Biology subjects

Muszewska, A.

Publications and source records attributed to Muszewska, A..

5 recordsLinked to original sources

bioRxiv2026

Domestication and deep lineage divergence define two discrete trajectories in Kluyveromyces marxianus

Although genomics has greatly improved our ability to detect population structure and genetic divergence, it remains difficult to determine when diversity within a recognized species reflects continuous variation and when it marks the emergence of discrete evolutionary lineages. In yeasts, population-genomic studies often reveal overlapping signatures of environmental association, admixture, and domestication, making this distinction especially challenging. By analyzing 178 globally sampled genomes from Kluyveromyces marxianus, an emerging yeast of biotechnological interest, we show that diversity within this species resolves into two contrasting evolutionary trajectories that do not map onto broad geographic origin. Most industrial and clinical isolates belong to a lineage marked by gene loss, aneuploidy, and reduced fertility, consistent with genomic hallmarks of domestication. In contrast, isolates confined to traditional agave fermentations in Mexico and South Africa form a highly distinct lineage, separated from the other lineages by up to 4.8% genome-wide nucleotide divergence, widespread reciprocal monophyly, no detectable recent gene flow, and reduced mating compatibility despite co-occurrence with other lineages. Together, these results show that within a single yeast species, domestication-associated genome remodeling and deep lineage divergence can define distinct trajectories, with implications for strain selection in biotechnology.

evolutionary biology↗

bioRxiv2021

Horizontal gene transfer in 44 early diverging fungi favors short, metabolic, extracellular proteins from associated bacteria

Numerous studies have been devoted to individual cases of horizontally acquired genes in fungi. It has been shown that such genes expand the hosts metabolic capabilities and contribute to their adaptations as parasites or symbionts. Some studies have provided an extensive characterization of the horizontal gene transfer (HGT) in Dikarya. However, in the early diverging fungi (EDF), a similar characterization is still missing. In order to fill this gap, we have designed a computational pipeline to obtain a statistical sample of reliable HGT events with a possibly minimal number of false detections. We have analyzed 44 EDF proteomes and identified 829 xenologs in fungi ranging from Chytridiomycota and Blastocladiomycota to Mucoromycota. We have identified several patterns and statistical properties of EDF HGT. Ancestrally aquatic fungi are generally more likely to acquire foreign genetic material than terrestrial ones. Endosymbiotic bacteria can be a source of useful xenologs, as exemplified by NOD-like receptors transferred to Mortierellomycota. Closely related fungi have similar rates of intronization of xenologs. The number of post-transfer paralogs of a protein can be described by a heavy-tailed Yule-Simons distribution. Post-transfer gene fusions complicate the landscape of HGT. We have designed a methodology to obtain a reliable, statistical sample of inter-kingdom xenologs across the tree of life of EDF to give a preliminary characterization of their general properties and patterns. We show that HGT is driven by bursts of gene exchange and duplication, resulting in highly divergent numbers and molecular properties of xenologs between fungal lineages. A close ecological relationship with another organism seems to be a predisposing condition for HGT, but does not always result in an extensive gene exchange. We argue that there is no universal approach for HGT identification and inter- and intra kingdom transfers require tailored identification methods. Our results help to better understand how and to what extent HGT has shaped the metabolic, adaptive, and immune capabilities of fungi.

genomics↗

bioRxiv2020

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

We describe the genomes of six Mucoromycotina fungi representing distant saprotrophic lineages within the subphylum (i.e. Umbelopsidales and Mucorales). We selected two Umbelopsis isolates from soil (i.e. U. isabellina, U. vinacea), two soil-derived Mucor isolates (i.e. M. circinatus, M. plumbeus), and two Mucorales representatives with extended proteolytic activity (i.e. Thamnidium elegans and Mucor saturninus). We complement genome analyses with a description of their digestive capabilities, their cell wall carbohydrate composition, and total lipid profiles. Finally, we link the presence of endohyphal bacteria with observed characteristics. One of the genomes, Thamnidium elegans, harbours a complete genome of an associated bacterium classified to Paenibacillus sp. This fungus displays multiple altered traits compared to remaining isolates regardless of their evolutionary distance. T. elegans has expanded carbon assimilation capabilities particularly efficiently degrades carboxylic acids, has a higher diacylglycerol: triacylglycerol ratio and phospholipid composition suggesting a more rigid cellular membrane. Comparison of early-diverging Umbelopsidales with evolutionary younger Mucorales points at several differences particularly in their carbon source preferences and encoded carbohydrate repertoire. All tested Mucoromycotina shares features including the ability to produce 18:3 gamma-linoleic acid and fucose as a cell wall component. Author SummaryIn our paper, we report on the genomic sequences of six Mucoromycotina strains and an associated bacterium from Paenibacillus genus. Mucoromycotina are often studied in pathogenic context albeit their basic biology remains understudied. This manuscript expands on the collection of currently sequenced Mucorales and Umbelopsidales, including the first sequenced Thamnidium isolate, which was sequenced together with a Paenibacillus bacterium. The interaction with a bacterial partner alters the metabolism, cell membrane composition but not the exoskeleton of the fungus. The associated bacterium provided multiple enzymes that significantly expanded the digestive capabilities of the fungal host. Parallel sequencing and phenotyping of Mucorales and Umbelopsidales enabled us to look at the differences of both lineages within Mucoromycotina. We demonstrate that the predicted digestive capabilities are in line with experimental validation. Based on the cell wall composition data and genomic underpinnings of carbohydrate metabolism we were able to confirm the universal presence of fucose in Mucoromycotina cell walls. Fatty acid, phospholipid and acylglycerol composition support the usage of 18:3 gamma-linoleic acid as a chemotaxonomic marker of Mucoromycotina and corroborate TAG as a dominant storage lipid in these organisms. Genomic features, digestive capabilities, fatty acid composition differ between Mucorales and Ubelopsidales pointing at subtle but significant changes in the course of Mucoromycotina radiation.

genomics↗

bioRxiv2020

Utilization of cobalamin is ubiquitous in early-branching fungal phyla

Cobalamin is a cofactor present in essential metabolic pathways in animals and one of the water-soluble vitamins. It is a complex compound synthesized solely by prokaryotes. Cobalamin dependence is scattered across the tree of life. In particular, fungi and plants were deemed devoid of cobalamin. We demonstrate that cobalamin is utilized by all fungal lineages, except for Dikarya. This observation is supported by the genomic presence of both B12 dependent enzymes and cobalamin modifying enzymes. Moreover, the genes identified are actively transcribed in many taxa. Most fungal cobalamin dependent enzymes and cobalamin metabolism proteins are highly similar to their animal homologs. Phylogenetic analyses support a scenario of vertical inheritance of the cobalamin trait with several losses. Cobalamin usage was probably lost in Mucorinae and at the base of Dikarya which groups most of the model organisms which hindered B12-dependent metabolism discovery in fungi. Our results indicate that cobalamin dependence was a widely distributed trait at least in Opisthokonta, across diverse microbial eukaryotes and likely in the LECA.

evolutionary biology↗

bioRxiv2017

A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.

genomics↗