Adaptive Evolution in the Photoreceptor Phytochrome A and its Role in the Ecological Success of the First Angiosperms

光信号的正确处理对于所有植物的成功至关重要。 因此，光感受器在植物发育中起着关键作用，作为信息分子，使植物能够确定它们在空间和时间中的位置，并使生长和发育与不断变化的光环境同步。 环境光条件对植物形态的控制，一个被称为光形态建成的过程，是由光敏色素介导的，光敏色素吸收红光和远红光，沿着不同的蓝光和紫外光吸收光感受器。 陆地植物光敏色素的进化是以一系列基因复制为标志的，这些基因复制导致了独立进化和功能不同的品系。 有花植物中光敏色素含量最高，也是陆生植物中最成功的一类。 它们总共约有25万种，数量超过所有其他植物群的总和，并主宰着地球上除两个以外的所有陆地植被带。 它们的起源伴随着自三叠纪以来一直占主导地位的植物群的衰落，但它们的起源模式和导致其惊人成功的因素仍然未知。 该项目将DNA序列分析与早期发散开花植物幼苗的生理特征相结合，以验证光感机制的进化对开花植物早期成功很重要的假设。 具体来说，它测试的假设，光敏色素A，一种独特的开花植物的光敏色素的进化，提高了早期被子植物在茂密的树荫下生存的能力。 序列分析将确定光敏色素A的功能分歧是通过正选择还是通过选择性限制的放松而发生的，并将确定将其与编码光敏色素C的姊妹基因区分开的功能分歧位点。 生理实验将确定早分化开花植物物种的幼苗是否表现出对密集遮荫的反应，这些反应已在更多衍生物种（例如拟南芥）中得到表征，并将确定是否在相关种子植物的幼苗中发现任何这些反应。 这些分析将一起测试的假设，光敏色素A的功能是一种适应性的创新，帮助显花植物获得立足点下的森林冠层曾经占主导地位的蕨类植物和裸子植物。 比较分子分析是评价非模式物种功能多样化的有效机制。 因此，在这个项目中进行的分析将进一步植物基因组学的一个目标，超越模型系统走向了解多样性的分子基础。 将生成的序列数据库将用于确定其他种子植物是否可能独立地获得对光环境的多个方面的复杂但平行的生理反应。 这个数据库也将是有用的，用于确定网站的功能规格的基因，其功能一直难以用传统的遗传学方法来表征。 以这种方式鉴定的位点的功能可以在诱变实验中进一步测试。 田间和温室生理实验将表征单个物种幼苗再生的最适光。 因此，他们将提供深入了解植物群落的组成可能会发生变化，以应对生态系统范围内的干扰或变化。

The proper processing of light signals is crucial for the success of all plants. Thus, photoreceptors play a critical role in plant development, serving as informational molecules that allow plants to determine where they are in space and time and to synchronize growth and development to a changing light regime. The control of plant form by ambient light conditions, a process known as photomorphogenesis, is mediated by phytochromes, which absorb red light and far-red light, along with distinct blue and ultra-violet absorbing photoreceptors. Phytochrome evolution in land plants is marked by a series of gene duplications that have led to independently evolving and functionally distinct lines. Flowering plants have the highest number of phytochromes and also are the most successful group of land plants. They total approximately 250,000 species, outnumbering all other plant groups combined, and dominate all but two of the earth's terrestrial vegetation zones. Their origin was followed by the decline of plant groups that had dominated since the Triassic, but their mode of origin and the factors that underlie their spectacular success remain unknown. This project integrates DNA sequence analyses with physiological characterization of seedlings from early-diverging flowering plants to test the hypothesis that evolution in light-sensing mechanisms was important for the early success of flowering plants. Specifically, it tests the hypothesis that the evolution of phytochrome A, a phytochrome unique to flowering plants, enhanced the ability of early angiosperms to survive in dense shade. Sequence analyses will determine whether functional divergence of phytochrome A occurred by positive selection or by relaxation of selective constraints, and will identify sites of functional divergence that distinguish it from its sister gene, which encodes phytochrome C. Physiological experiments will determine whether seedlings of early-diverging flowering plant species exhibit the responses to dense shade that have been characterized in more derived species such as Arabidopsis, and will determine whether any of these responses are found in seedlings of related seed plants. Together these analyses will test the hypothesis that phytochrome A function was an adaptive innovation that helped flowering plants gain a foothold under the forest canopy once dominated by ferns and gymnosperms. Comparative molecular analyses are an efficient mechanism for evaluating functional diversification in nonmodel species. Thus, the analyses undertaken in this project will further one goal of plant genomics, to move beyond model systems toward understanding the molecular basis of diversity. The sequence database that will be generated will be useful for determining whether other seed plants might have independently attained complex but parallel physiological responses to multiple facets of the light environment. This database also will be useful for identifying sites of functional specification in genes whose function has been difficult to characterize using traditional genetics approaches. The function of sites identified this way can be further tested in mutagenesis experiments. The physiological experiments in the field and greenhouse will characterize light optima for seedling regeneration of individual species. Thus, they will provide insight into how the composition of plant communities might change in response to ecosystem-wide disturbance or change.