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.

Impact of central carbon metabolism bypasses on the production of beta-carotene inYarrowia lipolytica

“…It can either assimilate lipids from the environment or synthesize triglycerides (TAGs) efficiently when ample carbon sources are available. However, there exists considerable variability in the lipid accumulation and synthesis abilities among individual Y. lipolytica strains (10). Although strain W29 is commonly used by numerous research groups, we opted to work with the strain YB-392 due to its superior lipid production capabilities (11).…”

Advances and perspectives in genetic expression and operation for the oleaginous yeast Yarrowia lipolytica

“…More recently, Liu et al [ 52 ] employed fluorescence-activated cell sorting (FACS) to construct an NHEJ-based GFP stochastic expression library. By screening the highly-expressed strains and analyzing possible integration sites, they identified new gene integration sites in Y. lipolytica [ 53 , 54 ]. These sites exhibited both high gene expression and integration efficiency, thus demonstrating the effectiveness of CRISPR/Cas9 gene editing for achieving successful integration in Y. lipolytica .…”

Whole-genome sequencing and phenotyping reveal specific adaptations ofLachancea thermotoleransto the winemaking environment

“…These include Torulaspora delbrueckki (Silva et al, 2023), Brettanomyces bruxellensis (Eberlein et al, 2021; Gounot et al, 2020), Hanseniaspora uvarum (Albertin et al, 2016), and Lachancea thermotolerans (Freel et al, 2014) (Hranilovic et al, 2017). Other yeasts genera associated with different industrial processes, such as Kluyveromyces lactis (Friedrich et al, 2023; Varela et al, 2019) or Yarrowia lypolitica (Bigey et al, 2023), as well as those of ecological significance as Saccharomyces uvarum (Almeida 2014), Lachancea cidri (Villarreal et al, 2024; Villarreal et al, 2022), and Schizosaccharomyces pombe (Jeffares et al, 2015) have gained attention. Notably, yeasts species of clinical relevance such as Candida glabrata (Wang et al, 2024), Candida auris (Chow et al, 2020) or Cryptococcus neoformans (Sephton-Clark et al, 2022), are also being studied.…”