Predicted Input of Uncultured Fungal Symbionts to a Lichen Symbiosis from Metagenome-Assembled Genomes

Abstract

Basidiomycete yeasts have recently been reported as stably associated secondary fungal symbionts (SFSs) of many lichens, but their role in the symbiosis remains unknown. Attempts to sequence their genomes have been hampered both by the inability to culture them and their low abundance in the lichen thallus alongside two dominant eukaryotes (an ascomycete fungus and chlorophyte alga). Using the lichen Alectoria sarmentosa, we selectively dissolved the cortex layer in which SFSs are embedded to enrich yeast cell abundance and sequenced DNA from the resulting slurries as well as bulk lichen thallus. In addition to yielding a near-complete genome of the filamentous ascomycete using both methods, metagenomes from cortex slurries yielded a 36- to 84-fold increase in coverage and near-complete genomes for two basidiomycete species, members of the classes Cystobasidiomycetes and Tremellomycetes. The ascomycete possesses the largest gene repertoire of the three. It is enriched in proteases often associated with pathogenicity and harbours the majority of predicted secondary metabolite clusters. The basidiomycete genomes possess ∼35% fewer predicted genes than the ascomycete and have reduced secretomes even compared to close relatives, while exhibiting signs of nutrient limitation and scavenging. Furthermore, both basidiomycetes are enriched in genes coding for enzymes producing secreted acidic polysaccharides, representing a potential contribution to the shared extracellular matrix. All three fungi retain genes involved in dimorphic switching, despite the ascomycete not being known to possess a yeast stage. The basidiomycete genomes are an important new resource for exploration of lifestyle and function in fungal-fungal interactions in lichen symbioses.

Functional convergence of Yunnan snub-nosed monkey and bamboo-eating panda gut microbiomes revealing the driving by dietary flexibility on mammal gut microbiome

“…Here, we found the difference in the relative abundance of the strain level (MAGs) between W and FP populations, which might be associated with the different diets. However, MAGs analyses such as this one should be taken with some caution due to the sequencing depth and the capability to assemble all MAGs in the metagenomes [54] , [55] .

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Lichen fungi do not depend on the alga for ATP production: A comment on Pogoda et al. (2018)

“…To test the hypothesis that the four species which Pogoda et al (2018) reported as lacking ATP9 in fact retain it, we searched for the gene in the recently published lecanoromycete genome of Alectoria sarmentosa (Tagirdzhanova et al, 2021), a close relative of A. fallacina , one of the four fungi reportedly lacking ATP9 . We identified one putative ATP9 homologue, ASARMPREDX12_000654, in the A. sarmentosa lecanoromycete nuclear genome.…”

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

“…Our sampling simultaneously represents a cross-section of lecanoromycete evolution, with 24 genomes from the subclass Ostropomycetidae , 17 from the subclass Lecanoromycetidae , and four and one each from the species-poor subclasses Acarosporomycetidae and Umbilicariomycetidae , respectively. Ten genomes were derived from cultured samples and 18 are metagenome-assembled genomes (MAGs) assembled and binned according to (63). Culture-derived genomes differed little from MAGs in estimated completeness and gene numbers (Supplementary Figures 1 and 2).…”