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 human 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.
authors.affiliation: The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02142, USA.
authors.forename: James E
authors.initials: JE
authors.lastname: Galagan
authors.forename: Sarah E
authors.initials: SE
authors.lastname: Calvo
authors.forename: Christina
authors.initials: C
authors.lastname: Cuomo
authors.forename: Li-Jun
authors.initials: LJ
authors.lastname: Ma
authors.forename: Jennifer R
authors.initials: JR
authors.lastname: Wortman
authors.forename: Serafim
authors.initials: S
authors.lastname: Batzoglou
authors.forename: Su-In
authors.initials: SI
authors.lastname: Lee
authors.forename: Meray
authors.initials: M
authors.lastname: Baştürkmen
authors.forename: Christina C
authors.initials: CC
authors.lastname: Spevak
authors.forename: John
authors.initials: J
authors.lastname: Clutterbuck
authors.forename: Vladimir
authors.initials: V
authors.lastname: Kapitonov
authors.forename: Jerzy
authors.initials: J
authors.lastname: Jurka
authors.forename: Claudio
authors.initials: C
authors.lastname: Scazzocchio
authors.forename: Mark
authors.initials: M
authors.lastname: Farman
authors.forename: Jonathan
authors.initials: J
authors.lastname: Butler
authors.forename: Seth
authors.initials: S
authors.lastname: Purcell
authors.forename: Steve
authors.initials: S
authors.lastname: Harris
authors.forename: Gerhard H
authors.initials: GH
authors.lastname: Braus
authors.forename: Oliver
authors.initials: O
authors.lastname: Draht
authors.forename: Silke
authors.initials: S
authors.lastname: Busch
authors.forename: Christophe
authors.initials: C
authors.lastname: D'Enfert
authors.forename: Christiane
authors.initials: C
authors.lastname: Bouchier
authors.forename: Gustavo H
authors.initials: GH
authors.lastname: Goldman
authors.forename: Deborah
authors.initials: D
authors.lastname: Bell-Pedersen
authors.forename: Sam
authors.initials: S
authors.lastname: Griffiths-Jones
authors.forename: John H
authors.initials: JH
authors.lastname: Doonan
authors.forename: Jaehyuk
authors.initials: J
authors.lastname: Yu
authors.forename: Kay
authors.initials: K
authors.lastname: Vienken
authors.forename: Arnab
authors.initials: A
authors.lastname: Pain
authors.forename: Michael
authors.initials: M
authors.lastname: Freitag
authors.forename: Eric U
authors.initials: EU
authors.lastname: Selker
authors.forename: David B
authors.initials: DB
authors.lastname: Archer
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Peñalva
authors.forename: Berl R
authors.initials: BR
authors.lastname: Oakley
authors.forename: Michelle
authors.initials: M
authors.lastname: Momany
authors.forename: Toshihiro
authors.initials: T
authors.lastname: Tanaka
authors.forename: Toshitaka
authors.initials: T
authors.lastname: Kumagai
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Asai
authors.forename: Masayuki
authors.initials: M
authors.lastname: Machida
authors.forename: William C
authors.initials: WC
authors.lastname: Nierman
authors.forename: David W
authors.initials: DW
authors.lastname: Denning
authors.forename: Mark
authors.initials: M
authors.lastname: Caddick
authors.forename: Michael
authors.initials: M
authors.lastname: Hynes
authors.forename: Mathieu
authors.initials: M
authors.lastname: Paoletti
authors.forename: Reinhard
authors.initials: R
authors.lastname: Fischer
authors.forename: Bruce
authors.initials: B
authors.lastname: Miller
authors.forename: Paul
authors.initials: P
authors.lastname: Dyer
authors.forename: Matthew S
authors.initials: MS
authors.lastname: Sachs
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Osmani
authors.forename: Bruce W
authors.initials: BW
authors.lastname: Birren
mesh_terms: D001232:Aspergillus fumigatus / Q000235:genetics* / Q000502:physiology; D001233:Aspergillus nidulans / Q000235:genetics* / Q000502:physiology; D001236:Aspergillus oryzae / Q000235:genetics* / Q000502:physiology; D001483:Base Sequence; D016384:Consensus Sequence / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D019143:Evolution, Molecular; D049770:Genes, Mating Type, Fungal / Q000235:genetics; D016681:Genome, Fungal / Q000235:genetics*; D023281:Genomics; D006801:Humans; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D020543:Proteome / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D017422:Sequence Analysis, DNA; D026801:Synteny / Q000235:genetics
chemical_list: D020543:Proteome