Centromeric DNA Facilitates Nonconventional Yeast Genetic Engineering

Mingfeng Cao; Meirong Gao; Carmen Lorena Lopez-Garcia; Yutong Wu; Arun Somwarpet Seetharam; Andrew Josef Severin; Zengyi Shao

doi:10.1021/acssynbio.7b00046

Centromeric DNA Facilitates Nonconventional Yeast Genetic Engineering

ACS Synthetic Biology ◽

10.1021/acssynbio.7b00046 ◽

2017 ◽

Vol 6 (8) ◽

pp. 1545-1553 ◽

Cited By ~ 24

Author(s):

Mingfeng Cao ◽

Meirong Gao ◽

Carmen Lorena Lopez-Garcia ◽

Yutong Wu ◽

Arun Somwarpet Seetharam ◽

...

Keyword(s):

Genetic Engineering ◽

Centromeric Dna ◽

Yeast Genetic ◽

Nonconventional Yeast

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Engineered yeast genomes accurately assembled from pure and mixed samples

Nature Communications ◽

10.1038/s41467-021-21656-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Joseph H. Collins ◽

Kevin W. Keating ◽

Trent R. Jones ◽

Shravani Balaji ◽

Celeste B. Marsan ◽

...

Keyword(s):

Genetic Engineering ◽

Metagenomic Sequencing ◽

Long Reads ◽

Whole Genomes ◽

Genome Features ◽

Engineered Yeast ◽

Yeast Genomes ◽

Yeast Genetic ◽

Yeast Plasmids ◽

Assembly Software

AbstractYeast 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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