Bug mapping and fitness testing of chemically synthesized chromosome X

Yi Wu; Bing Zhi Li; Meng Zhao; Leslie A. Mitchell; Ze Xiong Xie; Qiu Hui Lin; Xia Wang; Wen Hai Xiao; Ying Wang; Xiao Zhou; Hong Liu; Xia Li; Ming Zhu Ding; Duo Liu; Lu Zhang; Bao Li Liu; Xiao Le Wu; Fei Fei Li; Xiu Tao Dong; Bin Jia; Wen Zheng Zhang; Guo Zhen Jiang; Yue Liu; Xue Bai; Tian Qing Song; Yan Chen; Si Jie Zhou; Rui Ying Zhu; Feng Gao; Zheng Kuang; Xuya Wang; Michael Shen; Kun Yang; Giovanni Stracquadanio; Sarah M. Richardson; Yicong Lin; Lihui Wang; Roy Walker; Yisha Luo; Ping Sheng Ma; Huanming Yang; Yizhi Cai; Junbiao Dai; Joel S. Bader; Jef D. Boeke; Ying-Jin Yuan

doi:10.1126/science.aaf4706

Bug mapping and fitness testing of chemically synthesized chromosome X

Yi Wu, Bing Zhi Li, Meng Zhao, Leslie A. Mitchell, Ze Xiong Xie, Qiu Hui Lin, Xia Wang, Wen Hai Xiao, Ying Wang, Xiao Zhou, Hong Liu, Xia Li, Ming Zhu Ding, Duo Liu, Lu Zhang, Bao Li Liu, Xiao Le Wu, Fei Fei Li, Xiu Tao Dong, Bin JiaWen Zheng Zhang, Guo Zhen Jiang, Yue Liu, Xue Bai, Tian Qing Song, Yan Chen, Si Jie Zhou, Rui Ying Zhu, Feng Gao, Zheng Kuang, Xuya Wang, Michael Shen, Kun Yang, Giovanni Stracquadanio, Sarah M. Richardson, Yicong Lin, Lihui Wang, Roy Walker, Yisha Luo, Ping Sheng Ma, Huanming Yang, Yizhi Cai, Junbiao Dai, Joel S. Bader, Jef D. Boeke, Ying-Jin Yuan^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

Debugging a genome sequence is imperative for successfully building a synthetic genome. As part of the effort to build a designer eukaryotic genome, yeast synthetic chromosome X (synX), designed as 707,459 base pairs, was synthesized chemically. SynX exhibited good fitness under a wide variety of conditions. A highly efficient mapping strategy called pooled PCRTag mapping (PoPM), which can be generalized to any watermarked synthetic chromosome, was developed to identify genetic alterations that affect cell fitness ("bugs"). A series of bugs were corrected that included a large region bearing complex amplifications, a growth defect mapping to a recoded sequence in FIP1, and a loxPsym site affecting promoter function of ATP2. PoPM is a powerful tool for synthetic yeast genome debugging and an efficient strategy for phenotype-genotype mapping.

Original language	English
Article number	eaaf4706
Journal	Science
Volume	355
Issue number	6329
DOIs	https://doi.org/10.1126/science.aaf4706
Publication status	Published - 10 Mar 2017

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10.1126/science.aaf4706

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Wu, Y., Li, B. Z., Zhao, M., Mitchell, L. A., Xie, Z. X., Lin, Q. H., Wang, X., Xiao, W. H., Wang, Y., Zhou, X., Liu, H., Li, X., Ding, M. Z., Liu, D., Zhang, L., Liu, B. L., Wu, X. L., Li, F. F., Dong, X. T., ... Yuan, Y-J. (2017). Bug mapping and fitness testing of chemically synthesized chromosome X. Science, 355(6329), [eaaf4706]. https://doi.org/10.1126/science.aaf4706

Wu, Yi ; Li, Bing Zhi ; Zhao, Meng ; Mitchell, Leslie A. ; Xie, Ze Xiong ; Lin, Qiu Hui ; Wang, Xia ; Xiao, Wen Hai ; Wang, Ying ; Zhou, Xiao ; Liu, Hong ; Li, Xia ; Ding, Ming Zhu ; Liu, Duo ; Zhang, Lu ; Liu, Bao Li ; Wu, Xiao Le ; Li, Fei Fei ; Dong, Xiu Tao ; Jia, Bin ; Zhang, Wen Zheng ; Jiang, Guo Zhen ; Liu, Yue ; Bai, Xue ; Song, Tian Qing ; Chen, Yan ; Zhou, Si Jie ; Zhu, Rui Ying ; Gao, Feng ; Kuang, Zheng ; Wang, Xuya ; Shen, Michael ; Yang, Kun ; Stracquadanio, Giovanni ; Richardson, Sarah M. ; Lin, Yicong ; Wang, Lihui ; Walker, Roy ; Luo, Yisha ; Ma, Ping Sheng ; Yang, Huanming ; Cai, Yizhi ; Dai, Junbiao ; Bader, Joel S. ; Boeke, Jef D. ; Yuan, Ying-Jin. / Bug mapping and fitness testing of chemically synthesized chromosome X. In: Science. 2017 ; Vol. 355, No. 6329.

@article{9272a9d669d748669d4fa2240182ec9e,

title = "Bug mapping and fitness testing of chemically synthesized chromosome X",

abstract = "Debugging a genome sequence is imperative for successfully building a synthetic genome. As part of the effort to build a designer eukaryotic genome, yeast synthetic chromosome X (synX), designed as 707,459 base pairs, was synthesized chemically. SynX exhibited good fitness under a wide variety of conditions. A highly efficient mapping strategy called pooled PCRTag mapping (PoPM), which can be generalized to any watermarked synthetic chromosome, was developed to identify genetic alterations that affect cell fitness ({"}bugs{"}). A series of bugs were corrected that included a large region bearing complex amplifications, a growth defect mapping to a recoded sequence in FIP1, and a loxPsym site affecting promoter function of ATP2. PoPM is a powerful tool for synthetic yeast genome debugging and an efficient strategy for phenotype-genotype mapping.",

author = "Yi Wu and Li, {Bing Zhi} and Meng Zhao and Mitchell, {Leslie A.} and Xie, {Ze Xiong} and Lin, {Qiu Hui} and Xia Wang and Xiao, {Wen Hai} and Ying Wang and Xiao Zhou and Hong Liu and Xia Li and Ding, {Ming Zhu} and Duo Liu and Lu Zhang and Liu, {Bao Li} and Wu, {Xiao Le} and Li, {Fei Fei} and Dong, {Xiu Tao} and Bin Jia and Zhang, {Wen Zheng} and Jiang, {Guo Zhen} and Yue Liu and Xue Bai and Song, {Tian Qing} and Yan Chen and Zhou, {Si Jie} and Zhu, {Rui Ying} and Feng Gao and Zheng Kuang and Xuya Wang and Michael Shen and Kun Yang and Giovanni Stracquadanio and Richardson, {Sarah M.} and Yicong Lin and Lihui Wang and Roy Walker and Yisha Luo and Ma, {Ping Sheng} and Huanming Yang and Yizhi Cai and Junbiao Dai and Bader, {Joel S.} and Boeke, {Jef D.} and Ying-Jin Yuan",

note = "No AAM from Patrick Cai. Not compliant. Not REF eligible.",

year = "2017",

month = mar,

day = "10",

doi = "10.1126/science.aaf4706",

language = "English",

volume = "355",

journal = "Science",

issn = "0036-8075",

publisher = "AMER ASSOC ADVANCEMENT SCIENCE",

number = "6329",

}

Wu, Y, Li, BZ, Zhao, M, Mitchell, LA, Xie, ZX, Lin, QH, Wang, X, Xiao, WH, Wang, Y, Zhou, X, Liu, H, Li, X, Ding, MZ, Liu, D, Zhang, L, Liu, BL, Wu, XL, Li, FF, Dong, XT, Jia, B, Zhang, WZ, Jiang, GZ, Liu, Y, Bai, X, Song, TQ, Chen, Y, Zhou, SJ, Zhu, RY, Gao, F, Kuang, Z, Wang, X, Shen, M, Yang, K, Stracquadanio, G, Richardson, SM, Lin, Y, Wang, L, Walker, R, Luo, Y, Ma, PS, Yang, H, Cai, Y, Dai, J, Bader, JS, Boeke, JD & Yuan, Y-J 2017, 'Bug mapping and fitness testing of chemically synthesized chromosome X', Science, vol. 355, no. 6329, eaaf4706. https://doi.org/10.1126/science.aaf4706

Bug mapping and fitness testing of chemically synthesized chromosome X. / Wu, Yi; Li, Bing Zhi; Zhao, Meng; Mitchell, Leslie A.; Xie, Ze Xiong; Lin, Qiu Hui; Wang, Xia; Xiao, Wen Hai; Wang, Ying; Zhou, Xiao; Liu, Hong; Li, Xia; Ding, Ming Zhu; Liu, Duo; Zhang, Lu; Liu, Bao Li; Wu, Xiao Le; Li, Fei Fei; Dong, Xiu Tao; Jia, Bin; Zhang, Wen Zheng; Jiang, Guo Zhen; Liu, Yue; Bai, Xue; Song, Tian Qing; Chen, Yan; Zhou, Si Jie; Zhu, Rui Ying; Gao, Feng; Kuang, Zheng; Wang, Xuya; Shen, Michael; Yang, Kun; Stracquadanio, Giovanni; Richardson, Sarah M.; Lin, Yicong; Wang, Lihui; Walker, Roy; Luo, Yisha; Ma, Ping Sheng; Yang, Huanming; Cai, Yizhi; Dai, Junbiao; Bader, Joel S.; Boeke, Jef D.; Yuan, Ying-Jin.

In: Science, Vol. 355, No. 6329, eaaf4706, 10.03.2017.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Bug mapping and fitness testing of chemically synthesized chromosome X

AU - Wu, Yi

AU - Li, Bing Zhi

AU - Zhao, Meng

AU - Mitchell, Leslie A.

AU - Xie, Ze Xiong

AU - Lin, Qiu Hui

AU - Wang, Xia

AU - Xiao, Wen Hai

AU - Wang, Ying

AU - Zhou, Xiao

AU - Liu, Hong

AU - Li, Xia

AU - Ding, Ming Zhu

AU - Liu, Duo

AU - Zhang, Lu

AU - Liu, Bao Li

AU - Wu, Xiao Le

AU - Li, Fei Fei

AU - Dong, Xiu Tao

AU - Jia, Bin

AU - Zhang, Wen Zheng

AU - Jiang, Guo Zhen

AU - Liu, Yue

AU - Bai, Xue

AU - Song, Tian Qing

AU - Chen, Yan

AU - Zhou, Si Jie

AU - Zhu, Rui Ying

AU - Gao, Feng

AU - Kuang, Zheng

AU - Wang, Xuya

AU - Shen, Michael

AU - Yang, Kun

AU - Stracquadanio, Giovanni

AU - Richardson, Sarah M.

AU - Lin, Yicong

AU - Wang, Lihui

AU - Walker, Roy

AU - Luo, Yisha

AU - Ma, Ping Sheng

AU - Yang, Huanming

AU - Cai, Yizhi

AU - Dai, Junbiao

AU - Bader, Joel S.

AU - Boeke, Jef D.

AU - Yuan, Ying-Jin

N1 - No AAM from Patrick Cai. Not compliant. Not REF eligible.

PY - 2017/3/10

Y1 - 2017/3/10

N2 - Debugging a genome sequence is imperative for successfully building a synthetic genome. As part of the effort to build a designer eukaryotic genome, yeast synthetic chromosome X (synX), designed as 707,459 base pairs, was synthesized chemically. SynX exhibited good fitness under a wide variety of conditions. A highly efficient mapping strategy called pooled PCRTag mapping (PoPM), which can be generalized to any watermarked synthetic chromosome, was developed to identify genetic alterations that affect cell fitness ("bugs"). A series of bugs were corrected that included a large region bearing complex amplifications, a growth defect mapping to a recoded sequence in FIP1, and a loxPsym site affecting promoter function of ATP2. PoPM is a powerful tool for synthetic yeast genome debugging and an efficient strategy for phenotype-genotype mapping.

AB - Debugging a genome sequence is imperative for successfully building a synthetic genome. As part of the effort to build a designer eukaryotic genome, yeast synthetic chromosome X (synX), designed as 707,459 base pairs, was synthesized chemically. SynX exhibited good fitness under a wide variety of conditions. A highly efficient mapping strategy called pooled PCRTag mapping (PoPM), which can be generalized to any watermarked synthetic chromosome, was developed to identify genetic alterations that affect cell fitness ("bugs"). A series of bugs were corrected that included a large region bearing complex amplifications, a growth defect mapping to a recoded sequence in FIP1, and a loxPsym site affecting promoter function of ATP2. PoPM is a powerful tool for synthetic yeast genome debugging and an efficient strategy for phenotype-genotype mapping.

UR - http://www.scopus.com/inward/record.url?scp=85014820348&partnerID=8YFLogxK

U2 - 10.1126/science.aaf4706

DO - 10.1126/science.aaf4706

M3 - Article

AN - SCOPUS:85014820348

VL - 355

JO - Science

JF - Science

SN - 0036-8075

IS - 6329

M1 - eaaf4706

ER -

Bug mapping and fitness testing of chemically synthesized chromosome X

Abstract

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Edinburgh Genome Foundry

Building national hardware and software infrastructure for UK DNA foundries

14 ERASynBio - IESY - Inducible Evolution of Synthetic Yeast genomes

Cite this

Bug mapping and fitness testing of chemically synthesized chromosome X

Abstract

Access to Document

Other files and links

Fingerprint

Projects

Edinburgh Genome Foundry

Building national hardware and software infrastructure for UK DNA foundries

14 ERASynBio - IESY - Inducible Evolution of Synthetic Yeast genomes

Cite this