Abstract
The widespread use of Next-Generation Sequencing has opened a new era in the study of biological systems by significantly increasing the catalog of fungal genomes sequences and identifying gene clusters for known secondary metabolites as well as novel cryptic ones. However, most of these clusters still need to be examined in detail to completely understand the pathway steps and the regulation of the biosynthesis of metabolites. Genome sequencing approach led to the identification of the biosynthetic genes cluster of ochratoxin A (OTA) in a number of producing fungal species. Ochratoxin A is a potent pentaketide nephrotoxin produced by Aspergillus and Penicillium species and found as widely contaminant in food, beverages and feed. The increasing availability of several new genome sequences of OTA producer species in JGI Mycocosm and/or GenBank databanks led us to analyze and update the gene cluster structure in 19 Aspergillus and 2 Penicillium OTA producing species, resulting in a well conserved organization of OTA core genes among the species. Furthermore, our comparative genome analyses evidenced the presence of an additional gene, previously undescribed, located between the polyketide and non-ribosomal synthase genes in the cluster of all the species analyzed. The presence of a SnoaL cyclase domain in the sequence of this gene supports its putative role in the polyketide cyclization reaction during the initial steps of the OTA biosynthesis pathway. The phylogenetic analysis showed a clustering of OTA SnoaL domains in accordance with the phylogeny of OTA producing species at species and section levels. The characterization of this new OTA gene, its putative role and its expression evidence in three important representative producing species, are reported here for the first time.
Highlights
Next-generation sequencing (NGS) technologies have opened a new era in the study of biological systems by significantly increasing the catalog of fungal genomes sequences available for analysis
On the basis of this first general phylogenetic results evidencing the robustness of ochratoxin A (OTA) cyclases SnoaL domain clustering, we focused our phylogenetic analysis on the 23 cyclases from OTA
Next-generation sequencing technologies continue to drive a new era in mycology by greatly increasing the catalog of fungal genomes sequences available for analysis
Summary
Next-generation sequencing (NGS) technologies have opened a new era in the study of biological systems by significantly increasing the catalog of fungal genomes sequences available for analysis. In parallel with increased genome sequencing throughput, transcriptomic data from fungi have become attainable with RNA-seq approaches enabling current gene modeling pipelines to combine genome sequences with deep transcript sequencing data This integrated approach has led to improvements in genome annotation and de novo gene model generation, allowing the identification of previously “unseen” genes that are often comparatively small in size and missed by prior automated annotation pipelines (Grigoriev et al, 2014). This revolutionary approach to genome characterization has enabled a large-scale in silico identification of putative genes encoding novel enzymes, metabolic pathways, and bioactive compounds. Protein sequences were aligned by using muscle algorithm and the functional domain was detected by SMART6 analysis
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