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

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.

Keywords: diversity; killer toxin; phenotype; population genomics; transposable elements.

Figure 1

Maximum likelihood phylogenetic tree obtained from 133,528 biallelic SNPs present in at least two strains using RAxML (evolution model: GTRGAMMA). Only bootstrap values under 100 are indicated.

Figure 2

Region of 32 kb on chromosome Yali0B is duplicated in strain CBS 7326 between positions 2,239,806 and 2,271,919 of the E150 reference genome. (A) read mapping depth plot of the region, (B) list of genes present in this region, (C) maximum likelihood phylogenetic tree obtained using IQ-TREE (best evolution model according to BIC: HKY + F + I). The two copies of the region present in CBS 7326 are in red. Bootstrap values are indicated.

Figure 3

Analysis of transposable elements in the population of 56 strains. (A) overall amount of TEs as a fraction of the genome, (B) relative amount of TEs in each strain.

Figure 4

Analysis of the sensitivity to Debaryomyces hansenii killer toxin. (A) picture of the inhibition zone around D. hansenii cells expressing the two killer toxins (AII4bR vertical line, AII4bS horizontal line), (B) boxplot of the size of the inhibition zone according to the clades, each with a different colour. Letters mark significant differences between clades according to Tukey’s HSD (Honest Significant Difference) test.

Figure 5

Lipase activity on tributyrin. (A) halo formation around colonies grown on media containing tributyrin and YNB, (B) halo size as a function of the clade as obtained on the YNB media, (C) halo formation around colonies grown on media containing tributyrin and YP, (D) halo size as a function of the clade as obtained on the YP media.

Figure 6

Lipid synthesis and accumulation were monitored as described in the materials and methods section. (A) lipid content for each strain of Y. lipolytica. Strain numbers in black correspond to the ID in Supplementary Table S1. The number of replicated measures is in white. (B) lipid content as a function of clade. (C) microscopic photography showing yeast cells with lipid bodies colored in green with BODIPY^®.

Figure 7

Nucleotide variations found in XPR2. Comparison is relative to gene YALIH222S02e00408g of Y. lipolytica strain H222. Variants specific to strains showing no halo on the skimmed milk medium are shown. Yellow stars indicate the nucleotide position of the mutations.