Transcriptome analysis of different growth stages of Aspergillus oryzae reveals dynamic changes of distinct classes of genes during growth

Abstract

Background: The gene expression profile and metabolic pathways of Aspergillus oryzae underlying the anatomical and morphological differentiation across different growth stages have not been fully characterized. The rapid development of next-generation sequencing technologies provides advanced knowledge of the genomic organization of A. oryzae.

Results: In this study, we characterized the growth and development of A. oryzae at different growth stages, including the adaptive phase, logarithmic phase, and stationary phase. Our results revealed that A. oryzae undergoes physiological and morphological differentiation across the different stages. RNA-seq was employed to analyze the three stages of A. oryzae, which generated more than 27 million high-quality reads per sample. The analysis of differential gene expression showed more genes expressed differentially upon transition from the adaptive phase to the logarithmic and stationary phases, while relatively steady trend was observed during the transition from the logarithmic phase to the stationary phase. GO classification of the differentially expressed genes among different growth stages revealed that most of these genes were enriched for single-organism process, metabolic process, and catalytic activity. These genes were then subjected to a clustering analysis. The results showed that the cluster with the majority of genes with increased expression upon transition from the adaptive phase to the logarithmic phase, and steady expression from the logarithmic phase to the stationary phase was mainly involved in the carbohydrate and amino acid metabolism.

Conclusion: Our results provide a foundation for identifying developmentally important genes and understanding the biological processes across various growth stages.

Keywords: Aspergillus oryzae; Gene clusters; Growth stages; Transcriptome.

Fig. 1

The growth and development of A. oryzae at different growth stages. a The dry biomass at different growth stages (24 h, 36 h, 48 h, 60 h and 72 h). The mycelia were collected by peeling off from the plates and dried overnight for the determination of biomass; b The density of spores in the salinity treatments (24 h, 36 h, 48 h, 60 h and 72 h); c The phenotype of A. oryzae at different growth stages (from left to right: 24 h, 48 h and 72 h). The color of colony was began as white and then changed from kelly green to olive green

Fig. 2

Different types of alternative splicing events at different growth stages. The horizontal axis indicates the type of alternative splicing; the vertical axis indicates the number of alternative splicing. Intergenic (junctions start from and/or end up with the area between genes), P5_splice (junctions start inside an exon, end up with initiation site of another exon), P3_splice (junctions start from an exon termination site and end up inside another exon), ES (junctions start from an exon termination site and end at another termination site), IR (junctions start and end in the same exon), AFS/TSS (junctions start from the 5’ end of exon initiation site and end up with another exon), ALS/TTS (junctions start at the 3’ end of the last exon initiation site and end up with another exon) and Others (junctions that do not belong to any of the above categories). Ao_24_1, 2, 3: samples at 24 h after incubation; Ao_48_1, 2, 3: samples at 48 h after incubation; Ao_72_1, 2, 3: samples at 72 h after incubation

Fig. 3

Analysis of DEGs between fungal growth stages. a DEGs’ distribution between each two samples; b Venn diagram exhibiting the DEUs’ distribution in three libraries. Ao_24: samples at 24 h after incubation; Ao_48: samples at 48 h after incubation; Ao: samples at 72 h after incubation

Fig. 4

GO enrichment of DEGs between growth stages in A. oryzae. a The enriched GO terms of up-regulated DEGs between growth stages. b The enriched GO terms of down-regulated DEGs between growth stages

Fig. 5

Clustering of gene expression profiles across three growth stages. a Eight gene clusters with different expression patterns. b The number of genes for each gene cluster. c Functional annotation of each gene clusters