Biology subjects

Muggia, L.

Publications and source records attributed to Muggia, L..

5 recordsLinked to original sources

bioRxiv2025

Does more data solve the problem of deep support? A phylogenomic approach to clarifying evolutionary relationships in the Lecanoraceae

The family Lecanoraceae is one of the most diverse groups within Lecanoromycetes, yet its internal relationships have remained unresolved despite previous multilocus studies. Here we present the first phylogenomic reconstruction of the family, based on 1003 nuclear orthologous genes from 65 genome assemblies representing the major species groups and genera. Phylogenetic trees inferred from coalescent-based analyses, together with Quartet Sampling (QS) evaluation, confirm the monophyly of Lecanoraceae and recover several well-supported lineages. The Lecanora subfusca group is resolved as polyphyletic, comprising three major clades together with Zeora and Vainionora. Additional strongly supported lineages correspond to Glaucomaria s. lat., the MPRPS clade, and Lecidella s. lat., while Bryonora and Frutidella represent early-diverging members of the family. The L. fuscescens group and Miriquidica form a distinct lineage sister to Lecanoraceae, whereas Ramboldia (Ramboldiaceae) constitutes another sister family. Backbone support was generally improved, and QS analyses showed counter-support for only a few deep nodes, indicating a complex evolutionary history likely shaped by incomplete lineage sorting, hybridization, or rapid radiation. Our results demonstrate that genome-scale data improve the resolution of Lecanoraceae, but increasing the number of genes alone can not fully resolve the backbone relationships of the family.

molecular biology↗

bioRxiv2025

Symbiotic versatility in action: Trebouxia diversity expands the niche of the lichen Xanthoria parietina

AimWe explored the phylogenetic diversity of the mycobiont Xanthoria parietina and its associated Trebouxia phycobionts across the Mediterranean region and examined how photobiont climatic preferences may shape the ecological amplitude and spatial distribution of the lichen. LocationSpecimens were collected in different localities in the central and western Mediterranean Basin (Iberian and Italian peninsulas), with additional Atlantic and boreal localities used for comparison. MethodsGenetic diversity and phylogenies of both lichen symbionts were inferred from nrITS data. Mycobiont-phycobiont interaction networks were constructed, and ecological niches of associated Trebouxia species were modelled using 19 bioclimatic variables from WorldClim v. 2.1. ResultsPhylogenetic analyses revealed high diversity within Xanthoria parietina and clarified the placement of poorly studied species within the genus Xanthoria (e.g., X. monofoliosa and X. aureola s. lat.), and revealed a novel lineage (Xanthoria sp. hydra). All the photobionts belonged to Trebouxia clade A; nine Trebouxia species-level lineages were detected, including a previously unrecognized lineage (Trebouxia sp. A56). Trebouxia decolorans (A33) was the most frequent photobiont and exhibited the broadest climatic niche, whereas T. solaris (A35) and T. tabarcae ad int. (A48) showed a more specialized climatic niche. Ensemble species-distribution models indicated widespread suitability for T. decolorans across Europe, and more coastal-Mediterranean suitability for T. tabarcae ad int. Main ConclusionXanthoria parietina displays remarkable symbiont flexibility in associating with various Trebouxia lineages within clade A, which contribute to its ecological success in heterogeneous Mediterranean environments. Climatic niche modelling suggests that the association with different phycobionts may expand the ecological niche of the lichen, potentially enhancing its capacity to inhabit a wider range of environmental conditions.

ecology↗

bioRxiv2023

Introgressive descent and hypersexuality drive the evolution of sexual parasitism and morphological reduction in a fungal species complex.

Taxonomists consider species as discrete units of biological organization, which are subject to a continuous process of evolutionary change and are connected through their shared ancestry. However, the continuous nature of evolutionary change is difficult to reconcile with the discrete outcome of speciation, especially where species boundaries are permeable. A good example of this inconsistency is the lichen genus Pyrenodesmia, which shows a high morphologic and genetic diversity that that defies systematization by taxonomic or phylogenetic methods. Here we show that hybridization explains the presence of discordant morphs and that European species are interconnected through cross-mating in a single reproductive network, a syngameon, despite which species remain largely distinct and distinguishable. Whole genome data reflect the important role played by genome defense mechanisms in the genomic stabilization of fungal hybrids. The recurrence of Repeat Induced Point mutations (RIP) shapes genomes with islands of suppressed recombination and loss of gene content, which in turn generates a feedback loop reinforcing the lack of reproductive isolation through the loss of heterokaryon incompatibility and a tendency towards morphological reduction.

evolutionary biology↗

bioRxiv2021

Large differences in carbohydrate degradation and transport potential in the genomes of lichen fungal symbionts

Lichen symbioses are generally thought to be stabilized by the transfer of fixed carbon compounds from a photosynthesizing unicellular symbiont to a fungus. In other fungal symbioses, carbohydrate subsidies correlate with genomic reductions in the number of genes for plant cell wall-degrading enzymes (PCWDEs), but whether this is the case with lichen fungal symbionts (LFSs) is unknown. We predicted genes encoding carbohydrate-active enzymes (CAZymes) and sugar transporters in 17 existing and 29 newly sequenced genomes from across the class Lecanoromycetes, the largest extant clade of LFSs. Despite possessing lower mean numbers of PCWDE genes compared to non-symbiont Ascomycota, all LFS genomes possessed a robust suite of predicted PCWDEs. The largest CAZyme gene numbers, on par with model species such as Penicillium, were retained in genomes from the subclass Ostropomycetidae, which are found in crust lichens with highly specific ecologies. The lowest numbers were in the subclass Lecanoromycetidae, which are symbionts of many generalist macrolichens. Our results suggest that association with phototroph symbionts does not in itself result in functional loss of PCWDEs and that PCWDE losses may have been driven by adaptive processes within the evolution of specific LFS lineages. The inferred capability of some LFSs to access a wide range of carbohydrates suggests that some lichen symbioses may augment fixed CO2 with carbon from external sources. SignificanceLichen symbioses are considered self-contained autotrophic systems in which the total carbon economy is the sum of phototroph-fixed CO2, supplied to a fungus as sugars. In other fungal-plant symbioses, such as mycorrhizae, plant-derived sugar subsidies are associated with loss of plant cell wall-degrading enzymes (PCWDEs). We compared PCWDE inventories in 46 genomes from the largest group of lichen fungal symbionts (LFSs) with non-symbionts from across Ascomycota. We found that despite lower overall gene numbers, all LFSs retain PCWDEs, and some possess gene numbers and functional diversity on par with non-symbionts. Our results suggest that association with a phototroph does not necessarily result in PCWDE loss, and some lichens may obtain carbon from sources other than CO2 fixation.

genomics↗

bioRxiv2020

Metagenomic data reveal diverse fungal and algal communities associated with the lichen symbiosis

Lichens have traditionally been considered the symbiotic phenotype from the interactions of a single fungal partner and one or few photosynthetic partners. However, the lichen symbiosis has been shown to be far more complex and may include a wide range of other interacting organisms, including non-photosynthetic bacteria, accessory fungi, and algae. In this study, we analyzed metagenomic shotgun sequences to better characterize lichen mycobiomes. Specifically, we inferred the range of fungi associated within lichen thalli from five groups of lichens - horsehair lichens (mycobiont=Bryoria spp.), shadow lichens (taxa in Physciaceae), rock posies (Rhizoplaca spp.), rock tripes (Umbilicaria spp.), and green rock shields (Xanthoparmelia spp.). Metagenomic reads from the multi-copy nuclear ribosomal internal transcribed spacer region, the standard DNA barcode region for fungi, were extracted, clustered, and used to infer taxonomic assignments. Our data revealed diverse lichen-associated mycobiomes, and closely related mycobionts tended to have more similar mycobiomes. Many of the members of the lichen-associated mycobiomes identified here have not previously been found in association with lichens. We found little evidence supporting the ubiquitous presence of Cystobasidiales yeasts in macrolichens, although reads representing this putative symbiotic partner were found in samples of horsehair lichens, albeit in low abundance. Our study further highlights the ecosystem-like features of lichens, with partners and interactions far from being completely understood. Future research is needed to more fully and accurately characterize lichen mycobiomes and how these fungi interact with the major lichen components - the photo- and mycobionts.

ecology↗