Abstract
The de novo synthesis of genomes has made unprecedented progress and achieved milestones, particularly in bacteria and yeast. However, the process of synthesizing a multicellular plant genome has not progressed at the same pace, due to the complexity of multicellular plant genomes, technical difficulties associated with large genome size and structure, and the intricacies of gene regulation and expression in plants. Here we outline the bottom-up design principles for the de novo synthesis of the Physcomitrium patens (that is, earthmoss) genome. To facilitate international collaboration and accessibility, we have developed and launched a public online design platform called GenoDesigner. This platform offers an intuitive graphical interface enabling users to efficiently manipulate extensive genome sequences, even up to the gigabase level. This tool is poised to greatly expedite the synthesis of the P. patens genome, offering an essential reference and roadmap for the synthesis of plant genomes.
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Data availability
All genome data used in the design of SynMoss are available via Figshare at https://doi.org/10.6084/m9.figshare.22975925.v5 (ref. 51).
Code availability
The source code and instructions for GenoDesigner are available at https://github.com/SynMoss/GenoDesigner. The server is accessible at http://49.51.34.198:3000/client/chromosome/en/#/. Related Python and R programs are available at https://github.com/WenfeiY/P.patens_geno_design.
Change history
07 June 2024
A Correction to this paper has been published: https://doi.org/10.1038/s41477-024-01734-8
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Acknowledgements
This study was supported by the National Key R&D Program of China (grant nos 2022YFF1201800, 2021YFF1201700 and 2019YFA0903900), the National Natural Science Foundation of China (grant no. 32201207), the Innovation Program of the Chinese Academy of Agricultural Sciences, the Shenzhen Science and Technology Program (grant nos KQTD20180413181837372 and RCYX20221008092950122), the Shenzhen Outstanding Talents Training Fund, the CAS Project for Young Scientists in Basic Research (grant no. YSBR-078) and the Strategic Priority Research Program (Precision Seed Design and Breeding, grant no. XDA24020103).
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J.Y., Q.Z., B.M., Y.W., Y.J., Y.M., X.H., W.Q. and J.D. conceived and designed the project. X.H., W.Q. and J.D. supervised the research. W.Y., S. Zhang and X.H. completed the programming. S. Zhao analysed the RNA-seq data. L.-g.C., J.C. and H.Y. performed the experiments. W.Y., S. Zhang, X.H., W.Q. and J.D. wrote the manuscript.
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Yu, W., Zhang, S., Zhao, S. et al. Designing a synthetic moss genome using GenoDesigner. Nat. Plants 10, 848–856 (2024). https://doi.org/10.1038/s41477-024-01693-0
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DOI: https://doi.org/10.1038/s41477-024-01693-0
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