Journal Article

Bug mapping and fitness testing of chemically synthesized chromosome X

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

2017

Overview

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.

• Publisher: American Association for the Advancement of Science,The American Association for the Advancement of Science,American Association for the Advancement of Science (AAAS)
• Subject: Artificial chromosomes / Base pairs / Base Sequence / Biology / Chromosomes / Chromosomes, Artificial, Yeast - chemistry / Chromosomes, Artificial, Yeast - genetics / Debugging / Defects / Deoxyribonucleic acid / Design / DNA / Fitness / Flexibility / Gene Duplication / Gene mapping / Genes / Genetic crosses / Genetic Fitness / Genetics / Genome, Fungal / Genomes / Genomics / Genotype & phenotype / Genotypes / High-Throughput Nucleotide Sequencing - methods / Mapping / Meiosis / Nucleotide sequence / Open reading frames / Phenotypes / Physical Chromosome Mapping - methods / Polymerase chain reaction / Reproductive fitness / RESEARCH ARTICLE SUMMARY / Saccharomyces cerevisiae - genetics / Strain analysis / Strains (organisms) / Strategy / Synthesis / Synthetic Biology / Troubleshooting / Yeast