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Engineered yeast genomes accurately assembled from pure and mixed samples
Joseph H Collins1, Kevin W Keating1, Trent R Jones1
1Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA.
Nature Communications
|March 6, 2021
Summary
Prymetime is a new tool for yeast whole genome sequencing (WGS) that identifies genetic engineering. It accurately assembles plasmids and genomes, even in complex metagenomic samples, enabling WGS-based detection of engineered yeast.
Area of Science:
- Synthetic Biology
- Genomics
- Bioinformatics
Background:
- Whole genome sequencing (WGS) workflows for yeast often lack comprehensive identification of genetic engineering.
- Accurate assembly of engineered sequences in both plasmids and chromosomes is crucial for understanding genetic modifications.
Purpose of the Study:
- To present Prymetime, a novel hybrid workflow for yeast WGS that assembles plasmids and chromosomes.
- To annotate genetic engineering sequences within the yeast genome.
- To establish WGS-based identification of yeast genetic engineering.
Main Methods:
- Developed a hybrid WGS workflow utilizing both short and long sequencing reads.
- Implemented separate linear and circular assembly steps to resolve genetic engineering sequences.
- Applied the workflow to diverse engineered yeast strains and metagenomic samples.
Main Results:
- Prymetime successfully assembled yeast plasmids and chromosomes, annotating genetic engineering.
- The workflow identified unintended deletions and integrations in engineered yeasts.
- High-quality whole genomes were produced, though highly repetitive regions posed challenges.
- Plasmids and genome integrations were assembled from metagenomic data, even at low frequencies (1 in 1000 cells).
Conclusions:
- Prymetime provides an end-to-end solution for identifying genetic engineering in yeast using WGS.
- The tool enables accurate assembly and annotation of engineered sequences in plasmids and genomes.
- This work serves as a blueprint for developing WGS workflows for genetic engineering identification.
