Engineered yeast genomes accurately assembled from pure and mixed samples

Joseph H. Collins, Kevin W. Keating, Trent R. Jones, Shravani Balaji, Celeste B. Marsan, Marina Çomo, Zachary J. Newlon, Tom Mitchell, Bryan Bartley, Aaron Adler, Nicholas Roehner and Eric M. Young ()
Additional contact information
Joseph H. Collins: Worcester Polytechnic Institute
Kevin W. Keating: Worcester Polytechnic Institute
Trent R. Jones: Worcester Polytechnic Institute
Shravani Balaji: Worcester Polytechnic Institute
Celeste B. Marsan: Worcester Polytechnic Institute
Marina Çomo: Worcester Polytechnic Institute
Zachary J. Newlon: Worcester Polytechnic Institute
Tom Mitchell: Raytheon BBN Technologies
Bryan Bartley: Raytheon BBN Technologies
Aaron Adler: Raytheon BBN Technologies
Nicholas Roehner: Raytheon BBN Technologies
Eric M. Young: Worcester Polytechnic Institute

Nature Communications, 2021, vol. 12, issue 1, 1-15

Abstract: 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.

Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-21656-9

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DOI: 10.1038/s41467-021-21656-9

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