Proximal and ultimate causes of adaptive lateral gene transfers in land plants

陆地植物适应性横向基因转移的近端和最终原因

• 批准号: NE/M00208X/1
• 负责人: Pascal-Antoine Christin
• 金额: $ 45.5万
• 依托单位: University of Sheffield
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FM00208X%2F1
• 关键词: Proximal; ultimate; causes; adaptive; lateral

In multicellular organisms, evolution is classically thought to proceed exclusively through natural selection on mutations occurring within genes present in the genome of a single species. This paradigm has been challenged by recent reports of lateral gene transfers among multicellular animals and plants. In particular, we have recently shown that laterally acquired genes were integrated into the basic metabolism of some grasses and contributed to the adaptation of their photosynthetic apparatus through the optimization of a novel photosynthetic pathway, namely C4 photosynthesis. This trait increases the productivity of plants living in warm and dry conditions and would consequently lead to an increase of yield if introduced into crops using the ancestral C3 photosynthetic pathway, including rice and wheat. Elucidating the mechanisms behind naturally occurring adaptive transfers of genes for C4 photosynthesis among grasses would open new potential strategies for this endeavour. We currently do not understand how or why these gene transfers occurred. We propose to tackle these issues by sequencing and comparing the genomes of closely related grasses that differ in their photosynthetic types and in the number of laterally acquired genes they possess. This project will capitalize on the availability of high-throughput sequencing, using comparative genomics to address a key question in evolutionary biology. Complete genomes will be generated de novo for four closely related taxa of the grass genus Alloteropsis, two of which belong to the same species complex but use C3 and C4 photosynthesis, respectively. Thirty additional individuals from the same species complex, sampled from different continents and with different laterally acquired genes, will be selected for re-sequencing, and their genomes will be assembled using the de novo assemblies as a reference. All markers generated for Alloteropsis will be analysed within a phylogenetic framework that will incorporate publicly available complete genomes for model grasses, two of which are closely related to the donors of laterally transferred genes. All Alloteropsis genes that are statistically more closely related to their equivalents in species outside Alloteropsis will be identified as laterally acquired genes. The genomic regions surrounding them will be investigated to test alternative hypotheses about the mechanism responsible for the transfer. Finally, the evolutionary history of key C4 genes, including gradual C4-adaptive changes and loss of function, will be used to infer the photosynthetic type of the plants that received the gene transfers, shedding new light on the adaptive significance of the foreign genetic material incorporated. This multifaceted project will determine how and why adaptive lateral gene transfers occurred in grasses, enabling new understanding of the conditions that allow the lateral spread of functional traits among distantly related species. In addition, this fundamental research project will have a direct impact on the efforts to engineer rice using C4 photosynthesis to feed the growing human population, by elucidating the conditions that allowed successful transfers in the wild. Finally, the proposed project will generate the first genomes for closely related taxa that use different photosynthetic types, providing new and valuable resources for the identification of the fine-scale genetic (especially regulatory) changes that allow photosynthetic adaptation in grasses, the ecologically and economically most important group of plants.

在多细胞生物中，进化被经典地认为是通过自然选择对单个物种基因组中存在的基因内发生的突变进行的。这种模式受到了挑战，最近的报告横向基因转移之间的多细胞动物和植物。特别是，我们最近已经表明，横向收购的基因被整合到一些草的基本代谢，并通过优化一种新的光合作用途径，即C4光合作用，有助于其光合机构的适应。这种特性增加了生活在温暖和干燥条件下的植物的生产力，因此如果引入使用祖先C3光合途径的作物（包括水稻和小麦）中，将导致产量增加。阐明背后的机制自然发生的适应性转移基因C4光合作用之间的草将开辟新的潜在战略，这一努力。我们目前还不清楚这些基因转移是如何发生的，以及为什么会发生。我们建议通过测序和比较密切相关的草的基因组来解决这些问题，这些草在光合作用类型和横向获得的基因数量上有所不同。该项目将利用高通量测序的可用性，使用比较基因组学来解决进化生物学中的一个关键问题。完整的基因组将从头产生的四个密切相关的类群的草属Alloteropsis，其中两个属于同一物种的复合体，但使用C3和C4光合作用，分别。将选择来自不同大陆的同一物种复合体的另外30个个体进行重新测序，并将使用从头组装作为参考来组装它们的基因组。将在系统发育框架内分析为Alloteropsis产生的所有标记，该框架将纳入公开可用的模式草的完整基因组，其中两个与横向转移基因的供体密切相关。所有在统计学上与异拟属以外物种中的等同物更密切相关的异拟属基因将被鉴定为横向获得基因。将研究它们周围的基因组区域，以测试有关转移机制的替代假设。最后，关键C4基因的进化历史，包括逐渐C4适应性变化和功能丧失，将被用来推断接受基因转移的植物的光合作用类型，为引入的外源遗传物质的适应性意义提供新的线索。这个多方面的项目将确定如何以及为什么适应性横向基因转移发生在草，使新的理解的条件，允许功能性状的横向传播之间的远亲物种。此外，该基础研究项目将通过阐明允许在野外成功转移的条件，对利用C4光合作用设计水稻以养活不断增长的人口的努力产生直接影响。最后，拟议的项目将产生第一个基因组的密切相关的类群，使用不同的光合作用类型，提供新的和有价值的资源，用于识别精细尺度的遗传（特别是监管）的变化，使光合适应草，生态和经济上最重要的植物组。

项目成果

Genome biogeography reveals the intraspecific spread of adaptive mutations for a complex trait.

• DOI: 10.1111/mec.13914
• 发表时间: 2016-12
• 期刊: Molecular ecology
• 影响因子: 4.9
• 作者: Olofsson JK;Bianconi M;Besnard G;Dunning LT;Lundgren MR;Holota H;Vorontsova MS;Hidalgo O;Leitch IJ;Nosil P;Osborne CP;Christin PA
• 通讯作者: Christin PA

Gene duplication and dosage effects during the early emergence of C4 photosynthesis in the grass genus Alloteropsis.

• DOI: 10.1093/jxb/ery029
• 发表时间: 2018-04-09
• 期刊: Journal of experimental botany
• 影响因子: 6.9
• 作者: Bianconi ME;Dunning LT;Moreno-Villena JJ;Osborne CP;Christin PA
• 通讯作者: Christin PA

The recent and rapid spread of Themeda triandra

• DOI: 10.1080/23818107.2017.1391120
• 发表时间: 2017-01-01
• 期刊: BOTANY LETTERS
• 影响因子: 1.5
• 作者: Dunning, Luke T.;Liabot, Anne-Lise;Lehmann, Caroline E. R.
• 通讯作者: Lehmann, Caroline E. R.

Leaf anatomy explains the strength of C4 activity within the grass species Alloteropsis semialata.

叶子解剖学解释了草种 Alloteropsis semialata 内 C4 活性的强度。

• DOI: 10.1111/pce.14607
• 发表时间: 2023
• 期刊: Plant, cell & environment
• 作者: Alenazi AS

Highly Expressed Genes Are Preferentially Co-Opted for C4 Photosynthesis.

• DOI: 10.1093/molbev/msx269
• 发表时间: 2018-01-01
• 期刊: Molecular biology and evolution
• 影响因子: 10.7
• 作者: Moreno-Villena JJ;Dunning LT;Osborne CP;Christin PA
• 通讯作者: Christin PA