{"doi":"10.1371/journal.pgen.1011396","title":"An integrative taxonomy approach reveals Saccharomyces chiloensis sp. nov. as a newly discovered species from Coastal Patagonia","abstract":"<jats:p>\n                    Species delineation in microorganisms is challenging due to the limited markers available for accurate species assignment. Here, we applied an integrative taxonomy approach, combining extensive sampling, whole-genome sequence-based classification, phenotypic profiling, and assessment of interspecific reproductive isolation. Our work reveals the presence of a distinct\n                    <jats:italic>Saccharomyces</jats:italic>\n                    lineage in\n                    <jats:italic>Nothofagus</jats:italic>\n                    forests of coastal Patagonia. This lineage, designated\n                    <jats:italic>Saccharomyces chiloensis</jats:italic>\n                    sp. nov., exhibits 7% genetic divergence from its sister species\n                    <jats:italic>S</jats:italic>\n                    .\n                    <jats:italic>uvarum</jats:italic>\n                    , as revealed by whole-genome sequencing and population analyses. The South America-C (SA-C) coastal Patagonia population forms a unique clade closely related to a previously described divergent\n                    <jats:italic>S</jats:italic>\n                    .\n                    <jats:italic>uvarum</jats:italic>\n                    population from Oceania (AUS, found in Australia and New Zealand). Our species reclassification is supported by a low Ortho Average Nucleotide Identity (OANI) of 93% in SA-C and AUS relative to\n                    <jats:italic>S</jats:italic>\n                    .\n                    <jats:italic>uvarum</jats:italic>\n                    , which falls below the suggested species delineation threshold of 95%, indicating an independent evolutionary lineage. Hybrid spore viability assessment provided compelling evidence that SA-C and AUS are reproductively isolated from\n                    <jats:italic>S</jats:italic>\n                    .\n                    <jats:italic>uvarum</jats:italic>\n                    . In addition, we found unique structural variants between\n                    <jats:italic>S</jats:italic>\n                    .\n                    <jats:italic>chiloensis</jats:italic>\n                    sp. nov. lineages, including large-scale chromosomal translocations and inversions, together with a distinct phenotypic profile, emphasizing their intraspecies genetic distinctiveness. We suggest that\n                    <jats:italic>S</jats:italic>\n                    .\n                    <jats:italic>chiloensis</jats:italic>\n                    sp. nov diverged from\n                    <jats:italic>S</jats:italic>\n                    .\n                    <jats:italic>uvarum</jats:italic>\n                    in allopatry due to glaciation, followed by post-glacial dispersal, resulting in distinct lineages on opposite sides of the Pacific Ocean. The discovery of\n                    <jats:italic>S</jats:italic>\n                    .\n                    <jats:italic>chiloensis</jats:italic>\n                    sp. nov. illustrates the uniqueness of Patagonia’s coastal biodiversity and underscores the importance of adopting an integrative taxonomic approach in species delineation to unveil cryptic microbial species. The holotype of\n                    <jats:italic>S</jats:italic>\n                    .\n                    <jats:italic>chiloensis</jats:italic>\n                    sp. nov. is CBS 18620\n                    <jats:sup>T</jats:sup>\n                    .\n                  </jats:p>","journal":"PLOS Genetics","year":2024,"id":608849,"datarank":0.41588830833596724,"base_score":2.772588722239781,"endowment":2.772588722239781,"self_citation_contribution":0.41588830833596724,"citation_network_contribution":0.0,"self_endowment_contribution":0.41588830833596724,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":15,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"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":1564236,"name":"Pablo Villarreal","orcid":"0000-0002-2254-0417","position":1,"is_corresponding":false},{"id":1564237,"name":"Nicolas Agier","orcid":null,"position":2,"is_corresponding":false},{"id":381267,"name":"Matteo De Chiara","orcid":"0000-0003-1014-350X","position":3,"is_corresponding":false},{"id":1564238,"name":"Tomas Barría","orcid":null,"position":4,"is_corresponding":false},{"id":1564239,"name":"Kamila Urbina","orcid":null,"position":5,"is_corresponding":false},{"id":1564240,"name":"Carlos A. Villarroel","orcid":"0000-0002-6089-3088","position":6,"is_corresponding":false},{"id":1564241,"name":"Ana R. O. Santos","orcid":"0000-0001-9320-7673","position":7,"is_corresponding":false},{"id":1018613,"name":"Carlos A. Rosa","orcid":"0000-0002-0056-9075","position":8,"is_corresponding":false},{"id":844481,"name":"Roberto F. Nespolo","orcid":"0000-0003-0825-9618","position":9,"is_corresponding":false},{"id":381270,"name":"Gianni Liti","orcid":"0000-0002-2318-0775","position":10,"is_corresponding":false},{"id":1564242,"name":"Gilles Fischer","orcid":"0000-0001-5732-2682","position":11,"is_corresponding":false},{"id":76019,"name":"Francisco A. Cubillos","orcid":"0000-0003-3022-469X","position":12,"is_corresponding":false},{"id":1564235,"name":"Tomas A. Peña","orcid":"0009-0003-3201-743X","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"An integrative taxonomy approach reveals Saccharomyces chiloensis sp. nov. as a newly discovered species from Coastal Patagonia","abstract":"<jats:p>\n                    Species delineation in microorganisms is challenging due to the limited markers available for accurate species assignment. Here, we applied an integrative taxonomy approach, combining extensive sampling, whole-genome sequence-based classification, phenotypic profiling, and assessment of interspecific reproductive isolation. Our work reveals the presence of a distinct\n                    <jats:italic>Saccharomyces</jats:italic>\n                    lineage in\n                    <jats:italic>Nothofagus</jats:italic>\n                    forests of coastal Patagonia. This lineage, designated\n                    <jats:italic>Saccharomyces chiloensis</jats:italic>\n                    sp. nov., exhibits 7% genetic divergence from its sister species\n                    <jats:italic>S</jats:italic>\n                    .\n                    <jats:italic>uvarum</jats:italic>\n                    , as revealed by whole-genome sequencing and population analyses. The South America-C (SA-C) coastal Patagonia population forms a unique clade closely related to a previously described divergent\n                    <jats:italic>S</jats:italic>\n                    .\n                    <jats:italic>uvarum</jats:italic>\n                    population from Oceania (AUS, found in Australia and New Zealand). Our species reclassification is supported by a low Ortho Average Nucleotide Identity (OANI) of 93% in SA-C and AUS relative to\n                    <jats:italic>S</jats:italic>\n                    .\n                    <jats:italic>uvarum</jats:italic>\n                    , which falls below the suggested species delineation threshold of 95%, indicating an independent evolutionary lineage. Hybrid spore viability assessment provided compelling evidence that SA-C and AUS are reproductively isolated from\n                    <jats:italic>S</jats:italic>\n                    .\n                    <jats:italic>uvarum</jats:italic>\n                    . In addition, we found unique structural variants between\n                    <jats:italic>S</jats:italic>\n                    .\n                    <jats:italic>chiloensis</jats:italic>\n                    sp. nov. lineages, including large-scale chromosomal translocations and inversions, together with a distinct phenotypic profile, emphasizing their intraspecies genetic distinctiveness. We suggest that\n                    <jats:italic>S</jats:italic>\n                    .\n                    <jats:italic>chiloensis</jats:italic>\n                    sp. nov diverged from\n                    <jats:italic>S</jats:italic>\n                    .\n                    <jats:italic>uvarum</jats:italic>\n                    in allopatry due to glaciation, followed by post-glacial dispersal, resulting in distinct lineages on opposite sides of the Pacific Ocean. The discovery of\n                    <jats:italic>S</jats:italic>\n                    .\n                    <jats:italic>chiloensis</jats:italic>\n                    sp. nov. illustrates the uniqueness of Patagonia’s coastal biodiversity and underscores the importance of adopting an integrative taxonomic approach in species delineation to unveil cryptic microbial species. The holotype of\n                    <jats:italic>S</jats:italic>\n                    .\n                    <jats:italic>chiloensis</jats:italic>\n                    sp. nov. is CBS 18620\n                    <jats:sup>T</jats:sup>\n                    .\n                  </jats:p>","is_dataset_classified":null,"base_score":2.70805020110221,"endowment":2.70805020110221,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"39241096","pmcid":"PMC11410238","openalex_id":"https://openalex.org/W4402300803","authors":[],"funders":[{"funder_name":"Agencia Nacional de Investigación y Desarrollo","grant_id":"ICN17_022","title":null},{"funder_name":"Agencia Nacional de Investigación y Desarrollo","grant_id":"NCN2021_050","title":null},{"funder_name":"Agencia Nacional de Investigación y Desarrollo","grant_id":"FONDECYT 1220026","title":null},{"funder_name":"Agencia Nacional de Investigación y Desarrollo","grant_id":"21221095","title":null},{"funder_name":"Agencia Nacional de Investigación y Desarrollo","grant_id":"FONDECYT INICIACIÓN 11240649","title":null},{"funder_name":"FONDECYT INICIACIÓN","grant_id":"11230724","title":null},{"funder_name":"FONDECYT","grant_id":"1221073","title":null},{"funder_name":"Agencia Nacional de Investigación y Desarrollo","grant_id":"ECOS230001","title":null},{"funder_name":"Conselho Nacional de Desenvolvimento Científico e Tecnológico","grant_id":"406564/2022-1","title":null},{"funder_name":"Conselho Nacional de Desenvolvimento Científico e Tecnológico","grant_id":"#406564/2022-1, and grants 313088/2020-9 and 408733/2021","title":null},{"funder_name":"Fundação do Amparo a Pesquisa do Estado de Minas Gerais","grant_id":"APQ-03071–17","title":null}],"total_grants":11,"fwci":2.3049,"citation_percentile":0.89069436,"influential_citations":0,"citation_trend":[{"year":2024,"count":2},{"year":2025,"count":8},{"year":2026,"count":4}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://doi.org/10.1371/journal.pgen.1011396","host_type":"journal"},{"url":"https://doi.org/10.1371/journal.pgen.1011396","host_type":"publisher"},{"url":"https://dx.plos.org/10.1371/journal.pgen.1011396","host_type":"publisher"},{"url":"https://pubmed.ncbi.nlm.nih.gov/39241096","host_type":"repository"},{"url":"https://hal.science/hal-04797405","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11410238","host_type":"repository"},{"url":"https://hal.science/hal-04797405/document","host_type":"repository"},{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11410238/pdf/pgen.1011396.pdf","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC11410238","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC11410238?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Yeasts and Rust Fungi Studies","Plant Pathogens and Fungal Diseases","Mycorrhizal Fungi and Plant Interactions"],"mesh_terms":["Whole Genome Sequencing","Phylogeny","Saccharomyces","Reproductive Isolation"],"keywords":["Biology","Allopatric speciation","Reproductive isolation","Lineage (genetic)","Evolutionary biology","Population","Biological dispersal","Clade","Phylogenetics","Genetics","Gene"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life below water"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"gen"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-30T23:05:18.779384Z","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":[]}