ArticleNature communications2021
Engineered yeast genomes accurately assembled from pure and mixed samples.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed.
- Loss of Heterozygosity associated with ubiquitous environments in yeast.PLoS genetics · 2025Article
- Omics-driven onboarding of the carotenoid producing red yeast Xanthophyllomyces dendrorhous CBS 6938.Applied microbiology and biotechnology · 2024Article
- The need for adaptability in detection, characterization, and attribution of biosecurity threats.Nature communications · 2024Review
- Cyanamide-inducible expression of homing nucleaseSynthetic and systems biotechnology · 2024Article
- A correlative study of the genomic underpinning of virulence traits and drug tolerance ofInfection and immunity · 2024Article
- Synsor: a tool for alignment-free detection of engineered DNA sequences.Frontiers in bioengineering and biotechnology · 2024Article
- Isolation and sequencing of the spoilage yeastMicrobiology resource announcements · 2023Article
- Draft genome of theMicrobiology resource announcements · 2023Article
- High quality de novo genome assembly of the non-conventional yeast Kazachstania bulderi describes a potential low pH production host for biorefineries.Communications biology · 2023Article
- Profiling proteomic responses to hexokinase-II depletion in terpene-producingEngineering microbiology · 2023Article
- Genetic basis for probiotic yeast phenotypes revealed by nanopore sequencing.G3 (Bethesda, Md.) · 2023Article
- Automation protocol for high-efficiency and high-quality genomic DNA extraction from Saccharomyces cerevisiae.PloS one · 2023Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Yeast whole genome sequencing (WGS) lacks end-to-end workflows that identify genetic engineering. Here we present Prymetime, a tool that assembles yeast plasmids and chromosomes and annotates genetic engineering sequences. It is a hybrid workflow-it uses short and long reads as inputs to perform separate linear and circular assembly steps. This structure is necessary to accurately resolve genetic engineering sequences in plasmids and the genome. We show this by assembling diverse engineered yeasts, in some cases revealing unintended deletions and integrations. Furthermore, the resulting whole genomes are high quality, although the underlying assembly software does not consistently resolve highly repetitive genome features. Finally, we assemble plasmids and genome integrations from metagenomic sequencing, even with 1 engineered cell in 1000. This work is a blueprint for building WGS workflows and establishes WGS-based identification of yeast genetic engineering.
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Registered trials
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