BackgroundThe fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus.ResultsWe have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli.ConclusionsMany aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1151-0) contains supplementary material, which is available to authorized users.

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Mycobacterium sp.Spyr1 is a newly isolated strain that occurs in a creosote contaminated site in Greece. It was isolated by an enrichment method using pyrene as sole carbon and energy source and is capable of degrading a wide range of PAH substrates including pyrene, fluoranthene, fluorene, anthracene and acenapthene. Here we describe the genomic features of this organism, together with the complete sequence and annotation. The genome consists of a 5,547,747 bp chromosome and two plasmids, a larger and a smaller one with sizes of 211,864 and 23,681 bp, respectively. In total, 5,588 genes were predicted and annotated.

A polycyclic aromatic hydrocarbon (PAH)-degrading bacterial strain Spyr1 was isolated from Greek creosote polluted soil by an enrichment method using pyrene as sole carbon and energy source. Spyr1 was identified as Mycobacterium sp. based on 16S rDNA analysis and it was capable of degrading pyrene, fluoranthene, fluorene, anthracene, and acenaphthene. The effect of entrapment in glass beads and alginate/starch mixtures on the survival and pyrene degradation ability of Spyr1 cells in liquid suspensions and soil microcosms was tested and compared with that of freely suspended cells. In general, free cells showed higher degradation of pyrene and other PAH than immobilized cells. However, immobilized cells could better tolerate PAH and they maintained their viability and PAH degradation capability for at least 1 year after storage at 4 degrees C. Entrapped cells in glass beads exhibited better pyrene biodegradation performance than alginate/starch entrapped cells in liquid suspensions and could be used effectively for at least ten repeated cycles. Alginate/starch entrapped cells exhibited better yields than glass beads entrapped cells for removing pyrene as well as mixtures of PAH in soil microcosms.