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SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes

Shen, Y and Stracquadanio, G and Wang, Y and Yang, K and Mitchell, LA and Xue, Y and Cai, Y and Chen, T and Dymond, JS and Kang, K and Gong, J and Zeng, X and Zhang, Y and Li, Y and Feng, Q and Xu, X and Wang, J and Wang, J and Yang, H and Boeke, JD and Bader, JS (2016) 'SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes.' Genome Research, 26 (1). 36 - 49. ISSN 1088-9051

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Abstract

© 2016 Shen et al. Synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) generates combinatorial genomic diversity through rearrangements at designed recombinase sites. We applied SCRaMbLE to yeast synthetic chromosome arm synIXR (43 recombinase sites) and then used a computational pipeline to infer or unscramble the sequence of recombinations that created the observed genomes. Deep sequencing of 64 synIXR SCRaMbLE strains revealed 156 deletions, 89 inversions, 94 duplications, and 55 additional complex rearrangements; several duplications are consistent with a double rolling circle mechanism. Every SCRaMbLE strain was unique, validating the capability of SCRaMbLE to explore a diverse space of genomes. Rearrangements occurred exclusively at designed loxPsym sites, with no significant evidence for ectopic rearrangements or mutations involving synthetic regions, the 99% nonsynthetic nuclear genome, or the mitochondrial genome. Deletion frequencies identified genes required for viability or fast growth. Replacement of 3Œ UTR by non-UTR sequence had surprisingly little effect on fitness. SCRaMbLE generates genome diversity in designated regions, reveals fitness constraints, and should scale to simultaneous evolution of multiple synthetic chromosomes.

Item Type: Article
Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Divisions: Faculty of Science and Health > Computer Science and Electronic Engineering, School of
Depositing User: Giovanni Stracquadanio
Date Deposited: 13 Jan 2017 14:05
Last Modified: 30 Jan 2019 16:19
URI: http://repository.essex.ac.uk/id/eprint/18690

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