MarpoDB: An open registry for Marchantia polymorpha genetic parts

Delmans, Mihails; Pollak, Bernardo; Haseloff, Jim

doi:10.1093/pcp/pcw201

Title: MarpoDB: An open registry for Marchantia polymorpha genetic parts

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Abstract

Marchantia polymorpha is an extant relative of the earliest terrestrial plants and has attracted a substantial interest as a model organism for evolutionary and developmental studies. Given its relatively simple genome, compact gene families, simple morphology, ease of propagation and transformation, M. polymorpha is becoming a promising platform for plant synthetic biology. Modular genetic parts have been essential for development of synthetic biology approaches, so we sought to design an engineering oriented database for M. polymorpha genetic parts where each gene is a standalone functional unit. MarpoDB is a database of M. polymorpha genes and genetic parts, which is tailored to become an integral tool for a synthetic biology workflow. Among its features are precompiled cross-database querying to InterPro, Pfam signatures and non-redundant Viridiplantae BLAST annotations; BLAST querying to M. polymorpha genes; sequence export in GenBank format; recoding of sequences to the common syntax for type IIS assembly and exchange of DNA parts; and a minimalistic, intuitive and interactive user interface for gene models and sequence exploration. Furthermore, we have implemented user input to encourage feedback, collaboration and exchange between the MarpoDB community. MarpoDB source-code is released on GitHub to promote development of computational tools for synthetic biology.

Authors:

Delmans, Mihails ^[1]; Pollak, Bernardo ^[1]; Haseloff, Jim ^[1]

Univ. of Cambridge (United Kingdom). Dept. of Plant Sciences

Publication Date:: Fri Jan 27 00:00:00 EST 2017

Research Org.:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

OSTI Identifier:: 1625583

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Accepted Manuscript

Journal Name:: Plant and Cell Physiology

Additional Journal Information:: Journal Volume: 58; Journal Issue: 1; Journal ID: ISSN 0032-0781

Publisher:: Japanese Society of Plant Physiologists

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; plant sciences; cell biology; genetic parts; genetic databases; Marchantia polymorpha; open source database; plant synthetic biology

Citation Formats


                    Delmans, Mihails, Pollak, Bernardo, and Haseloff, Jim. MarpoDB: An open registry for Marchantia polymorpha genetic parts.  United States: N. p., 2017. 
Web.  doi:10.1093/pcp/pcw201.

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                    Delmans, Mihails, Pollak, Bernardo, & Haseloff, Jim. MarpoDB: An open registry for Marchantia polymorpha genetic parts.  United States.  https://doi.org/10.1093/pcp/pcw201

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                    Delmans, Mihails, Pollak, Bernardo, and Haseloff, Jim. Fri .  
"MarpoDB: An open registry for Marchantia polymorpha genetic parts".  United States.  https://doi.org/10.1093/pcp/pcw201.  https://www.osti.gov/servlets/purl/1625583.

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@article{osti_1625583,

  title        = {MarpoDB: An open registry for Marchantia polymorpha genetic parts},

  author       = {Delmans, Mihails and Pollak, Bernardo and Haseloff, Jim},

  abstractNote = {Marchantia polymorpha is an extant relative of the earliest terrestrial plants and has attracted a substantial interest as a model organism for evolutionary and developmental studies. Given its relatively simple genome, compact gene families, simple morphology, ease of propagation and transformation, M. polymorpha is becoming a promising platform for plant synthetic biology. Modular genetic parts have been essential for development of synthetic biology approaches, so we sought to design an engineering oriented database for M. polymorpha genetic parts where each gene is a standalone functional unit. MarpoDB is a database of M. polymorpha genes and genetic parts, which is tailored to become an integral tool for a synthetic biology workflow. Among its features are precompiled cross-database querying to InterPro, Pfam signatures and non-redundant Viridiplantae BLAST annotations; BLAST querying to M. polymorpha genes; sequence export in GenBank format; recoding of sequences to the common syntax for type IIS assembly and exchange of DNA parts; and a minimalistic, intuitive and interactive user interface for gene models and sequence exploration. Furthermore, we have implemented user input to encourage feedback, collaboration and exchange between the MarpoDB community. MarpoDB source-code is released on GitHub to promote development of computational tools for synthetic biology.},

  doi          = {10.1093/pcp/pcw201},

  journal      = {Plant and Cell Physiology},

  number       = 1,

  volume       = 58,

  place        = {United States},

  year         = {Fri Jan 27 00:00:00 EST 2017},

  month        = {Fri Jan 27 00:00:00 EST 2017}

}

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