Collaborative Research: Phylogenomics and Cytonuclear Coevolution of Papilionoid

Project: Research project

Project Details

Description

Overview
Plant cell function is directed by three genomes in separate cellular compartments (nucleus, mitochondrion, plastid) that are interdependent as their maintenance and expression are tightly coordinated. Recent studies in two unrelated angiosperm families provided a glimpse into coevolution between these three genomes, however, the patterns and causes of this coordination were distinct in each group. Both lineages share a syndrome of organelle features, including highly rearranged plastid genomes (plastomes), remarkably accelerated rates of nucleotide substitutions in organellar genes, plastid biparental inheritance and plastome-genome incompatibility (PGI). Some papilionoid legumes, which comprise the largest and most economically important legume clade, share this syndrome. Despite considerable effort, reliance on a few genes has not resolved relationships among the major papilionoid lineages. The proposed research will generate genomic data to reconstruct a more fully resolved and supported phylogeny of papilionoids, and to use this as a framework to conduct a comprehensive investigation of cytonuclear coevolution in this group. The proposed work has the following three broad aims: (1) generate a fully resolved and well supported phylogeny of the major clades of papilionoids using multiple genes from all three genomes; (2) examine coevolution of nuclear, mitochondrial and plastid genes; and (3) determine if changes in nuclear encoded DNA repair, replication and recombination genes are correlated with mitochondrial and plastid genome complexity. To address these aims, whole organellar genomic and nuclear transcriptomic data will be produced for 56 species of papilionoids, and combined with publicly available data for six species from this group. Genes will be mined from each of the three genomes to reconstruct phylogenetic relationships among the major clades of papilionoid legumes. This phylogeny will be used as a framework for molecular evolutionary analyses to address the two coevolutionary aims.
Intellectual Merit
Cytonuclear coevolution is an important phenomenon that has implications for species diversification and crop breeding that few comparative genomic investigations have addressed. The results of this project will not only deepen our understanding of phylogenetic relationships in papilionoids, it will enhance our understanding of cytonuclear coevolution and compartmental crosstalk between the nucleus and organelle genomes. This project represents the most comprehensive phylogenomic investigation of papilionoid legumes to date and will significantly advance our understanding of this diverse and economically important lineage of flowering plants. The proposed work will be of broad interest to legume and other plant biologists, and the general public. The results will provide a robust phylogenetic framework to advance studies by other investigators working on questions in legume biology, including the origin(s) of nodulation and whole genome duplications, biosynthesis of quinolizidine alkaloids and non-protein amino acids, and developmental evolution of floral structure and symmetry. This project will substantially increase the number of legume species with genome scale data, providing an invaluable resource for future studies by other researchers.
Broader Impacts
The project provides excellent student education and training opportunities at the undergraduate, graduate and postdoctoral levels in areas including genomics, computational biology, phylogenetics and evolutionary biology. The undergraduate training components of this project will utilize established research education and training programs at the University of Texas at Austin (FRI) and Arizona State University (SOLUR, IMSD). These programs are designed to recruit students from minority groups historically underrepresented in the sciences. Data and findings will be communicated via traditional scientific presentations and publications, public databases (GenBank, treeBASE, Dryad) and other publicly accessible internet resources. Outreach activities will include development of teaching modules and activities for the Ask-A-Biologist educational website at Arizona State University and research internships for high school students in Austin, Texas.

StatusActive
Effective start/end date9/1/198/31/22

Funding

  • National Science Foundation (NSF): $297,617.00

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