PROJECT SUMMARY
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.
PROPOSED TAXON SAMPLING
Table 1. Proposed sampling of genera in recognized papilionoid subclades. A single species will be examined from 56 of the 72 genera listed below that are most readily available, plus 4 caesalpinioid outgroups. Some specifically targeted species are indicated.
Angylocalyceae (Angylocalyx) clade: Alexa*
Dipterygeae: Monopteryx*, Dipteryx*, Pterodon*, Taralea*
Amburaneae (Amburana) clade: Petaldenium*
Swartzieae (Swartzioid) clade: Ateleia*, Swartzia*, Trischidium*
Cladrastis clade: Cladrastis lutea†, Pickeringia montana†, Styphnolobium japonicum†
Exostyleae (Lecointeoid) clade: Zollernia*, Exostyles*, Holocalyx*, Harleyodendron*
Vataireoid clade: Vatairea*, Luetzelbergia*
Andira clade: Andira*, Hymenolobium*
Orphan genera: Aldina*, Amphimas*, Dermatophyllum (sp. arizonicum/secundiflorum†)
Ormosieae (Ormosia) clade: Ormosia*, Clathrotropis*
Brongniartieae clade: Cyclobium*, Harpalyce*, Poecilanthe*
Leptolobieae (Bowdichia) clade: Bowdichia*, Diplotropis*, Leptolobium*
Sophoreae clade: Sophora†, Baptisia†, Thermopsis rhombifolia†
Crotalarieae clade: Crotalaria†
Genisteae clade: Genista†, Spartium†, Ulex†
Amorpheae clade: Amorpha†, Dalea†, Psorothamnus†
Dalbergieae clade: Aeschynomene*†, Dalbergia*†, Geoffroea*†, Arachis†, Tipuana†
Baphioid clade: Airyantha*, Baphia*
Indigoferoids-Millettioids clade: Canavalia*, Clitoria*, Cologania†, Desmodium†, Dioclea*, Erythrina†, Indigofera†, Lonchocarpus*†, Millettia†, Pueraria†, Rupertia†, Tephrosia†
Robinioids clade: Coursetia glandulosa†, Robinia neomexicana†, Sesbania†
IRLC: Alhagi†, Caragana†, Hedysarum†, Melilotus†, Parochetus, Wisteria†
Outgroups from Caesalpinioids s.l.: Ceratonia†, Gleditsia†, Parkinsonia†, Senna†
* Taxa can be obtained from botanical gardens in USA, Mexico, Brazil, and/or by field collections in eastern and central Brazil
† Taxa can be obtained from botanical gardens in USA, by field collections in the USA and Mexico, or from reputable seed banks (e.g., USDA GRIN National Genetic Resources Program and the Desert Legume Program, Boyce Thompson Arboretum/University of Arizona, Tucson).
Taxa in tribes Baphieae (Africa), Bossiaeeae (Australia), Camoensieae (Africa), Crotalarieae (Africa), Mirbelieae (Australasian), and Podalyrieae (Africa) not planned for sampling unless we can obtain fresh material from botanical gardens.
PUBLICATIONS
Choi I-S, Ruhlman TA, Jansen RK. 2020. Comparative mitogenome analysis of the genus Trifolium reveals independent gene fission of ccmFn and intracellular gene transfers in Fabaceae. Internat J Mol Sci 21: 1959.
Click here for list of other relevant pubications on Papilionoid legumes
Click here for list of previous publications on Papilionoid legumes
PARTICIPANTS
PI and co-PIs: Robert K. Jansen and Tracey A. Ruhlman, University of Texas at Austin; Martin Wojciechowski. Arizona State University.
Postdoctoral Fellows: Insu Choi, Arizona State University and University of Texas at Austin
Graduate Students: Chaehee Lee, PhD candidate, University of Texas at Austin
Collaborators: Domingos Cardoso, Universidade Federal da Bahia (UFBA), Instituto de Biologia, Salvador, Bahia, Brazil.
Luciano Paganucci de Queiroz, Universidade Estadual de Feira de Santana (UEFS), Dept. Ciências Biológicas, Feira de Santana, Bahia, Brazil.
Haroldo C. de Lima, Instituto de Pesquisas, Jardim Botanico do Rio de Janeiro, Rio de Janeiro, Brazil.
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| Camoensia scandens | Castanospermum australe |
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| Strongylodon macrobotys | Tabaroa caatingicola |
