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Background  Fungal conidia are usually dormant unless the extracellular conditions are right for germination. Despite the importance of dormancy, little is known about the molecular mechanism underlying entry to, maintenance of, and exit from dormancy. To gain comprehensive and inter-species insights, transcriptome analyses were conducted across  Aspergillus fumigatus ,  Aspergillus niger , and  Aspergillus oryzae .    Results  We found transcripts of 687, 694, and 812 genes were enriched in the resting conidia compared with hyphae in  A. fumigatus ,  A. niger , and  A. oryzae , respectively (conidia-associated genes). Similarly, transcripts of 766, 1,241, and 749 genes were increased in the 1 h-cultured conidia compared with the resting conidia (germination-associated genes). Among the three  Aspergillus  species, we identified orthologous 6,172 genes, 91 and 391 of which are common conidia- and germination-associated genes, respectively. A variety of stress-related genes, including the catalase genes, were found in the common conidia-associated gene set, and ribosome-related genes were significantly enriched among the germination-associated genes. Among the germination-associated genes, we found that  calA -family genes encoding a thaumatin-like protein were extraordinary expressed in early germination stage in all  Aspergillus  species tested here. In  A. fumigatus  63 % of the common conidia-associated genes were expressed in a bZIP-type transcriptional regulator AtfA-dependent manner, indicating that AtfA plays a pivotal role in the maintenance of resting conidial physiology. Unexpectedly, the precocious expression of the germination-associated  calA  and an abnormal metabolic activity were detected in the resting conidia of the  atfA  mutant, suggesting that AtfA was involved in the retention of conidial dormancy.    Conclusions  A comparison among transcriptomes of hyphae, resting conidia, and 1 h-grown conidia in the three  Aspergillus  species revealed likely common factors involved in conidial dormancy. AtfA positively regulates conidial stress-related genes and negatively mediates the gene expressions related to germination, suggesting a major role for AtfA in  Aspergillus  conidial dormancy.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2689-z) contains supplementary material, which is available to authorized users.

bmc genomics

Comparative transcriptome analysis revealing dormant conidia and germination associated genes in Aspergillus species: an essential role for AtfA in conidial dormancy