Collaborative Research: Phylogenomics and Cytonuclear Coevolution of Papilionoid Legumes

每种植物都有三个基因组，分别位于细胞核、线粒体和叶绿体中，它们的活动是紧密协调的。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，才能进行必要的过程，如光合作用。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分化的个体产生可行的杂交后代。这种基因组协调，或共同进化，被假设为推动植物物种多样化，但在密切相关的物种中很大程度上没有特征。该项目将使用豆科类植物来研究这一现象，其中包括重要的经济作物，如大豆、紫花苜蓿和花生，以及对生态有重大影响的固氮物种。研究人员将使用来自所有三个基因组的DNA序列数据来解析这一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这一谱系随着时间的扩展中所起的作用。该项目将在本科生、研究生和研究生阶段提供基因组学、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。外联活动包括为K-12学生开发教学单元和职业跟踪经验。该项目将提供一个强大的框架来解决关于豆科植物系统学和基因组共同进化的悬而未决的问题。蝶形豆科植物在细胞器基因组中的核苷酸替换速度加快，高度重排的质体表现出双亲遗传和质体-基因组不亲和性，这使得它们成为描述谱系多样化过程中基因组共同进化的理想模式。根据叶绿体和线粒体基因组数据以及代表22个主要分支中每一个的56个物种的核转录本，将推断蝶形豆科植物的系统发育关系，包括早期的分歧和鲜为人知的谱系。细胞核协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换率。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蝶形目系统发育的同一分支上，这将表明共同进化协调。这项研究的最终目的将进一步测试核编码的DNA修复、重组和复制基因的高序列进化速度与线粒体和叶绿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共享。这项研究的结果将为管理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。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.