Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae.
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.
Galagan
James E
JE
The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02142, USA.
Calvo
Sarah E
SE
Cuomo
Christina
C
Ma
Li-Jun
LJ
Wortman
Jennifer R
JR
Batzoglou
Serafim
S
Lee
Su-In
SI
Baştürkmen
Meray
M
Spevak
Christina C
CC
Clutterbuck
John
J
Kapitonov
Vladimir
V
Jurka
Jerzy
J
Scazzocchio
Claudio
C
Farman
Mark
M
Butler
Jonathan
J
Purcell
Seth
S
Harris
Steve
S
Braus
Gerhard H
GH
Draht
Oliver
O
Busch
Silke
S
D'Enfert
Christophe
C
Bouchier
Christiane
C
Goldman
Gustavo H
GH
Bell-Pedersen
Deborah
D
Griffiths-Jones
Sam
S
Doonan
John H
JH
Yu
Jaehyuk
J
Vienken
Kay
K
Pain
Arnab
A
Freitag
Michael
M
Selker
Eric U
EU
Archer
David B
DB
Peñalva
Miguel A
MA
Oakley
Berl R
BR
Momany
Michelle
M
Tanaka
Toshihiro
T
Kumagai
Toshitaka
T
Asai
Kiyoshi
K
Machida
Masayuki
M
Nierman
William C
WC
Denning
David W
DW
Caddick
Mark
M
Hynes
Michael
M
Paoletti
Mathieu
M
Fischer
Reinhard
R
Miller
Bruce
B
Dyer
Paul
P
Sachs
Matthew S
MS
Osmani
Stephen A
SA
Birren
Bruce W
BW
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
D020543:Proteome