Complete diploid genome of the type strain Yarrowia lipolytica YB-423 (ATCC 18942™)

Abstract

Here, we present the first complete, fully phased diploid genome of type strain Yarrowia lipolytica YB-423 (=ATCC 18942™), constructed using a combination of Oxford Nanopore long-read and Illumina short-read sequencing. Yarrowia lipolytica is an industrially relevant yeast species known for its metabolic versatility, particularly its ability to degrade hydrophobic compounds and express useful products such as fatty acids. Despite its growing use in biotechnology, a high-quality genome assembly of the species’ diploid type-strain has been lacking. The assembly and annotations presented here span six chromosomes of paired “haplotigs” and a mitochondrial genome, capturing large-scale structural variations and prominent levels of genome-wide heterozygosity. Variant analysis revealed 13,908 heterozygous alleles, of which 3,201 alleles were distributed among 1,237 protein-coding genes. Gene set enrichment analysis showed that these variants are enriched among genes involved in transmembrane transport, suggesting a role in environmental adaptability. Comparative analysis of matched haplotigs for the same chromosome uncovered multiple inversions and transpositions, as well as allele-specific insertions of retrotransposons, providing new insights into the structural complexity and evolutionary dynamics of the genome. The fully phased, finished diploid genome of Y. lipolytica YB-423 represents a crucial step toward unlocking the full genetic potential of Y. lipolytica. Our work will provide a valuable foundation for future comparative and functional genomics and strain engineering studies, particularly for industrial microbiology and biotechnology applications. One-sentence summary This study presents the first fully phased diploid genome of Yarrowia lipolytica type strain YB-423, revealing extensive structural variation and heterozygosity that enhance understanding of its genetic adaptability and industrial potential.