Fosker, N., Fraser, A., Harris, D., Larke, N., Murphy, L., Humphray, S., O'Neil, S., Pertea, M., Price, C., Rabbinowitsch, E., Rajandream, M. A., Salzberg, S., Saunders, D., ... Hall, N. (2004). Insight into the genome of Aspergillus fumigatus: Analysis of a 922 kb region encompassing the nitrate assimilation gene cluster. Fungal Genetics and Biology, 41(4), 443-453. https://doi.org/10.1016/j.fgb.2003.12.003

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title = "Insight into the genome of Aspergillus fumigatus: Analysis of a 922 kb region encompassing the nitrate assimilation gene cluster",

abstract = "Aspergillus fumigatus is the most ubiquitous opportunistic filamentous fungal pathogen of human. As an initial step toward sequencing the entire genome of A. fumigatus, which is estimated to be ∼30Mb in size, we have sequenced a 922kb region, contained within 16 overlapping bacterial artificial chromosome (BAC) clones. Fifty-four percent of the DNA is predicted to be coding with 341 putative protein coding genes. Functional classification of the proteins showed the presence of a higher proportion of enzymes and membrane transporters when compared to those of Saccharomyces cerevisiae. In addition to the nitrate assimilation gene cluster, the quinate utilisation gene cluster is also present on this 922kb genomic sequence. We observed large scale synteny between A. fumigatus and Aspergillus nidulans by comparing this sequence to the A. nidulans genetic map of linkage group VIII.",

keywords = "Annotation, Aspergillus fumigatus, BAC-end sequencing, Comparative genomics, Gene-cluster, Genome, Synteny",

author = "Arnab Pain and John Woodward and Quail, \{Michael A.\} and Anderson, \{Michael J.\} and Richard Clark and Matthew Collins and Nigel Fosker and Audrey Fraser and David Harris and Natasha Larke and Lee Murphy and Sean Humphray and Susan O'Neil and Mihaela Pertea and Claire Price and Ester Rabbinowitsch and Rajandream, \{Marie Adele\} and Steven Salzberg and David Saunders and Kathy Seeger and Sarah Sharp and Tim Warren and Denning, \{David W.\} and Bart Barrell and Neil Hall",

note = "Funding Information: We are indebted to Rod Warren for having the forethought to save the clinical isolate that was selected for sequencing and for providing extensive clinical details on this strain. Also thanks to Caroline Moore for susceptibility testing, to Stephan Bretagne for microsattelite typing, to David Geiser for his phylogenetic analysis, to Mike Bromley for providing the niaD gene sequence and to Jonathon Ross for performing the orthology analysis between A. fumigatus and A. nidulans. We are also indebted to the Wellcome Trust and the Fungal Research Trust for funding the work. We are grateful to Hubert Renauld for advice and corrections to the manuscript.",

year = "2004",

month = apr,

doi = "10.1016/j.fgb.2003.12.003",

language = "English (US)",

volume = "41",

pages = "443--453",

journal = "Fungal Genetics and Biology",

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Pain, A, Woodward, J, Quail, MA, Anderson, MJ, Clark, R, Collins, M, Fosker, N, Fraser, A, Harris, D, Larke, N, Murphy, L, Humphray, S, O'Neil, S, Pertea, M, Price, C, Rabbinowitsch, E, Rajandream, MA, Salzberg, S, Saunders, D, Seeger, K, Sharp, S, Warren, T, Denning, DW, Barrell, B & Hall, N 2004, 'Insight into the genome of Aspergillus fumigatus: Analysis of a 922 kb region encompassing the nitrate assimilation gene cluster', Fungal Genetics and Biology, vol. 41, no. 4, pp. 443-453. https://doi.org/10.1016/j.fgb.2003.12.003

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T2 - Analysis of a 922 kb region encompassing the nitrate assimilation gene cluster

AU - Pain, Arnab

AU - Woodward, John

AU - Quail, Michael A.

AU - Anderson, Michael J.

AU - Clark, Richard

AU - Collins, Matthew

AU - Fosker, Nigel

AU - Fraser, Audrey

AU - Harris, David

AU - Larke, Natasha

AU - Murphy, Lee

AU - Humphray, Sean

AU - O'Neil, Susan

AU - Pertea, Mihaela

AU - Price, Claire

AU - Rabbinowitsch, Ester

AU - Rajandream, Marie Adele

AU - Salzberg, Steven

AU - Saunders, David

AU - Seeger, Kathy

AU - Sharp, Sarah

AU - Warren, Tim

AU - Denning, David W.

AU - Barrell, Bart

AU - Hall, Neil

N1 - Funding Information: We are indebted to Rod Warren for having the forethought to save the clinical isolate that was selected for sequencing and for providing extensive clinical details on this strain. Also thanks to Caroline Moore for susceptibility testing, to Stephan Bretagne for microsattelite typing, to David Geiser for his phylogenetic analysis, to Mike Bromley for providing the niaD gene sequence and to Jonathon Ross for performing the orthology analysis between A. fumigatus and A. nidulans. We are also indebted to the Wellcome Trust and the Fungal Research Trust for funding the work. We are grateful to Hubert Renauld for advice and corrections to the manuscript.

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KW - BAC-end sequencing

KW - Comparative genomics

KW - Gene-cluster

KW - Genome

KW - Synteny

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Insight into the genome of Aspergillus fumigatus: Analysis of a 922 kb region encompassing the nitrate assimilation gene cluster

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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