Differential adaptation of the yeast Candida anglica to fermented food

A single strain of Candida anglica, isolated from apple cider, is present in international yeast collections. Here, we present 7 new strains isolated from French PDO cheese. A high quality genome assembly with 8 near complete telomere-to-telomere chromosomes was obtained for strain 29B2s-10. Two other genomes of cheese strains and that of the cider strain were also sequenced and assembled. A high quality genome annotation was produced after extensive expert manual curation leading to a core genome composed of 5,966 CDS. Presence of a non-LTR retrotransposon of the L1 superfamily was reported. Analysis of the mating-type locus showed that the cider strain has a MATa locus whereas all cheese strains arbored a MATalpha locus, with a similar organisation as Candida albicans. We also gathered genetic (SNPs and indels) and phenotypic (quantitative traits in 37 conditions) data for the 8 strains. These results show that the cider strain is genetically divergent from the cheese strains which are all very closely related. Variations in phenotypic traits were observed within the cheese population under stress conditions (ethanol and hygromycin resistance, SDS sensitivity). Finally, we found that the cider strain has a much greater growth capacity under all the growing conditions used.