Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France.
Station Biologique de Roscoff, Plateforme ABiMS, CNRS: FR2424, Sorbonne Université (UPMC), Paris VI, Place Georges Teissier, 74 29682, Roscoff Cedex, BP, France.
BMC Genomics. 2020 Feb 10;21(1):135. doi: 10.1186/s12864-019-6256-2.
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.
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.
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.
尽管对早期分化真菌的研究越来越多，但相应的谱系并没有像子囊菌或担子菌那样得到广泛的描述。属于这些谱系之一的毛霉属也不例外。迄今为止，公开提供的毛霉属注释基因组数量有限，主要对应于参考物种毛霉circ inelloides 和与医学相关的物种。然而，毛霉属由大量普遍存在的物种以及少数报道仅在特定栖息地出现的物种组成。本研究旨在扩大可用的毛霉属基因组范围，并确定毛霉属不同环境和生活方式适应的潜在基因组印记。
在这项研究中，我们报告了从非临床环境中分离的四个新测序的毛霉属分离物的基因组，这些分离物属于具有不同生活方式的物种，即毛霉 fuscus 和毛霉 lanceolatus，这两种物种用于奶酪生产（在成熟过程中），毛霉 racemosus，一种经常出现的奶酪变质菌，有时被描述为机会性动物和人类病原体，以及毛霉 endophyticus，一种植物内生菌。将这些新基因组与之前为六个毛霉属和两个根霉属（以前鉴定为毛霉 racemosus）分离物提供的基因组进行比较，允许进行全局结构和功能描述，例如它们的 TE 含量、核心和物种特异性基因以及专门基因。我们提出了涉及铁代谢的基因候选物；其中一些基因已知与致病性有关；并描述了一些模式，例如在用于奶酪成熟的物种和内生分离物中 CAZymes 的数量减少，这可能与毛霉属内不同环境和生活方式的适应有关。
这项研究扩展了毛霉属基因组的描述性数据集，指出了即使使用多个基因家族也很难获得稳健的系统发育，并确定了与潜在生活方式相关的基因库的复杂性。获得的数据将允许进一步研究遗传与生物学数据之间的联系，特别是在适应特定栖息地方面。
