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Gallegos JE, Rogers MF, Cialek CA, Peccoud J. Rapid, robust plasmid verification by de novo assembly of short sequencing reads. Nucleic Acids Res 2020; 48:e106. [PMID: 32890398 PMCID: PMC7544192 DOI: 10.1093/nar/gkaa727] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/07/2020] [Accepted: 08/24/2020] [Indexed: 12/13/2022] Open
Abstract
Plasmids are a foundational tool for basic and applied research across all subfields of biology. Increasingly, researchers in synthetic biology are relying on and developing massive libraries of plasmids as vectors for directed evolution, combinatorial gene circuit tests, and for CRISPR multiplexing. Verification of plasmid sequences following synthesis is a crucial quality control step that creates a bottleneck in plasmid fabrication workflows. Crucially, researchers often elect to forego the cumbersome verification step, potentially leading to reproducibility and—depending on the application—security issues. In order to facilitate plasmid verification to improve the quality and reproducibility of life science research, we developed a fast, simple, and open source pipeline for assembly and verification of plasmid sequences from Illumina reads. We demonstrate that our pipeline, which relies on de novo assembly, can also be used to detect contaminating sequences in plasmid samples. In addition to presenting our pipeline, we discuss the role for verification and quality control in the increasingly complex life science workflows ushered in by synthetic biology.
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Affiliation(s)
- Jenna E Gallegos
- Department of Chemical & Biological Engineering, Colorado State University, USA
| | | | - Charlotte A Cialek
- GenoFAB, Inc.,Department of Biochemistry and Molecular Biology, Colorado State University, USA
| | - Jean Peccoud
- Department of Chemical & Biological Engineering, Colorado State University, USA.,GenoFAB, Inc
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Coll A, Wilson ML, Gruden K, Peccoud J. GenoCAD Plant Grammar to Design Plant Expression Vectors for Promoter Analysis. Methods Mol Biol 2016; 1482:219-232. [PMID: 27557770 DOI: 10.1007/978-1-4939-6396-6_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
With the rapid advances in prediction tools for discovery of new promoters and their cis-elements, there is a need to improve plant expression methodologies in order to facilitate a high-throughput functional validation of these promoters in planta. The promoter-reporter analysis is an indispensible approach for characterization of plant promoters. It requires the design of complex plant expression vectors, which can be challenging. Here, we describe the use of a plant grammar implemented in GenoCAD that will allow the users to quickly design constructs for promoter analysis experiments but also for other in planta functional studies. The GenoCAD plant grammar includes a library of plant biological parts organized in structural categories to facilitate their use and management and a set of rules that guides the process of assembling these biological parts into large constructs.
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Affiliation(s)
- Anna Coll
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.
| | - Mandy L Wilson
- Biocomplexity Institute of Virginia Tech, 1015 Life Science Circle, Blacksburg, VA, 24061-0477, USA
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Jean Peccoud
- Department of Chemical & Biological Engineering, Colorado State University, Fort Collins, CO, USA
- GenoFAB, LLC, 548 Market Street, #46143, San Francisco, CA, USA
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Coll A, Wilson ML, Gruden K, Peccoud J. Rule-Based Design of Plant Expression Vectors Using GenoCAD. PLoS One 2015; 10:e0132502. [PMID: 26148190 PMCID: PMC4492961 DOI: 10.1371/journal.pone.0132502] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 06/15/2015] [Indexed: 01/28/2023] Open
Abstract
Plant synthetic biology requires software tools to assist on the design of complex multi-genic expression plasmids. Here a vector design strategy to express genes in plants is formalized and implemented as a grammar in GenoCAD, a Computer-Aided Design software for synthetic biology. It includes a library of plant biological parts organized in structural categories and a set of rules describing how to assemble these parts into large constructs. Rules developed here are organized and divided into three main subsections according to the aim of the final construct: protein localization studies, promoter analysis and protein-protein interaction experiments. The GenoCAD plant grammar guides the user through the design while allowing users to customize vectors according to their needs. Therefore the plant grammar implemented in GenoCAD will help plant biologists take advantage of methods from synthetic biology to design expression vectors supporting their research projects.
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Affiliation(s)
- Anna Coll
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Mandy L. Wilson
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Jean Peccoud
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America
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Adames NR, Wilson ML, Fang G, Lux MW, Glick BS, Peccoud J. GenoLIB: a database of biological parts derived from a library of common plasmid features. Nucleic Acids Res 2015; 43:4823-32. [PMID: 25925571 PMCID: PMC4446419 DOI: 10.1093/nar/gkv272] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 03/18/2015] [Indexed: 11/12/2022] Open
Abstract
Synthetic biologists rely on databases of biological parts to design genetic devices and systems. The sequences and descriptions of genetic parts are often derived from features of previously described plasmids using ad hoc, error-prone and time-consuming curation processes because existing databases of plasmids and features are loosely organized. These databases often lack consistency in the way they identify and describe sequences. Furthermore, legacy bioinformatics file formats like GenBank do not provide enough information about the purpose of features. We have analyzed the annotations of a library of ∼2000 widely used plasmids to build a non-redundant database of plasmid features. We looked at the variability of plasmid features, their usage statistics and their distributions by feature type. We segmented the plasmid features by expression hosts. We derived a library of biological parts from the database of plasmid features. The library was formatted using the Synthetic Biology Open Language, an emerging standard developed to better organize libraries of genetic parts to facilitate synthetic biology workflows. As proof, the library was converted into GenoCAD grammar files to allow users to import and customize the library based on the needs of their research projects.
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Affiliation(s)
- Neil R Adames
- Virginia Bioinformatics Institute, Virginia Tech, 1015 Life Science Circle, Blacksburg, VA 24061, USA
| | - Mandy L Wilson
- Virginia Bioinformatics Institute, Virginia Tech, 1015 Life Science Circle, Blacksburg, VA 24061, USA
| | - Gang Fang
- Virginia Bioinformatics Institute, Virginia Tech, 1015 Life Science Circle, Blacksburg, VA 24061, USA School of Biological Technology, Xi'an University of Arts and Science, Xi'an, Shaanxi Province 710065, China
| | - Matthew W Lux
- Virginia Bioinformatics Institute, Virginia Tech, 1015 Life Science Circle, Blacksburg, VA 24061, USA Biosciences Division, Edgewood Chemical Biological Center, 5183 Blackhawk Rd Aberdeen Proving Grounds MD 21010, USA
| | - Benjamin S Glick
- Molecular Genetics & Cell Biology, University of Chicago, 920 E. 58th St., Chicago, IL 60637, USA GSL Biotech LLC, 5211 S. Kenwood Ave., Chicago, IL 60615, USA
| | - Jean Peccoud
- Virginia Bioinformatics Institute, Virginia Tech, 1015 Life Science Circle, Blacksburg, VA 24061, USA
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Ullrich KK, Hiss M, Rensing SA. Means to optimize protein expression in transgenic plants. Curr Opin Biotechnol 2015; 32:61-67. [DOI: 10.1016/j.copbio.2014.11.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 10/29/2014] [Accepted: 11/10/2014] [Indexed: 11/24/2022]
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