Collaborative Research: Phylogenomics and Cytonuclear Coevolution of Papilionoid Legumes

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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.