Insights into the Genomic and Phenotypic Landscape of the Oleaginous Yeast Yarrowia lipolytica - Archive ouverte HAL Access content directly
Journal Articles Journal of Fungi Year : 2023

Insights into the Genomic and Phenotypic Landscape of the Oleaginous Yeast Yarrowia lipolytica

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1
Frédéric Bigey
Emilie Pasteur
  • Function : Author
Xymena Połomska
Stéphane Thomas
  • Function : Author
Anne-Marie Crutz-Le Coq
  • Function : Author
Cécile Neuvéglise

Abstract

Although Yarrowia lipolytica is a model yeast for the study of lipid metabolism, its diversity is poorly known, as studies generally consider only a few standard laboratory strains. To extend our knowledge of this biotechnological workhorse, we investigated the genomic and phenotypic diversity of 56 natural isolates. Y. lipolytica is classified into five clades with no correlation between clade membership and geographic or ecological origin. A low genetic diversity (π = 0.0017) and a pan-genome (6528 genes) barely different from the core genome (6315 genes) suggest Y. lipolytica is a recently evolving species. Large segmental duplications were detected, totaling 892 genes. With three new LTR-retrotransposons of the Gypsy family (Tyl4, Tyl9, and Tyl10), the transposable element content of genomes appeared diversified but still low (from 0.36% to 3.62%). We quantified 34 traits with substantial phenotypic diversity, but genome-wide association studies failed to evidence any associations. Instead, we investigated known genes and found four mutational events leading to XPR2 protease inactivation. Regarding lipid metabolism, most high-impact mutations were found in family-belonging genes, such as ALK or LIP, and therefore had a low phenotypic impact, suggesting that the huge diversity of lipid synthesis and accumulation is multifactorial or due to complex regulations.

Dates and versions

hal-03942758 , version 1 (17-01-2023)

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Frédéric Bigey, Emilie Pasteur, Xymena Połomska, Stéphane Thomas, Anne-Marie Crutz-Le Coq, et al.. Insights into the Genomic and Phenotypic Landscape of the Oleaginous Yeast Yarrowia lipolytica. Journal of Fungi, 2023, 9 (1), pp.76. ⟨10.3390/jof9010076⟩. ⟨hal-03942758⟩
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