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 inFIP1, and a loxPsym site affecting promoter function ofATP2PoPM is a powerful tool for synthetic yeast genome debugging and an efficient strategy for phenotype-genotype mapping.
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Yi
authors.identifier: 0000-0002-2539-9228
authors.initials: Y
authors.lastname: Wu
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Bing-Zhi
authors.identifier: 0000-0003-4121-3048
authors.initials: BZ
authors.lastname: Li
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Meng
authors.identifier: 0000-0001-6253-8154
authors.initials: M
authors.lastname: Zhao
authors.affiliation: Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University (NYU) Langone Medical Center, New York City, NY 10016, USA.
authors.forename: Leslie A
authors.identifier: 0000-0001-7869-9817
authors.initials: LA
authors.lastname: Mitchell
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Ze-Xiong
authors.identifier: 0000-0002-6214-9009
authors.initials: ZX
authors.lastname: Xie
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Qiu-Hui
authors.initials: QH
authors.lastname: Lin
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Xia
authors.initials: X
authors.lastname: Wang
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Wen-Hai
authors.initials: WH
authors.lastname: Xiao
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Hong
authors.initials: H
authors.lastname: Liu
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Xia
authors.identifier: 0000-0001-8554-6245
authors.initials: X
authors.lastname: Li
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Ming-Zhu
authors.initials: MZ
authors.lastname: Ding
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Duo
authors.initials: D
authors.lastname: Liu
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Lu
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Bao-Li
authors.initials: BL
authors.lastname: Liu
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Xiao-Le
authors.initials: XL
authors.lastname: Wu
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Fei-Fei
authors.initials: FF
authors.lastname: Li
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Xiu-Tao
authors.initials: XT
authors.lastname: Dong
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Bin
authors.initials: B
authors.lastname: Jia
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Wen-Zheng
authors.initials: WZ
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Guo-Zhen
authors.initials: GZ
authors.lastname: Jiang
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Yue
authors.identifier: 0000-0002-8051-5156
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Xue
authors.identifier: 0000-0002-8636-3843
authors.initials: X
authors.lastname: Bai
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Tian-Qing
authors.identifier: 0000-0003-3483-3695
authors.initials: TQ
authors.lastname: Song
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Yan
authors.identifier: 0000-0001-7245-6574
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Si-Jie
authors.initials: SJ
authors.lastname: Zhou
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Rui-Ying
authors.identifier: 0000-0002-8309-457X
authors.initials: RY
authors.lastname: Zhu
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Feng
authors.identifier: 0000-0002-9563-3841
authors.initials: F
authors.lastname: Gao
authors.affiliation: Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University (NYU) Langone Medical Center, New York City, NY 10016, USA.
authors.forename: Zheng
authors.identifier: 0000-0001-5855-8371
authors.initials: Z
authors.lastname: Kuang
authors.affiliation: Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University (NYU) Langone Medical Center, New York City, NY 10016, USA.
authors.forename: Xuya
authors.initials: X
authors.lastname: Wang
authors.affiliation: Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University (NYU) Langone Medical Center, New York City, NY 10016, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Shen
authors.affiliation: High Throughput Biology Center and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.
authors.forename: Kun
authors.identifier: 0000-0002-1060-8082
authors.initials: K
authors.lastname: Yang
authors.affiliation: High Throughput Biology Center and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.|School of Computer Science and Electronic Engineering, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
authors.forename: Giovanni
authors.identifier: 0000-0001-9819-3645
authors.initials: G
authors.lastname: Stracquadanio
authors.affiliation: High Throughput Biology Center and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.
authors.forename: Sarah M
authors.identifier: 0000-0002-9820-9421
authors.initials: SM
authors.lastname: Richardson
authors.affiliation: Key laboratory of Industrial Biocatalysis (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, PR China.
authors.forename: Yicong
authors.initials: Y
authors.lastname: Lin
authors.affiliation: Key laboratory of Industrial Biocatalysis (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, PR China.
authors.forename: Lihui
authors.identifier: 0000-0002-8479-7859
authors.initials: L
authors.lastname: Wang
authors.affiliation: School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK.
authors.forename: Roy
authors.identifier: 0000-0003-0960-4591
authors.initials: R
authors.lastname: Walker
authors.affiliation: School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK.
authors.forename: Yisha
authors.identifier: 0000-0002-4228-7527
authors.initials: Y
authors.lastname: Luo
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Ping-Sheng
authors.initials: PS
authors.lastname: Ma
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, PR China.|James D. Watson Institute of Genome Sciences, Hangzhou 310058, PR China.
authors.forename: Huanming
authors.identifier: 0000-0003-1703-3012
authors.initials: H
authors.lastname: Yang
authors.affiliation: School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK.
authors.forename: Yizhi
authors.identifier: 0000-0003-1663-2865
authors.initials: Y
authors.lastname: Cai
authors.affiliation: Key laboratory of Industrial Biocatalysis (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, PR China.
authors.forename: Junbiao
authors.identifier: 0000-0002-5299-4700
authors.initials: J
authors.lastname: Dai
authors.affiliation: High Throughput Biology Center and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.
authors.forename: Joel S
authors.identifier: 0000-0002-6020-4625
authors.initials: JS
authors.lastname: Bader
authors.affiliation: Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University (NYU) Langone Medical Center, New York City, NY 10016, USA.
authors.forename: Jef D
authors.identifier: 0000-0001-5322-4946
authors.initials: JD
authors.lastname: Boeke
authors.affiliation: Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China. yjyuan@tju.edu.cn.|SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China.
authors.forename: Ying-Jin
authors.identifier: 0000-0003-0553-0089
authors.initials: YJ
authors.lastname: Yuan
mesh_terms: D001483:Base Sequence; D018244:Chromosomes, Artificial, Yeast / Q000737:chemistry* / Q000235:genetics*; D020440:Gene Duplication; D056084:Genetic Fitness; D016681:Genome, Fungal; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D020161:Physical Chromosome Mapping / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D058615:Synthetic Biology