ArticlePloS one2016
Sequence Assembly of Yarrowia lipolytica Strain W29/CLIB89 Shows Transposable Element Diversity.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Intron location and sequence modulate gene expression in Yarrowia lipolytica.Nucleic acids research · 2026Article
- Review
- Complete diploid genome of the type strain Yarrowia lipolytica YB-423 (ATCC 18942™).Journal of industrial microbiology & biotechnology · 2026Article
- Genome sequence assembly and annotation ofNAR genomics and bioinformatics · 2025Article
- Identification of theMicrobiology (Reading, England) · 2025Article
- Patterns of spontaneous and induced genomic alterations inApplied and environmental microbiology · 2025Article
- Balanced Training Sets Improve Deep Learning-Based Prediction of CRISPR sgRNA Activity.ACS synthetic biology · 2024Article
- The Key Enzymes of Carbon Metabolism and the Glutathione Antioxidant System ProtectJournal of fungi (Basel, Switzerland) · 2024Article
- Genome-scale transcriptional activation by non-homologous end joining-mediated integration in Yarrowia lipolytica.Biotechnology for biofuels and bioproducts · 2024Article
- The second complete mitochondrial genome ofMitochondrial DNA. Part B, Resources · 2024Article
- acCRISPR: an activity-correction method for improving the accuracy of CRISPR screens.Communications biology · 2023Article
- Improving solubility and copy number of taxadiene synthase to enhance the titer of taxadiene inSynthetic and systems biotechnology · 2023Article
- Kinetic and Regulatory Properties ofInternational journal of molecular sciences · 2023Article
- Abolishing storage lipids induces protein misfolding and stress responses in Yarrowia lipolytica.Journal of industrial microbiology & biotechnology · 2023Article
- Copper Ion Mediates Yeast-to-Hypha Transition inJournal of fungi (Basel, Switzerland) · 2023Article
- Insights into the Genomic and Phenotypic Landscape of the Oleaginous YeastJournal of fungi (Basel, Switzerland) · 2023Article
- Article
- Genome-wide CRISPR-Cas9 screen reveals a persistent null-hyphal phenotype that maintains high carotenoid production in Yarrowia lipolytica.Biotechnology and bioengineering · 2022Article
- Engineering ofMetabolic engineering communications · 2022Review
- Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica.Nature communications · 2022Article
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Authors and funding
10 authors.
Funding
Abstract
Yarrowia lipolytica, an oleaginous yeast, is capable of accumulating significant cellular mass in lipid making it an important source of biosustainable hydrocarbon-based chemicals. In spite of a similar number of protein-coding genes to that in other Hemiascomycetes, the Y. lipolytica genome is almost double that of model yeasts. Despite its economic importance and several distinct strains in common use, an independent genome assembly exists for only one strain. We report here a de novo annotated assembly of the chromosomal genome of an industrially-relevant strain, W29/CLIB89, determined by hybrid next-generation sequencing. For the first time, each Y. lipolytica chromosome is represented by a single contig. The telomeric rDNA repeats were localized by Irys long-range genome mapping and one complete copy of the rDNA sequence is reported. Two large structural variants and retroelement differences with reference strain CLIB122 including a full-length, novel Ty3/Gypsy long terminal repeat (LTR) retrotransposon and multiple LTR-like sequences are described. Strikingly, several of these are adjacent to RNA polymerase III-transcribed genes, which are almost double in number in Y. lipolytica compared to other Hemiascomycetes. In addition to previously-reported dimeric RNA polymerase III-transcribed genes, tRNA pseudogenes were identified. Multiple full-length and truncated LINE elements are also present. Therefore, although identified transposons do not constitute a significant fraction of the Y. lipolytica genome, they could have played an active role in its evolution. Differences between the sequence of this strain and of the existing reference strain underscore the utility of an additional independent genome assembly for this economically important organism.
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