Sequencing and functional annotation of the whole genome of the filamentous fungus Aspergillus westerdijkiae

Abstract

BackgroundAspergillus 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.ResultsWe 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2974-x) contains supplementary material, which is available to authorized users.

Production, purification, and characterization of a novel serine‐esterase from Aspergillus westerdijkiae

“…The MS analysis revealed a peptide with the sequence TWGLG and other small peptide sequences. A search in the A. westerdijkiae sequenced complete genome found a protein containing those sequences (awe06028), which had one identical mass peak and two other very close in size with our experimental MS data (not shown). This serine hydrolase protein (sequence deposited in GenBank as AN BK010323) has 303 amino acids with a predicted mass of 33.9 kDa (Fig.…”

“…In (A) CV for enzymatic activity was 21% and for mycelium dry weight was 9.3%. In (B) CV for enzymatic activity was 9% and for mycelium dry weight was 15.1% sequenced complete genome [17] found a protein containing those sequences (awe06028), which had one identical mass peak and two other very close in size with our experimental MS data (not shown). This serine hydrolase protein (sequence deposited in GenBank as AN BK010323) has 303 amino acids with a predicted mass of 33.9 kDa (Fig.…”

Genome Sequencing and Analysis of the Hypocrellin-Producing Fungus Shiraia bambusicola S4201

“…However, its GT coding ability was the weakest, lower than other selected strains. The proteins containing CAZy domains in the GH, PL, and CE groups may act as plant polysaccharide degradation (PDD) enzymes (Han et al, 2016). Regarding the PDD enzyme Table S7).…”

“…Fungi have specialized in using plant biomass as a carbon source by producing enzymes that degrade cell wall polysaccharides into metabolizable sugars for nutrition (Rytioja et al, 2014;Han et al, 2016). Carbohydrate-active enzymes (CAZy) are enzymes involved in the synthesis, metabolism, modification, and transport of carbohydrates.…”

A scalable platform to identify fungal secondary metabolites and their gene clusters

“…It is estimated that there are between five hundred thousand and three million ascomycete fungal species on earth 1 , containing on the order of 50 to 90 BGCs encoding the production of secondary metabolites 2 – 4 . However, translating this vast biosynthetic potential of fungal genomes into defined and renewable chemical libraries has proven challenging, with most progress being made in only the handful of fungal species with well-established genetic tools, such as Aspergillus nidulans 5 – 7 .…”