Chromosome-level assemblies from diverse clades reveal limited structural and gene content variation in the genome of Candida glabrata

• Published in: BMC biology Vol. 20; no. 1; pp. 1 - 226
• Main Authors: Marcet-Houben, Marina, Alvarado, María, Ksiezopolska, Ewa, Saus, Ester, de Groot, Piet W. J, Gabaldón, Toni
• Format: Journal Article
• Language: English
• Published: London BioMed Central Ltd 08.10.2022; BioMed Central; BMC
• Subjects: Adhesins; Assemblies; Candida; Candida glabrata; Cell adhesion molecules; Cell walls; Chromosomes; Datasets; Gene conversion; Gene duplication; Gene expression; Genetic aspects; Genetic diversity; Genomes; Genomics; Identification and classification; Natural history; Opportunist infection; Pan-genome; Pathogens; Phenotypic plasticity; Physiological aspects; Virulence; Yeasts; Spain
• ISSN: 1741-7007; 1741-7007
• DOI: 10.1186/s12915-022-01412-1

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. 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. 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.