title: Sequencing and functional annotation of the whole genome of the filamentous fungus Aspergillus westerdijkiae.
abstract: Aspergillus westerdijkiae produces ochratoxin A (OTA) in Aspergillus section Circumdati. It is responsible for the contamination of agricultural crops, fruits, and food commodities, as its secondary metabolite OTA poses a potential threat to animals and humans. As a member of the filamentous fungi family, its capacity for enzymatic catalysis and secondary metabolite production is valuable in industrial production and medicine. To understand the genetic factors underlying its pathogenicity, enzymatic degradation, and secondary metabolism, we analysed the whole genome of A. westerdijkiae and compared it with eight other sequenced Aspergillus species.
  
  
  
  We sequenced the complete genome of A. westerdijkiae and assembled approximately 36 Mb of its genomic DNA, in which we identified 10,861 putative protein-coding genes. We constructed a phylogenetic tree of A. westerdijkiae and eight other sequenced Aspergillus species and found that the sister group of A. westerdijkiae was the A. oryzae - A. flavus clade. By searching the associated databases, we identified 716 cytochrome P450 enzymes, 633 carbohydrate-active enzymes, and 377 proteases. By combining comparative analysis with Kyoto Encyclopaedia of Genes and Genomes (KEGG), Conserved Domains Database (CDD), and Pfam annotations, we predicted 228 potential carbohydrate-active enzymes related to plant polysaccharide degradation (PPD). We found a large number of secondary biosynthetic gene clusters, which suggested that A. westerdijkiae had a remarkable capacity to produce secondary metabolites. Furthermore, we obtained two more reliable and integrated gene sequences containing the reported portions of OTA biosynthesis and identified their respective secondary metabolite clusters. We also systematically annotated these two hybrid t1pks-nrps gene clusters involved in OTA biosynthesis. These two clusters were separate in the genome, and one of them encoded a couple of GH3 and AA3 enzyme genes involved in sucrose and glucose metabolism.
  
  
  
  The genomic information obtained in this study is valuable for understanding the life cycle and pathogenicity of A. westerdijkiae. We identified numerous enzyme genes that are potentially involved in host invasion and pathogenicity, and we provided a preliminary prediction for each putative secondary metabolite (SM) gene cluster. In particular, for the OTA-related SM gene clusters, we delivered their components with domain and pathway annotations. This study sets the stage for experimental verification of the biosynthetic and regulatory mechanisms of OTA and for the discovery of new secondary metabolites.
authors.affiliation: State Key Laboratory of Organ Failure Research, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China.|Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China.
authors.forename: Xiaolong
authors.initials: X
authors.lastname: Han
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Republic of Singapore.
authors.forename: Alolika
authors.initials: A
authors.lastname: Chakrabortti
authors.affiliation: State Key Laboratory of Organ Failure Research, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China.|Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China.
authors.forename: Jindong
authors.initials: J
authors.lastname: Zhu
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Republic of Singapore. zxliang@ntu.edu.sg.
authors.forename: Zhao-Xun
authors.initials: ZX
authors.lastname: Liang
authors.affiliation: State Key Laboratory of Organ Failure Research, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China. jmli@smu.edu.cn.|Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China. jmli@smu.edu.cn.
authors.forename: Jinming
authors.initials: J
authors.lastname: Li
mesh_terms: D001230:Aspergillus / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D055028:Comparative Genomic Hybridization; D030541:Databases, Genetic; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D016681:Genome, Fungal; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D010447:Peptide Hydrolases / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D014774:Virulence / Q000235:genetics
chemical_list: D005656:Fungal Proteins; D010447:Peptide Hydrolases
keywords: Aspergillus westerdijkiae; Comparative genomics; Fungi; Orthologues; Phylogeny; Secondary metabolite