A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice

Shayne D. Wierbowski, Tommy V. Vo, Pascal Falter-Braun, Timothy O. Jobe, Lars H. Kruse, Xiaomu Wei, Jin Liang, Michael J. Meyer, Nurten Akturk, Christen A. Rivera-Erick, Nicolas A. Cordero, Mauricio I. Paramo, Elnur E. Shayhidin, Marta Bertolotti, Nathaniel D. Tippens, Kazi Akther, Rita Sharma, Yuichi Katayose, Kourosh Salehi-Ashtiani, Tong HaoPamela C. Ronald, Joseph R. Ecker, Peter A. Schweitzer, Shoshi Kikuchi, Hiroshi Mizuno, David E. Hill, Marc Vidal, Gaurav D. Moghe, Susan R. McCouch, Haiyuan Yu

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number11836
JournalProceedings of the National Academy of Sciences of the United States of America
Volume117
Issue number21
DOIs
StatePublished - May 26 2020

Keywords

  • Networks
  • Next-generation sequencing
  • ORFeome
  • Protein-protein interaction
  • Rice

ASJC Scopus subject areas

  • General

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  • Cite this

    Wierbowski, S. D., Vo, T. V., Falter-Braun, P., Jobe, T. O., Kruse, L. H., Wei, X., Liang, J., Meyer, M. J., Akturk, N., Rivera-Erick, C. A., Cordero, N. A., Paramo, M. I., Shayhidin, E. E., Bertolotti, M., Tippens, N. D., Akther, K., Sharma, R., Katayose, Y., Salehi-Ashtiani, K., ... Yu, H. (2020). A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. Proceedings of the National Academy of Sciences of the United States of America, 117(21), [11836]. https://doi.org/10.1073/pnas.1918068117