Engineered yeast genomes accurately assembled from pure and mixed samples.

Szczegóły
Abstrakt

Tytuł:: Engineered yeast genomes accurately assembled from pure and mixed samples.
Autorzy:: Collins JH; Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA.
Keating KW; Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA.
Jones TR; Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA.
Balaji S; Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA.
Marsan CB; Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA.
Çomo M; Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA.
Newlon ZJ; Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA.
Mitchell T; Synthetic Biology, Raytheon BBN Technologies, Cambridge, MA, USA.
Bartley B; Synthetic Biology, Raytheon BBN Technologies, Cambridge, MA, USA.
Adler A; Synthetic Biology, Raytheon BBN Technologies, Cambridge, MA, USA.
Roehner N; Synthetic Biology, Raytheon BBN Technologies, Cambridge, MA, USA.
Young EM; Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA. .
Źródło:: Nature communications [Nat Commun] 2021 Mar 05; Vol. 12 (1), pp. 1485. Date of Electronic Publication: 2021 Mar 05.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
Język:: English
Imprint Name(s):: Original Publication: [London] : Nature Pub. Group
MeSH Terms:: Genome, Fungal*
Genetic Engineering/*methods
Saccharomyces cerevisiae/*genetics
Whole Genome Sequencing/*methods
Base Sequence ; Chromosomes ; Chromosomes, Artificial, Yeast ; Cloning, Molecular ; Computer Simulation ; Contig Mapping/methods ; Metagenome ; Metagenomics ; Plasmids ; Software ; Transformation, Genetic
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Entry Date(s):: Date Created: 20210306 Date Completed: 20210319 Latest Revision: 20240331
Update Code:: 20240331
PubMed Central ID:: PMC7935868
DOI:: 10.1038/s41467-021-21656-9
PMID:: 33674578
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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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