Description:
<jats:title>Abstract</jats:title><jats:sec>
<jats:title>Background</jats:title>
<jats:p>Despite a growing number of investigations on early diverging fungi, the corresponding lineages have not been as extensively characterized as <jats:italic>Ascomycota</jats:italic> or <jats:italic>Basidiomycota</jats:italic> ones. The <jats:italic>Mucor</jats:italic> genus, pertaining to one of these lineages is not an exception. To this date, a restricted number of <jats:italic>Mucor</jats:italic> annotated genomes is publicly available and mainly correspond to the reference species, <jats:italic>Mucor circinelloides,</jats:italic> and to medically relevant species. However, the <jats:italic>Mucor</jats:italic> genus is composed of a large number of ubiquitous species as well as few species that have been reported to specifically occur in certain habitats. The present study aimed to expand the range of <jats:italic>Mucor</jats:italic> genomes available and identify potential genomic imprints of adaptation to different environments and lifestyles in the <jats:italic>Mucor</jats:italic> genus.</jats:p>
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<jats:title>Results</jats:title>
<jats:p>In this study, we report four newly sequenced genomes of <jats:italic>Mucor</jats:italic> isolates collected from non-clinical environments pertaining to species with contrasted lifestyles, namely <jats:italic>Mucor fuscus</jats:italic> and <jats:italic>Mucor lanceolatus</jats:italic>, two species used in cheese production (during ripening), <jats:italic>Mucor racemosus</jats:italic>, a recurrent cheese spoiler sometimes described as an opportunistic animal and human pathogen, and <jats:italic>Mucor endophyticus</jats:italic>, a plant endophyte. Comparison of these new genomes with those previously available for six <jats:italic>Mucor</jats:italic> and two <jats:italic>Rhizopus</jats:italic> (formerly identified as <jats:italic>M. racemosus</jats:italic>) isolates allowed global structural and functional description such as their TE content, core and species-specific genes and specialized genes. We proposed gene candidates involved in iron metabolism; some of these genes being known to be involved in pathogenicity; and described patterns such as a reduced number of CAZymes in the species used for cheese ripening as well as in the endophytic isolate that might be related to adaptation to different environments and lifestyles within the <jats:italic>Mucor</jats:italic> genus.</jats:p>
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<jats:title>Conclusions</jats:title>
<jats:p>This study extended the descriptive data set for <jats:italic>Mucor</jats:italic> genomes, pointed out the complexity of obtaining a robust phylogeny even with multiple genes families and allowed identifying contrasting potentially lifestyle-associated gene repertoires. The obtained data will allow investigating further the link between genetic and its biological data, especially in terms of adaptation to a given habitat.</jats:p>
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