title: Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus.
abstract: We present the genome sequences of a new clinical isolate of the important human pathogen, Aspergillus fumigatus, A1163, and two closely related but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1. Comparative genomic analysis of A1163 with the recently sequenced A. fumigatus isolate Af293 has identified core, variable and up to 2% unique genes in each genome. While the core genes are 99.8% identical at the nucleotide level, identity for variable genes can be as low 40%. The most divergent loci appear to contain heterokaryon incompatibility (het) genes associated with fungal programmed cell death such as developmental regulator rosA. Cross-species comparison has revealed that 8.5%, 13.5% and 12.6%, respectively, of A. fumigatus, N. fischeri and A. clavatus genes are species-specific. These genes are significantly smaller in size than core genes, contain fewer exons and exhibit a subtelomeric bias. Most of them cluster together in 13 chromosomal islands, which are enriched for pseudogenes, transposons and other repetitive elements. At least 20% of A. fumigatus-specific genes appear to be functional and involved in carbohydrate and chitin catabolism, transport, detoxification, secondary metabolism and other functions that may facilitate the adaptation to heterogeneous environments such as soil or a mammalian host. Contrary to what was suggested previously, their origin cannot be attributed to horizontal gene transfer (HGT), but instead is likely to involve duplication, diversification and differential gene loss (DDL). The role of duplication in the origin of lineage-specific genes is further underlined by the discovery of genomic islands that seem to function as designated "gene dumps" and, perhaps, simultaneously, as "gene factories".
authors.affiliation: The J. Craig Venter Institute, Rockville, Maryland, United States of America.
authors.forename: Natalie D
authors.initials: ND
authors.lastname: Fedorova
authors.forename: Nora
authors.initials: N
authors.lastname: Khaldi
authors.forename: Vinita S
authors.initials: VS
authors.lastname: Joardar
authors.forename: Rama
authors.initials: R
authors.lastname: Maiti
authors.forename: Paolo
authors.initials: P
authors.lastname: Amedeo
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Anderson
authors.forename: Jonathan
authors.initials: J
authors.lastname: Crabtree
authors.forename: Joana C
authors.initials: JC
authors.lastname: Silva
authors.forename: Jonathan H
authors.initials: JH
authors.lastname: Badger
authors.forename: Ahmed
authors.initials: A
authors.lastname: Albarraq
authors.forename: Sam
authors.initials: S
authors.lastname: Angiuoli
authors.forename: Howard
authors.initials: H
authors.lastname: Bussey
authors.forename: Paul
authors.initials: P
authors.lastname: Bowyer
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Cotty
authors.forename: Paul S
authors.initials: PS
authors.lastname: Dyer
authors.forename: Amy
authors.initials: A
authors.lastname: Egan
authors.forename: Kevin
authors.initials: K
authors.lastname: Galens
authors.forename: Claire M
authors.initials: CM
authors.lastname: Fraser-Liggett
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Haas
authors.forename: Jason M
authors.initials: JM
authors.lastname: Inman
authors.forename: Richard
authors.initials: R
authors.lastname: Kent
authors.forename: Sebastien
authors.initials: S
authors.lastname: Lemieux
authors.forename: Iran
authors.initials: I
authors.lastname: Malavazi
authors.forename: Joshua
authors.initials: J
authors.lastname: Orvis
authors.forename: Terry
authors.initials: T
authors.lastname: Roemer
authors.forename: Catherine M
authors.initials: CM
authors.lastname: Ronning
authors.forename: Jaideep P
authors.initials: JP
authors.lastname: Sundaram
authors.forename: Granger
authors.initials: G
authors.lastname: Sutton
authors.forename: Geoff
authors.initials: G
authors.lastname: Turner
authors.forename: J Craig
authors.initials: JC
authors.lastname: Venter
authors.forename: Owen R
authors.initials: OR
authors.lastname: White
authors.forename: Brett R
authors.initials: BR
authors.lastname: Whitty
authors.forename: Phil
authors.initials: P
authors.lastname: Youngman
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Wolfe
authors.forename: Gustavo H
authors.initials: GH
authors.lastname: Goldman
authors.forename: Jennifer R
authors.initials: JR
authors.lastname: Wortman
authors.forename: Bo
authors.initials: B
authors.lastname: Jiang
authors.forename: David W
authors.initials: DW
authors.lastname: Denning
authors.forename: William C
authors.initials: WC
authors.lastname: Nierman
mesh_terms: D000485:Allergens / Q000235:genetics; D001230:Aspergillus / Q000145:classification / Q000235:genetics / Q000502:physiology; D001232:Aspergillus fumigatus / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity / Q000502:physiology; D015825:Chromosomes, Fungal / Q000235:genetics; D032641:Eurotiales / Q000145:classification / Q000235:genetics / Q000502:physiology; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000235:genetics / Q000276:immunology; D016681:Genome, Fungal; D044404:Genomic Islands; D006801:Humans; D010802:Phylogeny; D013045:Species Specificity; D014774:Virulence / Q000235:genetics
chemical_list: D000485:Allergens; D005656:Fungal Proteins