{"doi":"10.1186/s12864-024-10979-8","title":"Chromosome level assemblies of Nakaseomyces (Candida) bracarensis uncover two distinct clades and define its adhesin repertoire","abstract":"<jats:title>Abstract</jats:title><jats:sec>\n                <jats:title>Background</jats:title>\n                <jats:p>The <jats:italic>Nakaseomyces</jats:italic> clade is formed by at least nine described species among which three can be pathogenic to humans, namely <jats:italic>Nakaseomyces glabratus</jats:italic> (<jats:italic>Candida glabrata</jats:italic>), the second most-common cause of candidiasis worldwide, and two rarer emerging pathogens: <jats:italic>Nakaseomyces (Candida) nivarensis</jats:italic> and <jats:italic>Nakaseomyces (Candida) bracarensis.</jats:italic> Early comparative genomics analyses identified parallel expansions of subtelomeric adhesin genes in <jats:italic>N. glabratus</jats:italic> and <jats:italic>N. nivarensis/bracarensis</jats:italic>, and suggested possible links with the emergence of the virulence potential in these species. However, as shown for <jats:italic>N. glabratus</jats:italic>, the proper assessment of subtelomeric genes is hindered by the use of incomplete assemblies and reliance on a single isolate.</jats:p>\n              </jats:sec><jats:sec>\n                <jats:title>Results</jats:title>\n                <jats:p>Here we sequenced seven <jats:italic>N. bracarensis</jats:italic> isolates and reconstructed chromosome level assemblies of two divergent strains. We show that <jats:italic>N. bracarensis</jats:italic> isolates belong to two diverging clades that have slightly different genomic structures. We identified the set of encoded adhesins in the two complete assemblies, and uncovered the presence of a novel adhesin motif, found mainly in <jats:italic>N. bracarensis</jats:italic>. Our analysis revealed a larger adhesin content in <jats:italic>N. bracarensis</jats:italic> than previously reported, and similar in size to that of <jats:italic>N. glabratus</jats:italic>. We confirm the independent adhesin expansion in these two species, which could relate to their different levels of virulence.</jats:p>\n              </jats:sec><jats:sec>\n                <jats:title>Conclusion</jats:title>\n                <jats:p><jats:italic>N. bracarensis</jats:italic> clinical isolates belong to at least two differentiated clades. We describe a novel repeat motif found in <jats:italic>N. bracarensis</jats:italic> adhesins, which helps in their identification. Adhesins underwent independent expansions in <jats:italic>N. glabratus</jats:italic> and <jats:italic>N. bracarensis</jats:italic>, leading to repertoires that are qualitatively different but quantitatively similar. Given that adhesins are considered virulence factors, some of the observed differences could contribute to variations in virulence capabilities between <jats:italic>N. glabratus</jats:italic> and <jats:italic>N. bracarensis.</jats:italic></jats:p>\n              </jats:sec>","journal":"BMC Genomics","year":2024,"id":608961,"datarank":0.2615867067028836,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"self_citation_contribution":0.24141568686511508,"citation_network_contribution":0.02017101983776849,"self_endowment_contribution":0.24141568686511508,"citer_contribution":0.02017101983776849,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":4,"citers_with_citation_signal":1,"citers_with_endowment":1,"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":856424,"name":"Ewa Księżopolska","orcid":"0000-0002-2021-4343","position":1,"is_corresponding":false},{"id":856428,"name":"Toni Gabaldón","orcid":"0000-0001-6436-2914","position":2,"is_corresponding":false},{"id":1564715,"name":"Marina Marcet-Houben","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Chromosome level assemblies of Nakaseomyces (Candida) bracarensis uncover two distinct clades and define its adhesin repertoire","abstract":"<jats:title>Abstract</jats:title><jats:sec>\n                <jats:title>Background</jats:title>\n                <jats:p>The <jats:italic>Nakaseomyces</jats:italic> clade is formed by at least nine described species among which three can be pathogenic to humans, namely <jats:italic>Nakaseomyces glabratus</jats:italic> (<jats:italic>Candida glabrata</jats:italic>), the second most-common cause of candidiasis worldwide, and two rarer emerging pathogens: <jats:italic>Nakaseomyces (Candida) nivarensis</jats:italic> and <jats:italic>Nakaseomyces (Candida) bracarensis.</jats:italic> Early comparative genomics analyses identified parallel expansions of subtelomeric adhesin genes in <jats:italic>N. glabratus</jats:italic> and <jats:italic>N. nivarensis/bracarensis</jats:italic>, and suggested possible links with the emergence of the virulence potential in these species. However, as shown for <jats:italic>N. glabratus</jats:italic>, the proper assessment of subtelomeric genes is hindered by the use of incomplete assemblies and reliance on a single isolate.</jats:p>\n              </jats:sec><jats:sec>\n                <jats:title>Results</jats:title>\n                <jats:p>Here we sequenced seven <jats:italic>N. bracarensis</jats:italic> isolates and reconstructed chromosome level assemblies of two divergent strains. We show that <jats:italic>N. bracarensis</jats:italic> isolates belong to two diverging clades that have slightly different genomic structures. We identified the set of encoded adhesins in the two complete assemblies, and uncovered the presence of a novel adhesin motif, found mainly in <jats:italic>N. bracarensis</jats:italic>. Our analysis revealed a larger adhesin content in <jats:italic>N. bracarensis</jats:italic> than previously reported, and similar in size to that of <jats:italic>N. glabratus</jats:italic>. We confirm the independent adhesin expansion in these two species, which could relate to their different levels of virulence.</jats:p>\n              </jats:sec><jats:sec>\n                <jats:title>Conclusion</jats:title>\n                <jats:p><jats:italic>N. bracarensis</jats:italic> clinical isolates belong to at least two differentiated clades. We describe a novel repeat motif found in <jats:italic>N. bracarensis</jats:italic> adhesins, which helps in their identification. Adhesins underwent independent expansions in <jats:italic>N. glabratus</jats:italic> and <jats:italic>N. bracarensis</jats:italic>, leading to repertoires that are qualitatively different but quantitatively similar. Given that adhesins are considered virulence factors, some of the observed differences could contribute to variations in virulence capabilities between <jats:italic>N. glabratus</jats:italic> and <jats:italic>N. bracarensis.</jats:italic></jats:p>\n              </jats:sec>","is_dataset_classified":null,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"39511470","pmcid":"PMC11542307","openalex_id":"https://openalex.org/W4404147835","authors":[],"funders":[{"funder_name":"HORIZON EUROPE European Research Council","grant_id":"724173","title":"Reticulate evolution: patterns and impacts of non-vertical inheritance in eukaryotic genomes."},{"funder_name":"‘la Caixa’ Foundation","grant_id":"LCF/PR/HR21/00737","title":null}],"total_grants":2,"fwci":1.2227,"citation_percentile":0.79298921,"influential_citations":0,"citation_trend":[{"year":2025,"count":1},{"year":2026,"count":3}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-024-10979-8","host_type":"journal"},{"url":"https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-024-10979-8","host_type":"publisher"},{"url":"https://link.springer.com/content/pdf/10.1186/s12864-024-10979-8.pdf","host_type":"publisher"},{"url":"https://link.springer.com/article/10.1186/s12864-024-10979-8/fulltext.html","host_type":"publisher"},{"url":"https://doi.org/10.1186/s12864-024-10979-8","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/39511470","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11542307","host_type":"repository"},{"url":"https://doaj.org/article/bdde5f3a57f24d7995fdf17c06921da4","host_type":"repository"},{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11542307/pdf/12864_2024_Article_10979.pdf","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC11542307","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC11542307?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.1186/s12864-024-10979-8","host_type":""}],"fields_of_study":["Antifungal resistance and susceptibility","Fungal Infections and Studies","Infectious Diseases and Mycology","0301 basic medicine","0303 health sciences","03 medical and health sciences","Phylogeny","Candida","Chromosomes, Fungal","Fungal Proteins","Genomics","Genome, Fungal"],"mesh_terms":["Candida","Fungal Proteins","Phylogeny","Chromosomes, Fungal","Genome, Fungal","Genomics"],"keywords":["Biology","Repertoire","Clade","Bacterial adhesin","Genetics","Evolutionary biology","DNA microarray","Chromosome","Computational biology","Gene","Phylogenetics","Virulence","Genomics","Adhesins","Nanopore","Nakaseomyces","Research","QH426-470","Fungal Proteins","Chromosomes, Fungal","Genome, Fungal","TP248.13-248.65","Phylogeny","Biotechnology","Candida"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life in Land"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"bioproject"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-31T01:13:24.440137Z","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":[]}