{"doi":"10.7554/elife.71348","title":"Gene age shapes the transcriptional landscape of sexual morphogenesis in mushroom-forming fungi (Agaricomycetes)","abstract":"<jats:p>\n                    Multicellularity has been one of the most important innovations in the history of life. The role of gene regulatory changes in driving transitions to multicellularity is being increasingly recognized; however, factors influencing gene expression patterns are poorly known in many clades. Here, we compared the developmental transcriptomes of complex multicellular fruiting bodies of eight Agaricomycetes and\n                    <jats:italic>Cryptococcus neoformans</jats:italic>\n                    , a closely related human pathogen with a simple morphology. In-depth analysis in\n                    <jats:italic>Pleurotus ostreatus</jats:italic>\n                    revealed that allele-specific expression, natural antisense transcripts, and developmental gene expression, but not RNA editing or a ‘developmental hourglass,’ act in concert to shape its transcriptome during fruiting body development. We found that transcriptional patterns of genes strongly depend on their evolutionary ages. Young genes showed more developmental and allele-specific expression variation, possibly because of weaker evolutionary constraint, suggestive of nonadaptive expression variance in fruiting bodies. These results prompted us to define a set of conserved genes specifically regulated only during complex morphogenesis by excluding young genes and accounting for deeply conserved ones shared with species showing simple sexual development. Analysis of the resulting gene set revealed evolutionary and functional associations with complex multicellularity, which allowed us to speculate they are involved in complex multicellular morphogenesis of mushroom fruiting bodies.\n                  </jats:p>","journal":"eLife","year":2022,"id":611965,"datarank":0.9121103141781703,"base_score":3.4339872044851463,"endowment":3.4339872044851463,"self_citation_contribution":0.515098080672772,"citation_network_contribution":0.3970122335053984,"self_endowment_contribution":0.515098080672772,"citer_contribution":0.3970122335053984,"corpus_percentile":null,"corpus_rank":null,"citation_count":30,"citer_count":18,"citers_with_citation_signal":17,"citers_with_endowment":17,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1575376,"name":"Máté Virágh","orcid":null,"position":1,"is_corresponding":false},{"id":1575377,"name":"Emile Gluck-Thaler","orcid":null,"position":2,"is_corresponding":false},{"id":482267,"name":"Jason C. Slot","orcid":"0000-0001-6731-3405","position":3,"is_corresponding":false},{"id":1350220,"name":"Brigitta Kiss","orcid":null,"position":4,"is_corresponding":false},{"id":1575378,"name":"Torda Varga","orcid":null,"position":5,"is_corresponding":false},{"id":1575379,"name":"András Geösel","orcid":null,"position":6,"is_corresponding":false},{"id":1575380,"name":"Botond Hegedüs","orcid":null,"position":7,"is_corresponding":false},{"id":1575381,"name":"Balázs Bálint","orcid":null,"position":8,"is_corresponding":false},{"id":1388893,"name":"László G. Nagy","orcid":"0000-0002-4102-8566","position":9,"is_corresponding":false},{"id":1575375,"name":"Zsolt Merényi","orcid":"0000-0003-1114-3739","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Gene age shapes the transcriptional landscape of sexual morphogenesis in mushroom-forming fungi (Agaricomycetes)","abstract":"<jats:p>\n                    Multicellularity has been one of the most important innovations in the history of life. The role of gene regulatory changes in driving transitions to multicellularity is being increasingly recognized; however, factors influencing gene expression patterns are poorly known in many clades. Here, we compared the developmental transcriptomes of complex multicellular fruiting bodies of eight Agaricomycetes and\n                    <jats:italic>Cryptococcus neoformans</jats:italic>\n                    , a closely related human pathogen with a simple morphology. In-depth analysis in\n                    <jats:italic>Pleurotus ostreatus</jats:italic>\n                    revealed that allele-specific expression, natural antisense transcripts, and developmental gene expression, but not RNA editing or a ‘developmental hourglass,’ act in concert to shape its transcriptome during fruiting body development. We found that transcriptional patterns of genes strongly depend on their evolutionary ages. Young genes showed more developmental and allele-specific expression variation, possibly because of weaker evolutionary constraint, suggestive of nonadaptive expression variance in fruiting bodies. These results prompted us to define a set of conserved genes specifically regulated only during complex morphogenesis by excluding young genes and accounting for deeply conserved ones shared with species showing simple sexual development. Analysis of the resulting gene set revealed evolutionary and functional associations with complex multicellularity, which allowed us to speculate they are involved in complex multicellular morphogenesis of mushroom fruiting bodies.\n                  </jats:p>","is_dataset_classified":null,"base_score":3.4339872044851463,"endowment":3.4339872044851463,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"35156613","pmcid":null,"openalex_id":"https://openalex.org/W4213110856","authors":[],"funders":[{"funder_name":"Hungarian National Research, Development, and Innovation Office","grant_id":"GINOP-2.3.2-15-2016-00052","title":null},{"funder_name":"Hungarian Academy of Sciences","grant_id":"Momentum Program LP2019-13/2019","title":null},{"funder_name":"European Research Council","grant_id":"758161","title":"The genetic basis of the convergent evolution of fungal multicellularity"}],"total_grants":3,"fwci":4.383,"citation_percentile":0.94842877,"influential_citations":0,"citation_trend":[{"year":2021,"count":1},{"year":2022,"count":8},{"year":2023,"count":7},{"year":2024,"count":8},{"year":2025,"count":4},{"year":2026,"count":2}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://doi.org/10.7554/elife.71348","host_type":"journal"},{"url":"https://doi.org/10.7554/elife.71348","host_type":"publisher"},{"url":"https://cdn.elifesciences.org/articles/71348/elife-71348-v2.pdf","host_type":"publisher"},{"url":"https://cdn.elifesciences.org/articles/71348/elife-71348-v2.xml","host_type":"publisher"},{"url":"https://elifesciences.org/articles/71348","host_type":"publisher"},{"url":"https://pubmed.ncbi.nlm.nih.gov/35156613","host_type":"repository"},{"url":"https://doaj.org/article/6833d0813aa1445b9f900b92dd9e530f","host_type":"repository"},{"url":"http://hdl.handle.net/10831/114178","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8893723","host_type":"repository"},{"url":"https://elifesciences.org/download/aHR0cHM6Ly9jZG4uZWxpZmVzY2llbmNlcy5vcmcvYXJ0aWNsZXMvNzEzNDgvZWxpZmUtNzEzNDgtdjEucGRmP2Nhbm9uaWNhbFVyaT1odHRwczovL2VsaWZlc2NpZW5jZXMub3JnL2FydGljbGVzLzcxMzQ4/elife-71348-v1.pdf?_hash=yk%2BlCXrSVtXl5Pwc5pwiiXbQ9r5d819z8T0o9zixRLk%3D","host_type":""},{"url":"http://dx.doi.org/10.7554/eLife.71348","host_type":""},{"url":"http://dx.doi.org/10.7554/elife.71348","host_type":""},{"url":"https://doi.org/https://doi.org/10.7554/eLife.71348","host_type":""}],"fields_of_study":["Fungal Biology and Applications","Mycorrhizal Fungi and Plant Interactions","Fungal and yeast genetics research","0301 basic medicine","0303 health sciences","03 medical and health sciences"],"mesh_terms":["Agaricales","Ascomycota","Basidiomycota","Fungal Proteins","Gene Expression Regulation, Fungal","Fruiting Bodies, Fungal"],"keywords":["Agaricomycetes","Mushroom","Biology","Morphogenesis","Gene","Genetics","Evolutionary biology","Botany","Basidiomycota","developmental hourglass","QH301-705.5","Science","Q","R","mushroom-forming fungi","Pleurotus ostreatus","Fungal Proteins","Ascomycota","Coprinopsis cinerea","allelic imbalance","Gene Expression Regulation, Fungal","Cryptococcus neoformans","Medicine","Fruiting Bodies, Fungal","Biology (General)","QH301 Biology / biológia","Agaricales","Developmental Biology"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life in Land"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-02T00:20:54.095876Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}