Comparative genomics applied to Mucor species with different lifestyles

Abstract

Background: Despite a growing number of investigations on early diverging fungi, the corresponding lineages have not been as extensively characterized as Ascomycota or Basidiomycota ones. The Mucor genus, pertaining to one of these lineages is not an exception. To this date, a restricted number of Mucor annotated genomes is publicly available and mainly correspond to the reference species, Mucor circinelloides, and to medically relevant species. However, the Mucor 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 Mucor genomes available and identify potential genomic imprints of adaptation to different environments and lifestyles in the Mucor genus. Results: In this study, we report four newly sequenced genomes of Mucor isolates collected from non-clinical environments pertaining to species with contrasted lifestyles, namely Mucor fuscus and Mucor lanceolatus, two species used in cheese production (during ripening), Mucor racemosus, a recurrent cheese spoiler sometimes described as an opportunistic animal and human pathogen, and Mucor endophyticus, a plant endophyte. Comparison of these new genomes with those previously available for six Mucor and two Rhizopus (formerly identified as M. racemosus) 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 Mucor genus. Conclusions: This study extended the descriptive data set for Mucor 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.

Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina

“…Mucor genomes harbor also numerous Helitrons, known for their rolling circle replication mechanism. The presence of Helitrons has been observed in other Mucor species previously ( Lebreton et al, 2020 ). Noteworthy, Helitrons often hijack neighboring genes and are efficient vectors of HGT in other fungi ( Castanera et al, 2014 ).…”

Understanding Mucormycoses in the Age of “omics”

“…Sequencing of five different Mucor genomes from strains that represented different environments and lifestyles identified homologs of genes involved in different mechanisms of iron acquisition. Similar to R. delemar, the results suggested that Mucor species relied predominantly on Rhizoferrin for iron acquisition (Lebreton et al, 2020). However, the two strains associated with cheese production showed a reduced number of genes related to iron acquisition.…”

“…The genomes of Apophysomyces species show a unique profile of carbohydrate active enzymes (CAZymes) responsible for the generation of Apophysomyces cell wall polysaccharides, which may represent a novel antifungal target (Prakash et al, 2017). Difference patterns in CAZymes repertoire was also observed in the genomes of Mucor species that differed in lifestyle (Lebreton et al, 2020). Notably, Mucor species involved in cheese ripening had less CAZymes in their genome compared to more pathogenic and clinical isolates.…”

“…Protease gene families are one of the many gene families that are expanded due to the WGD of R. delemar , and may account for its invasive nature ( Ma et al, 2009 ). The genome of L. corymbifera, Mucor species and Apophysomyces species also contain a significant number of predicted secreted proteases ( Schwartze et al, 2014 ; Prakash et al, 2017 ; Lebreton et al, 2020 ). A clinical isolate of M ucor velutinosus , which was previously not thought to be a major cause of mucormycosis, showed the presence of unique secreted aspartyl proteases which contribute to skin dissemination ( Shelburne et al, 2015 ).…”

Metabolic potential, ecology and presence of endohyphal bacteria is reflected in genomic diversity of Mucoromycotina

“…Mucor genomes harbour also numerous Helitrons, known for their rolling circle replication mechanism. The presence of Helitrons has been observed in other Mucor species previously [41]. Noteworthy,…”