title: Genomic characteristics and comparative genomics analysis of Penicillium chrysogenum KF-25.
abstract: BACKGROUND
  Penicillium chrysogenum has been used in producing penicillin and derived β-lactam antibiotics for many years. Although the genome of the mutant strain P. chrysogenum Wisconsin 54-1255 has already been sequenced, the versatility and genetic diversity of this species still needs to be intensively studied. In this study, the genome of the wild-type P. chrysogenum strain KF-25, which has high activity against Ustilaginoidea virens, was sequenced and characterized.
  
  
  RESULTS
  The genome of KF-25 was about 29.9 Mb in size and contained 9,804 putative open reading frames (orfs). Thirteen genes were predicted to encode two-component system proteins, of which six were putatively involved in osmolarity adaption. There were 33 putative secondary metabolism pathways and numerous genes that were essential in metabolite biosynthesis. Several P. chrysogenum virus untranslated region sequences were found in the KF-25 genome, suggesting that there might be a relationship between the virus and P. chrysogenum in evolution. Comparative genome analysis showed that the genomes of KF-25 and Wisconsin 54-1255 were highly similar, except that KF-25 was 2.3 Mb smaller. Three hundred and fifty-five KF-25 specific genes were found and the biological functions of the proteins encoded by these genes were mainly unknown (232, representing 65%), except for some orfs encoding proteins with predicted functions in transport, metabolism, and signal transduction. Numerous KF-25-specific genes were found to be associated with the pathogenicity and virulence of the strains, which were identical to those of wild-type P. chrysogenum NRRL 1951.
  
  
  CONCLUSIONS
  Genome sequencing and comparative analysis are helpful in further understanding the biology, evolution, and environment adaption of P. chrysogenum, and provide a new tool for identifying further functional metabolites.
authors.forename: Qin
authors.initials: Q
authors.lastname: Peng
authors.forename: Yihui
authors.initials: Y
authors.lastname: Yuan
authors.affiliation: Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. mygao@wh.iov.cn.
authors.forename: Meiying
authors.initials: M
authors.lastname: Gao
authors.forename: Xupeng
authors.initials: X
authors.lastname: Chen
authors.forename: Biao
authors.initials: B
authors.lastname: Liu
authors.forename: Pengming
authors.initials: P
authors.lastname: Liu
authors.forename: Yan
authors.initials: Y
authors.lastname: Wu
authors.forename: Dandan
authors.initials: D
authors.lastname: Wu
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D058947:Bacterial Secretion Systems / Q000235:genetics; D055028:Comparative Genomic Hybridization; D019295:Computational Biology; D016681:Genome, Fungal; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D053858:Metabolic Networks and Pathways; D058977:Molecular Sequence Annotation; D010408:Penicillium chrysogenum / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D020506:Untranslated Regions / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D058947:Bacterial Secretion Systems; D020506:Untranslated Regions