Delmans Mihails, Pollak Bernardo, Haseloff Jim
Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, UK.
Plant Cell Physiol. 2017 Jan 1;58(1):e5. doi: 10.1093/pcp/pcw201.
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 stand-alone 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.
多形叶苔是最早的陆生植物现存的亲缘物种，作为进化和发育研究的模式生物，它已引起了广泛关注。鉴于其相对简单的基因组、紧凑的基因家族、简单的形态、易于繁殖和转化，多形叶苔正成为植物合成生物学一个很有前景的平台。模块化遗传元件对于合成生物学方法的发展至关重要，因此我们试图为多形叶苔遗传元件设计一个面向工程的数据库，其中每个基因都是一个独立的功能单元。MarpoDB是一个多形叶苔基因和遗传元件的数据库，旨在成为合成生物学工作流程中不可或缺的工具。其功能包括对InterPro、Pfam特征和非冗余绿藻植物BLAST注释进行预编译的跨数据库查询；对多形叶苔基因进行BLAST查询；以GenBank格式导出序列；将序列重新编码为用于IIS型组装和DNA元件交换的通用语法；以及一个简约、直观且交互式的用户界面，用于基因模型和序列探索。此外，我们还实现了用户输入，以鼓励MarpoDB社区之间的反馈、合作和交流。MarpoDB的源代码在GitHub上发布，以促进合成生物学计算工具的开发。
