1. A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice
- Author
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Wierbowski, Shayne D, Vo, Tommy V, Falter-Braun, Pascal, Jobe, Timothy O, Kruse, Lars H, Wei, Xiaomu, Liang, Jin, Meyer, Michael J, Akturk, Nurten, Rivera-Erick, Christen A, Cordero, Nicolas A, Paramo, Mauricio I, Shayhidin, Elnur E, Bertolotti, Marta, Tippens, Nathaniel D, Akther, Kazi, Sharma, Rita, Katayose, Yuichi, Salehi-Ashtiani, Kourosh, Hao, Tong, Ronald, Pamela C, Ecker, Joseph R, Schweitzer, Peter A, Kikuchi, Shoshi, Mizuno, Hiroshi, Hill, David E, Vidal, Marc, Moghe, Gaurav D, McCouch, Susan R, and Yu, Haiyuan
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Biotechnology ,Human Genome ,Generic health relevance ,Computational Biology ,DNA ,Plant ,Databases ,Genetic ,Genome ,Plant ,High-Throughput Nucleotide Sequencing ,Open Reading Frames ,Oryza ,Protein Interaction Mapping ,Protein Interaction Maps ,Sequence Analysis ,DNA ,protein-protein interaction ,rice ,ORFeome ,next-generation sequencing ,networks ,protein–protein interaction - Abstract
Systematic mappings of protein interactome networks have provided invaluable functional information for numerous model organisms. Here we develop PCR-mediated Linkage of barcoded Adapters To nucleic acid Elements for sequencing (PLATE-seq) that serves as a general tool to rapidly sequence thousands of DNA elements. We validate its utility by generating the ORFeome for Oryza sativa covering 2,300 genes and constructing a high-quality protein-protein interactome map consisting of 322 interactions between 289 proteins, expanding the known interactions in rice by roughly 50%. Our work paves the way for high-throughput profiling of protein-protein interactions in a wide range of organisms.
- Published
- 2020