Genomic comparison of five early diverging fungi encounter in different environments and belonging to the Mucor genus

The fungal genus Mucor belongs to the Mucoromycota phylum, one of the five groups of the early diverging fungi. Mucor species are ubiquitous, they show diverse lifestyles and may have contrasting impacts on human activities. Indeed, some opportunistic pathogenic Mucor species represent a threat for human health, some others can be involved in food spoilage whereas some few others are commonly used for Asian and African fermented food manufacturing or cheese ripening. Despite these impacts on human activities, little is known on the genus Mucor. Here, we are investigating on specificities linked to Mucor species lifestyles. We engaged a genomic comparison focused on five species: M. fuscus and M. lanceolatus, two technological species used in cheese ripening, M. racemosus, a recurrent cheese spoiler, M. circinelloides, a pathogenic species and M. endophyticus, a plant endophyte.

Strains of M. fuscus UBOCC 1.09.160, M. lanceolatus UBOCC 1.09.153, M. racemosus UBOCC 1.09.155 and M. endophyticus CBS 385-95 genomes were sequenced and assembled. Genes were structurally and functionally annotated following a standard pipeline including ab initio prediction and RNAseq data support, transposable elements were annotated using the REPET pipeline that includes a de novo prediction. These data were integrated in an instance of the genome viewer Apollo allowing experts to validate the gene prediction quality.

Investigating these four genomes along with genome of the reference species M. circinelloides (strain CBS 277.49), core and pan genomes were established. Genome structures were analyzed and compared between species showing, among others, a lack of synteny among species and questioning the existence of gene cluster organization. Gene functions were compared among Mucor species and among species with different lifestyles. Evolution of gene families was also studied in order to give new hints regarding adaptation to specific habitat and/or lifestyle.