Characterization of Natural Antisense Transcript, Sclerotia Development and Secondary Metabolism by Strand-Specific RNA Sequencing of Aspergillus flavus

Abstract

Aspergillus flavus has received much attention owing to its severe impact on agriculture and fermented products induced by aflatoxin. Sclerotia morphogenesis is an important process related to A. flavus reproduction and aflatoxin biosynthesis. In order to obtain an extensive transcriptome profile of A. flavus and provide a comprehensive understanding of these physiological processes, the isolated mRNA of A. flavus CA43 cultures was subjected to high-throughput strand-specific RNA sequencing (ssRNA-seq). Our ssRNA-seq data profiled widespread transcription across the A. flavus genome, quantified vast transcripts (73% of total genes) and annotated precise transcript structures, including untranslated regions, upstream open reading frames (ORFs), alternative splicing variants and novel transcripts. We propose natural antisense transcripts in A. flavus might regulate gene expression mainly on the post-transcriptional level. This regulation might be relevant to tune biological processes such as aflatoxin biosynthesis and sclerotia development. Gene Ontology annotation of differentially expressed genes between the mycelia and sclerotia cultures indicated sclerotia development was related closely to A. flavus reproduction. Additionally, we have established the transcriptional profile of aflatoxin biosynthesis and its regulation model. We identified potential genes linking sclerotia development and aflatoxin biosynthesis. These genes could be used as targets for controlled regulation of aflatoxigenic strains of A. flavus.

Integrative analyses reveal transcriptome-proteome correlation in biological pathways and secondary metabolism clusters in A. flavus in response to temperature

“…1B ). After excluding these genes from further analysis, 75.8% of genes were detected expressed at 28 °C or 37 °C, which was similar to the results in previous studies in A. flavus 25 26 . Compared with the results of single-end RNA seq of A. flavus at 30 °C and 37 °C 25 , we found that the expression data of transcripts correlated well between samples (Spearman correlation coefficient, rho = 0.73 for samples grown at 37 °C samples [ Fig.…”

“…In total, about 36 million 100-bp paired-end reads were obtained from the Illumina platform. Using the splice-aware aligner Tophat2 24 , 91.2% of reads were mapped to the A. flavus genome sequence, which represented much greater accuracy than earlier A. flavus transcriptome data 25 26 . More than 96% of reads were mapped to the exon region, including the 5′ untranslated region (UTR) and 3′ UTR region ( Fig.…”

Global Survey of Canonical Aspergillus flavus G Protein-Coupled Receptors

“…Interestingly, four GPCRs, encoded by gprC , gprH , gprM , and gprS , were differentially expressed on the germ versus the endosperm ( 55 ). Two separate studies compared genomic expression from mycelial growth versus sclerotial production, though the methods used were quite different between the two studies ( 55 , 57 ). The strains of A. flavus , media, and growth conditions (i.e., liquid versus solid culture) that were used varied, as did the methods for measuring gene expression (i.e., microarray versus transcriptome sequencing [RNA-seq]).…”

Association of fungal secondary metabolism and sclerotial biology

“…Functional genomic analysis is a powerful approach that has helped to elucidate the genetic connections between sclerotial formation and secondary metabolism. For instance, Wu et al (2014) compared the transcriptome of mycelium and sclerotium developmental stages and found that backbone genes of 38 secondary metabolite pathways were transcribed in both the mycelial and sclerotial cultures, including the AF biosynthetic pathway. A transcriptome study by Lin et al (2013) of A. flavus cultures treated with 5-azacytidine, an inactivator of DNA methyltransferase, provided further evidence that secondary metabolism and development are co-regulated.…”