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表型悖论：自然转录组进化对植物工程的启示

The Phenotype Paradox: Lessons From Natural Transcriptome Evolution on How to Engineer Plants.

作者信息

Law Justin, Ng Kangbo, Windram Oliver P F

机构信息

Grand Challenges in Ecosystems and the Environment, Imperial College London, Ascot, United Kingdom.

The Francis Crick Institute, London, United Kingdom.

出版信息

Front Plant Sci. 2020 Feb 18;11:75. doi: 10.3389/fpls.2020.00075. eCollection 2020.

DOI:10.3389/fpls.2020.00075
PMID:32133018
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7040092/
Abstract

Plants have evolved genome complexity through iterative rounds of single gene and whole genome duplication. This has led to substantial expansion in transcription factor numbers following preferential retention and subsequent functional divergence of these regulatory genes. Here we review how this simple evolutionary network rewiring process, regulatory gene duplication followed by functional divergence, can be used to inspire synthetic biology approaches that seek to develop novel phenotypic variation for future trait based breeding programs in plants.

摘要

植物通过单基因和全基因组重复的迭代轮次进化出基因组复杂性。这导致转录因子数量大幅增加，这些调控基因优先保留并随后发生功能分化。在这里，我们回顾了这种简单的进化网络重连过程，即调控基因复制后发生功能分化，如何能够启发合成生物学方法，这些方法旨在为未来基于性状的植物育种计划开发新的表型变异。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ab56/7040092/823d93234bd7/fpls-11-00075-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ab56/7040092/823d93234bd7/fpls-11-00075-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ab56/7040092/823d93234bd7/fpls-11-00075-g001.jpg

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本文引用的文献

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The Recruitment Model of Metabolic Evolution: Jasmonate-Responsive Transcription Factors and a Conceptual Model for the Evolution of Metabolic Pathways.代谢进化的招募模型：茉莉酸响应转录因子与代谢途径进化的概念模型
Front Plant Sci. 2019 May 14;10:560. doi: 10.3389/fpls.2019.00560. eCollection 2019.
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Computational methods for Gene Regulatory Networks reconstruction and analysis: A review.计算方法在基因调控网络重构和分析中的应用：综述。
Artif Intell Med. 2019 Apr;95:133-145. doi: 10.1016/j.artmed.2018.10.006. Epub 2018 Nov 9.
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The transcriptional landscape of polyploid wheat.
多倍体小麦的转录组图谱。
Science. 2018 Aug 17;361(6403). doi: 10.1126/science.aar6089.
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Draft genome sequence of var. provides insights into the evolution of the tea genome and tea quality.变种的基因组草图序列为研究茶树基因组和茶叶品质的演化提供了线索。
Proc Natl Acad Sci U S A. 2018 May 1;115(18):E4151-E4158. doi: 10.1073/pnas.1719622115. Epub 2018 Apr 20.
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HiDi: an efficient reverse engineering schema for large-scale dynamic regulatory network reconstruction using adaptive differentiation.HiDi：一种使用自适应分化进行大规模动态调控网络重构的高效反向工程模式。
Bioinformatics. 2017 Dec 15;33(24):3964-3972. doi: 10.1093/bioinformatics/btx501.
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A time series driven decomposed evolutionary optimization approach for reconstructing large-scale gene regulatory networks based on fuzzy cognitive maps.一种基于模糊认知图的时间序列驱动的分解进化优化方法，用于重建大规模基因调控网络。
BMC Bioinformatics. 2017 May 8;18(1):241. doi: 10.1186/s12859-017-1657-1.
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Engineering microbial phenotypes through rewiring of genetic networks.通过重新连接遗传网络来设计微生物表型。
Nucleic Acids Res. 2017 May 5;45(8):4984-4993. doi: 10.1093/nar/gkx197.
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The feasibility of genome-scale biological network inference using Graphics Processing Units.使用图形处理器进行全基因组规模生物网络推断的可行性。
Algorithms Mol Biol. 2017 Mar 20;12:8. doi: 10.1186/s13015-017-0100-5. eCollection 2017.
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Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families.植物 DNA 结合转录因子家族的多样性、扩张和进化新颖性。
Biochim Biophys Acta Gene Regul Mech. 2017 Jan;1860(1):3-20. doi: 10.1016/j.bbagrm.2016.08.005. Epub 2016 Aug 10.
10
Evolution of plant genome architecture.植物基因组结构的演变
Genome Biol. 2016 Mar 1;17:37. doi: 10.1186/s13059-016-0908-1.