Chromosome-level assemblies from diverse clades reveal limited structural and gene content variation in the genome of Candida glabrata
Abstract Background Candida glabrata is an opportunistic yeast pathogen thought to have a large genetic and phenotypic diversity and a highly plastic genome. However, the lack of chromosome-level genome assemblies representing this diversity limits our ability to accurately establish how chromosomal...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-10-01
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| Series: | BMC Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12915-022-01412-1 |
| _version_ | 1811226526035738624 |
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| author | Marina Marcet-Houben María Alvarado Ewa Ksiezopolska Ester Saus Piet W. J. de Groot Toni Gabaldón |
| author_facet | Marina Marcet-Houben María Alvarado Ewa Ksiezopolska Ester Saus Piet W. J. de Groot Toni Gabaldón |
| author_sort | Marina Marcet-Houben |
| collection | DOAJ |
| description | Abstract Background Candida glabrata is an opportunistic yeast pathogen thought to have a large genetic and phenotypic diversity and a highly plastic genome. However, the lack of chromosome-level genome assemblies representing this diversity limits our ability to accurately establish how chromosomal structure and gene content vary across strains. Results Here, we expanded publicly available assemblies by using long-read sequencing technologies in twelve diverse strains, obtaining a final set of twenty-one chromosome-level genomes spanning the known C. glabrata diversity. Using comparative approaches, we inferred variation in chromosome structure and determined the pan-genome, including an analysis of the adhesin gene repertoire. Our analysis uncovered four new adhesin orthogroups and inferred a rich ancestral adhesion repertoire, which was subsequently shaped through a still ongoing process of gene loss, gene duplication, and gene conversion. Conclusions C. glabrata has a largely stable pan-genome except for a highly variable subset of genes encoding cell wall-associated functions. Adhesin repertoire was established for each strain and showed variability among clades. |
| first_indexed | 2024-04-12T09:26:35Z |
| format | Article |
| id | doaj.art-24a60922742d4dd48b09e64fd97109b0 |
| institution | Directory Open Access Journal |
| issn | 1741-7007 |
| language | English |
| last_indexed | 2024-04-12T09:26:35Z |
| publishDate | 2022-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj.art-24a60922742d4dd48b09e64fd97109b02022-12-22T03:38:28ZengBMCBMC Biology1741-70072022-10-0120111710.1186/s12915-022-01412-1Chromosome-level assemblies from diverse clades reveal limited structural and gene content variation in the genome of Candida glabrataMarina Marcet-Houben0María Alvarado1Ewa Ksiezopolska2Ester Saus3Piet W. J. de Groot4Toni Gabaldón5Barcelona Supercomputing Centre (BSC-CNS)Regional Center for Biomedical Research, University of Castilla-La ManchaBarcelona Supercomputing Centre (BSC-CNS)Barcelona Supercomputing Centre (BSC-CNS)Regional Center for Biomedical Research, University of Castilla-La ManchaBarcelona Supercomputing Centre (BSC-CNS)Abstract Background Candida glabrata is an opportunistic yeast pathogen thought to have a large genetic and phenotypic diversity and a highly plastic genome. However, the lack of chromosome-level genome assemblies representing this diversity limits our ability to accurately establish how chromosomal structure and gene content vary across strains. Results Here, we expanded publicly available assemblies by using long-read sequencing technologies in twelve diverse strains, obtaining a final set of twenty-one chromosome-level genomes spanning the known C. glabrata diversity. Using comparative approaches, we inferred variation in chromosome structure and determined the pan-genome, including an analysis of the adhesin gene repertoire. Our analysis uncovered four new adhesin orthogroups and inferred a rich ancestral adhesion repertoire, which was subsequently shaped through a still ongoing process of gene loss, gene duplication, and gene conversion. Conclusions C. glabrata has a largely stable pan-genome except for a highly variable subset of genes encoding cell wall-associated functions. Adhesin repertoire was established for each strain and showed variability among clades.https://doi.org/10.1186/s12915-022-01412-1Candida glabrataGenomicsPan-genomeAdhesins |
| spellingShingle | Marina Marcet-Houben María Alvarado Ewa Ksiezopolska Ester Saus Piet W. J. de Groot Toni Gabaldón Chromosome-level assemblies from diverse clades reveal limited structural and gene content variation in the genome of Candida glabrata BMC Biology Candida glabrata Genomics Pan-genome Adhesins |
| title | Chromosome-level assemblies from diverse clades reveal limited structural and gene content variation in the genome of Candida glabrata |
| title_full | Chromosome-level assemblies from diverse clades reveal limited structural and gene content variation in the genome of Candida glabrata |
| title_fullStr | Chromosome-level assemblies from diverse clades reveal limited structural and gene content variation in the genome of Candida glabrata |
| title_full_unstemmed | Chromosome-level assemblies from diverse clades reveal limited structural and gene content variation in the genome of Candida glabrata |
| title_short | Chromosome-level assemblies from diverse clades reveal limited structural and gene content variation in the genome of Candida glabrata |
| title_sort | chromosome level assemblies from diverse clades reveal limited structural and gene content variation in the genome of candida glabrata |
| topic | Candida glabrata Genomics Pan-genome Adhesins |
| url | https://doi.org/10.1186/s12915-022-01412-1 |
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