Collaborative Research: Phylogenomics and Cytonuclear Coevolution of Papilionoid Legumes

每个植物物种都有三个基因组，分别位于细胞核、线粒体和叶绿体中，它们的活动紧密协调。叶绿体和线粒体基因组编码的蛋白质必须与核编码的蛋白质相互作用，才能进行光合作用等基本过程。因此，这些相互作用的蛋白质之间的不匹配可能会阻止遗传上不同的个体产生有活力的杂交后代。这种基因组协调或共同进化被假设为驱动植物物种多样化，但在密切相关的物种中基本上没有特征。本项目将利用类千花科豆类研究这一现象，其中包括经济上重要的作物，如大豆、苜蓿和花生，以及具有重大生态影响的固氮物种。研究人员将利用来自所有三个基因组的DNA序列数据来解决该群体主要谱系之间的进化关系，并将研究基因组共同进化在该谱系随着时间的推移而扩展中的作用。该项目将为本科生、研究生和研究生提供基因组学、植物生物学和进化生物学方面的培训，并将从代表性不足的群体中招收学生。拓展活动包括为K-12学生开发教学模块和工作见习体验。该项目将提供一个强有力的框架，以解决有关豆科植物系统学和基因组共同进化的突出问题。Papilionoid豆科植物在细胞器基因组、高度重排的质体、双亲本遗传和质体-基因组不相容方面具有加速的核苷酸替代速率，这使它们成为谱系多样化过程中表征基因组共同进化的理想模型。将利用代表22个主要分支的56个物种的质体和线粒体基因组数据以及核转录组，包括早期分化和鲜为人知的谱系，来推断出乳突豆科植物的系统发育关系。细胞核共同进化分析将比较其产物相互作用的细胞器和核基因之间的核苷酸替代率。然后，研究人员将确定基因产物之间的协调变化是否发生在乳突虫系统发育的同一分支上，这将表明共同进化的协调。这项研究的最终目的是进一步测试核编码DNA修复、重组和复制基因的高序列进化率与线粒体和质体基因组复杂性之间的相关性。研究结果将在出版物、公共数据库和其他可公开访问的互联网资源中广泛分享。研究结果将为控制物种边界的可能基因组机制提供新的见解，并将加强研究基础设施，以支持系统发育生物学和农业改良的进步。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Each plant species has three genomes housed in the nucleus, mitochondrion, and chloroplast whose activities are tightly coordinated. Proteins encoded by the chloroplast and mitochondrial genomes must interact with nuclear-encoded proteins in order for essential processes, such as photosynthesis, to occur. Consequently, mismatches among these interacting proteins may prevent genetically divergent individuals from producing viable hybrid offspring. This genomic coordination, or coevolution, is hypothesized to drive plant species diversification but is largely uncharacterized among closely related species. This project will examine this phenomenon using the papilionoid group of legumes, which include economically important crops, such as soybeans, alfalfa, and peanuts, and nitrogen-fixing species that have significant ecological impacts. Researchers will resolve the evolutionary relationships among the major lineages of this group using DNA sequence data from all three genomes and will study the role of genomic coevolution during this lineage's expansion over time. The project will provide training at the undergraduate, graduate and post-graduate levels in genomics, plant biology, and evolutionary biology and will recruit students from underrepresented groups. Outreach activities include the development of teaching modules and job-shadowing experiences for K-12 students. This project will provide a robust framework to address outstanding questions regarding legume systematics and genome coevolution. Papilionoid legumes have accelerated rates of nucleotide substitution in organellar genomes, highly rearranged plastomes that exhibit biparental inheritance and plastome-genome incompatibility, which make them ideal models for characterizing genomic coevolution during lineage diversification. Phylogenetic relationships of the papilionoid legumes will be inferred using plastid and mitochondrial genome data as well as nuclear transcriptomes for 56 species representing each of the 22 major clades, including early diverging and poorly known lineages. Cytonuclear coevolution analyses will compare nucleotide substitution rates between organelle and nuclear genes whose products interact. Researchers will then determine whether coordinated changes among the gene products are occurring on the same branch of the papilionoid phylogeny, which would indicate coevolutionary coordination. The final aim of the research will further test the correlation between high rates of sequence evolution in nuclear-encoded DNA repair, recombination and replication genes and mitochondrial and plastid genome complexity. Results of the research will be shared widely in publications, public databases and other publicly-accessible internet resources. Outcomes of the research will provide new insights into possible genomic mechanisms that govern species boundaries and will strengthen research infrastructure to support advances in phylogenetic biology and agricultural improvement.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.