ABSTRACT
CONTENTS 4.1 Introduction ................................................................................................................................. 43 4.2 Genome Characteristics .............................................................................................................. 44
4.2.1 Genome Assembly .......................................................................................................... 44 4.2.2 Genome Annotation and Analysis .................................................................................. 44 4.2.3 Repetitive Elements ........................................................................................................ 45 4.2.4 Functional Annotation and Common Protein Domains ................................................ 46 4.2.5 Secondary Metabolites ................................................................................................... 46 4.2.6 Physiology and Development ......................................................................................... 48
4.3 Gene Regulation ......................................................................................................................... 48 4.3.1 Conserved Noncoding Sequences and Prediction of Regulatory Motifs ....................... 48
4.4 Genome Evolution ....................................................................................................................... 48 4.4.1 Phylogenetic Relationships ............................................................................................. 50 4.4.2 Conserved Synteny ......................................................................................................... 50 4.4.3 Genome Size ................................................................................................................... 51 4.4.4 Reproductive Strategy ..................................................................................................... 52
4.5 Future of Aspergillus Genomics ................................................................................................. 53 Acknowledgments ................................................................................................................................ 53 References ............................................................................................................................................ 54
4.1 Introduction Perhaps no other fungal genus contains species that are so harmful and species that are so benefi cial to humans as the genus Aspergillus.1 The genome sequence of the model organism Aspergillus nidulans was sequenced by the Broad Institute,2 and the genomes of a number of other Aspergillus species have also been sequenced3-7 by several others. The profoundly different lifestyles exhibited by each of the Aspergillus species for which genome sequences are available coupled with the varying degrees of evolutionary affi nity shared by their genomes makes Aspergillus a model clade to address fundamental questions in functional and comparative genomics. Here we review the essential characteristics of the A. nidulans genome and place them in the larger evolutionary context of the genus Aspergillus and fi lamentous fungi.
