SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes

Yue Shen, Giovanni Stracquadanio, Yun Wang, Kun Yang, Leslie A. Mitchell, Yaxin Xue, Yizhi Cai, Tai Chen, Jessica S. Dymond, Kang Kang, Jianhui Gong, Xiaofan Zeng, Yongfen Zhang, Yingrui Li, Qiang Feng, Xun Xu, Jun Wang, Jian Wang, Huanming Yang, Jef D. BoekeJoel S. Bader

Research output: Contribution to journalArticle

Abstract

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 3ΠUTR 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.

Original languageEnglish (US)
Pages (from-to)36-49
Number of pages14
JournalGenome Research
Volume26
Issue number1
DOIs
StatePublished - Jan 1 2016

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Chromosomes
Genome
Recombinases
High-Throughput Nucleotide Sequencing
Mitochondrial Genome
3' Untranslated Regions
Gene Frequency
Genetic Recombination
Yeasts
Mutation
Growth

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Shen, Y., Stracquadanio, G., Wang, Y., Yang, K., Mitchell, L. A., Xue, Y., ... Bader, J. S. (2016). SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Genome Research, 26(1), 36-49. https://doi.org/10.1101/gr.193433.115

SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. / Shen, Yue; Stracquadanio, Giovanni; Wang, Yun; Yang, Kun; Mitchell, Leslie A.; Xue, Yaxin; Cai, Yizhi; Chen, Tai; Dymond, Jessica S.; Kang, Kang; Gong, Jianhui; Zeng, Xiaofan; Zhang, Yongfen; Li, Yingrui; Feng, Qiang; Xu, Xun; Wang, Jun; Wang, Jian; Yang, Huanming; Boeke, Jef D.; Bader, Joel S.

In: Genome Research, Vol. 26, No. 1, 01.01.2016, p. 36-49.

Research output: Contribution to journalArticle

Shen, Y, Stracquadanio, G, Wang, Y, Yang, K, Mitchell, LA, Xue, Y, Cai, Y, Chen, T, Dymond, JS, Kang, K, Gong, J, Zeng, X, Zhang, Y, Li, Y, Feng, Q, Xu, X, Wang, J, Wang, J, Yang, H, Boeke, JD & Bader, JS 2016, 'SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes', Genome Research, vol. 26, no. 1, pp. 36-49. https://doi.org/10.1101/gr.193433.115
Shen, Yue ; Stracquadanio, Giovanni ; Wang, Yun ; Yang, Kun ; Mitchell, Leslie A. ; Xue, Yaxin ; Cai, Yizhi ; Chen, Tai ; Dymond, Jessica S. ; Kang, Kang ; Gong, Jianhui ; Zeng, Xiaofan ; Zhang, Yongfen ; Li, Yingrui ; Feng, Qiang ; Xu, Xun ; Wang, Jun ; Wang, Jian ; Yang, Huanming ; Boeke, Jef D. ; Bader, Joel S. / SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. In: Genome Research. 2016 ; Vol. 26, No. 1. pp. 36-49.
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