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 humaloven 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.
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Acknowledgements The authors would like to thank M. Zody, X. Xie, M. Kellis, M. Kamal, J. Taylor, G. Turgeon and E. Lander for numerous helpful conversations, comments and critical readings of the paper. We also thank all members of the sequencing platform at the Broad Institute. We thank R. Dean for providing the BAC library used in sequencing. We especially thank M. Brudno for his help in using Mlagan to align the three genomes, and R. Morris for his many contributions to the A. nidulans sequencing project and subsequent analyses. This work was supported in part by grants from the NIH, as well as the NIH Research Supplement for Underrepresented Minorities, the DFG, the CMPB and the BBSRC.
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