{"entity": "researcher", "timestamp": "2026-11-12T12:46:54.506Z", "family": "Spribille", "given": "Toby", "initials": "T", "orcid": "0000-0002-9855-4591", "affiliations": ["Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/18b90e5c247f45db979b35cd50a13bf9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/18b90e5c247f45db979b35cd50a13bf9"}}, "publications": [{"entity": "publication", "iuid": "897231b191b14b378f75b6d57dc416ee", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/897231b191b14b378f75b6d57dc416ee.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/897231b191b14b378f75b6d57dc416ee"}}, "title": "Massive Gene Loss in the Fungus Sporothrix epigloea Accompanied a Shift to Life in a Glucuronoxylomannan-based Gel Matrix.", "authors": [{"family": "Allen", "given": "Carmen C G", "initials": "CCG", "orcid": "0000-0002-0318-4293", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e0047745454417bbc369d79d932c82c.json"}}, {"family": "D\u00edaz-Escand\u00f3n", "given": "David", "initials": "D", "orcid": "0000-0001-6588-6621", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c3d65614fae4317a61591439d45d75d.json"}}, {"family": "DeLong-Duhon", "given": "Sarah", "initials": "S", "orcid": "0000-0003-1865-2413", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4dc069df7c184898b26ae8da29b38df0.json"}}, {"family": "Tagirdzhanova", "given": "Gulnara", "initials": "G", "orcid": "0000-0002-8493-2387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bea413deb99d4292a70265fd906af4a1.json"}}, {"family": "Huereca", "given": "Alejandro", "initials": "A", "orcid": "0000-0002-6460-2380", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33c9108b09044812a3605359d03061bc.json"}}, {"family": "Reckseidler-Zenteno", "given": "Shauna", "initials": "S", "orcid": "0000-0003-1077-3755", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9e7c75afbfb4f179abb608f1422c3dd.json"}}, {"family": "Forbes", "given": "Andrew", "initials": "A", "orcid": "0000-0001-8332-6652", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/575cfc3e972448eea49b3fa0d79b1e52.json"}}, {"family": "Spribille", "given": "Toby", "initials": "T", "orcid": "0000-0002-9855-4591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18b90e5c247f45db979b35cd50a13bf9.json"}}], "type": "journal article", "published": "2025-02-03", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "17", "issue": "2", "issn-l": "1759-6653"}, "abstract": "Fungi are well-known for their ability to both produce and catabolize complex carbohydrates to acquire carbon, often in the most extreme of environments. Glucuronoxylomannan (GXM)-based gel matrices are widely produced by fungi in nature and though they are of key interest in medicine and pharmaceuticals, their biodegradation is poorly understood. Though some organisms, including other fungi, are adapted to life in and on GXM-like matrices in nature, they are almost entirely unstudied, and it is unknown if they are involved in matrix degradation. Sporothrix epigloea is an ascomycete fungus that completes its life cycle entirely in the short-lived secreted polysaccharide matrix of a white jelly fungus, Tremella fuciformis. To gain insight into how S. epigloea adapted to life in this unusual microhabitat, we compared the predicted protein composition of S. epigloea to that of 21 other Sporothrix species. We found that the genome of S. epigloea is smaller than that of any other sampled Sporothrix, with widespread functional gene loss, including those coding for serine proteases and biotin synthesis. In addition, many predicted CAZymes degrading both plant and fungal cell wall components were lost while a lytic polysaccharide monooxygenase with no previously established activity or substrate specificity, appears to have been gained. Phenotype assays suggest narrow use of mannans and other oligosaccharides as carbon sources. Taken together, the results suggest a streamlined machinery, including potential carbon sourcing from GXM building blocks, facilitates the hyperspecialized ecology of S. epigloea in the GXM-like milieu.", "doi": "10.1093/gbe/evaf015", "pmid": "39865500", "labels": {"Gulnara Tagirdzhanova": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11822852"}, {"db": "pii", "key": "7981255"}], "notes": [], "created": "2026-11-04T13:19:01.262Z", "modified": "2026-11-04T13:19:20.911Z"}, {"entity": "publication", "iuid": "04fd403116324309aac56c0c3f2b74f0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/04fd403116324309aac56c0c3f2b74f0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/04fd403116324309aac56c0c3f2b74f0"}}, "title": "Microbial occurrence and symbiont detection in a global sample of lichen metagenomes.", "authors": [{"family": "Tagirdzhanova", "given": "Gulnara", "initials": "G"}, {"family": "Saary", "given": "Paul", "initials": "P"}, {"family": "Cameron", "given": "Ellen S", "initials": "ES"}, {"family": "Allen", "given": "Carmen C G", "initials": "CCG"}, {"family": "Garber", "given": "Arkadiy I", "initials": "AI"}, {"family": "Escand\u00f3n", "given": "David D\u00edaz", "initials": "DD"}, {"family": "Cook", "given": "Andrew T", "initials": "AT"}, {"family": "Goyette", "given": "Spencer", "initials": "S"}, {"family": "Nogerius", "given": "Veera Tuovinen", "initials": "VT"}, {"family": "Passo", "given": "Alfredo", "initials": "A"}, {"family": "Mayrhofer", "given": "Helmut", "initials": "H"}, {"family": "Holien", "given": "H\u00e5kon", "initials": "H"}, {"family": "T\u00f8nsberg", "given": "Tor", "initials": "T"}, {"family": "Stein", "given": "Lisa Y", "initials": "LY"}, {"family": "Finn", "given": "Robert D", "initials": "RD", "orcid": "0000-0001-8626-2148", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6128c68b2dc4673bb80982e445e4de0.json"}}, {"family": "Spribille", "given": "Toby", "initials": "T", "orcid": "0000-0002-9855-4591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18b90e5c247f45db979b35cd50a13bf9.json"}}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "PLoS Biol.", "issn": "1545-7885", "volume": "22", "issue": "11", "pages": "e3002862", "issn-l": "1544-9173"}, "abstract": "In lichen research, metagenomes are increasingly being used for evaluating symbiont composition and metabolic potential, but the overall content and limitations of these metagenomes have not been assessed. We reassembled over 400 publicly available metagenomes, generated metagenome-assembled genomes (MAGs), constructed phylogenomic trees, and mapped MAG occurrence and frequency across the data set. Ninety-seven percent of the 1,000 recovered MAGs were bacterial or the fungal symbiont that provides most cellular mass. Our mapping of recovered MAGs provides the most detailed survey to date of bacteria in lichens and shows that 4 family-level lineages from 2 phyla accounted for as many bacterial occurrences in lichens as all other 71 families from 16 phyla combined. Annotation of highly complete bacterial, fungal, and algal MAGs reveals functional profiles that suggest interdigitated vitamin prototrophies and auxotrophies, with most lichen fungi auxotrophic for biotin, most bacteria auxotrophic for thiamine and the few annotated algae with partial or complete pathways for both, suggesting a novel dimension of microbial cross-feeding in lichen symbioses. Contrary to longstanding hypotheses, we found no annotations consistent with nitrogen fixation in bacteria other than known cyanobacterial symbionts. Core lichen symbionts such as algae were recovered as MAGs in only a fraction of the lichen symbioses in which they are known to occur. However, the presence of these and other microbes could be detected at high frequency using small subunit rRNA analysis, including in many lichens in which they are not otherwise recognized to occur. The rate of MAG recovery correlates with sequencing depth, but is almost certainly influenced by biological attributes of organisms that affect the likelihood of DNA extraction, sequencing and successful assembly, including cellular abundance, ploidy and strain co-occurrence. Our results suggest that, though metagenomes are a powerful tool for surveying microbial occurrence, they are of limited use in assessing absence, and their interpretation should be guided by an awareness of the interacting effects of microbial community complexity and sequencing depth.", "doi": "10.1371/journal.pbio.3002862", "pmid": "39509454", "labels": {"Gulnara Tagirdzhanova": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11542873"}, {"db": "pii", "key": "PBIOLOGY-D-24-00500"}], "notes": [], "created": "2026-11-04T13:19:03.388Z", "modified": "2026-11-04T13:19:22.863Z"}, {"entity": "publication", "iuid": "cda25c80800d458a870f052fc8019e29", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cda25c80800d458a870f052fc8019e29.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cda25c80800d458a870f052fc8019e29"}}, "title": "Evolutionary biology of lichen symbioses.", "authors": [{"family": "Spribille", "given": "Toby", "initials": "T", "orcid": "0000-0002-9855-4591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18b90e5c247f45db979b35cd50a13bf9.json"}}, {"family": "Resl", "given": "Philipp", "initials": "P", "orcid": "0000-0002-7841-6060", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f668746f83945dc8d616ae8022842f2.json"}}, {"family": "Stanton", "given": "Daniel E", "initials": "DE", "orcid": "0000-0002-6713-9328", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b2799c0904814734b811397f9f7343b0.json"}}, {"family": "Tagirdzhanova", "given": "Gulnara", "initials": "G", "orcid": "0000-0002-8493-2387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bea413deb99d4292a70265fd906af4a1.json"}}], "type": "journal article", "published": "2022-06-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "234", "issue": "5", "pages": "1566-1582", "issn-l": "0028-646X"}, "abstract": "Lichens are the symbiotic outcomes of open, interspecies relationships, central to which are a fungus and a phototroph, typically an alga and/or cyanobacterium. The evolutionary processes that led to the global success of lichens are poorly understood. In this review, we explore the goods and services exchange between fungus and phototroph and how this propelled the success of both symbiont and symbiosis. Lichen fungal symbionts count among the only filamentous fungi that expose most of their mycelium to an aerial environment. Phototrophs export carbohydrates to the fungus, which converts them to specific polyols. Experimental evidence suggests that polyols are not only growth and respiratory substrates but also play a role in anhydrobiosis, the capacity to survive desiccation. We propose that this dual functionality is pivotal to the evolution of fungal symbionts, enabling persistence in environments otherwise hostile to fungi while simultaneously imposing costs on growth. Phototrophs, in turn, benefit from fungal protection from herbivory and light stress, while appearing to exert leverage over fungal sex and morphogenesis. Combined with the recently recognized habit of symbionts to occur in multiple symbioses, this creates the conditions for a multiplayer marketplace of rewards and penalties that could drive symbiont selection and lichen diversification.", "doi": "10.1111/nph.18048", "pmid": "35302240", "labels": {"Gulnara Tagirdzhanova": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2026-11-04T13:26:58.912Z", "modified": "2026-11-04T13:26:59.002Z"}, {"entity": "publication", "iuid": "30d2d3695ad047b0b8918c724a7da176", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/30d2d3695ad047b0b8918c724a7da176.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/30d2d3695ad047b0b8918c724a7da176"}}, "title": "Lichen fungi do not depend on the alga for ATP production: A comment on Pogoda et al. (2018).", "authors": [{"family": "Tagirdzhanova", "given": "Gulnara", "initials": "G", "orcid": "0000-0002-8493-2387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bea413deb99d4292a70265fd906af4a1.json"}}, {"family": "McCutcheon", "given": "John P", "initials": "JP", "orcid": "0000-0002-5489-6039", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a9cf48ebccac45098e0f3f120ca1b6d9.json"}}, {"family": "Spribille", "given": "Toby", "initials": "T", "orcid": "0000-0002-9855-4591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18b90e5c247f45db979b35cd50a13bf9.json"}}], "type": "letter", "published": "2021-09-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "30", "issue": "17", "pages": "4155-4159", "issn-l": "0962-1083"}, "abstract": "Lichen fungi live in a symbiotic association with unicellular phototrophs and most have no known aposymbiotic stage. A recent study in Molecular Ecology postulated that some of them have lost mitochondrial oxidative phosphorylation and rely on their algal partners for ATP. This claim originated from an apparent lack of ATP9, a gene encoding one subunit of ATP synthase, from a few mitochondrial genomes. Here, we show that while these fungi indeed have lost the mitochondrial ATP9, each retain a nuclear copy of this gene. Our analysis reaffirms that lichen fungi produce their own ATP.", "doi": "10.1111/mec.16010", "pmid": "34232528", "labels": {"Gulnara Tagirdzhanova": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "Dryad", "key": "10.5061/dryad.xgxd254gd"}], "notes": [], "created": "2026-11-04T13:27:03.266Z", "modified": "2026-11-04T13:27:03.398Z"}]}