Abstract Detail



Macroevolution

Kates, Heather [1], Folk, Ryan [2], Kirst, Matias [3], Roy, Sushmita [4], Ane, Jean-Michel [5], Guralnick, Robert [6], Soltis, Douglas [7], Soltis, Pamela [2].

Phylogenomics of the Nitrogen-Fixing Clade to Uncover Genomic Novelties Required for Evolution of Root Nodule Symbioses.

Robust phylogenetic inferences on the origin of the predisposition to nodulation, and how and if nodulation has been gained and lost, are key to understanding the evolutionary lability and thus likelihood of successful transferability of N-fixing symbioses among lineages of angiosperms. A well-resolved and well-sampled N-fixing clade phylogeny is therefore a prerequisite to the discovery of genes that determine nodule development. Multiple phylogenetic analyses have been conducted on the N-fixing clade with the aim of elucidating the origins of N-fixing symbioses; however, these analyses have relied on trees estimated using a few genes and in which species sampling in the N-fixing clade was limited.            
We present our current phylogeny based on deliberate and extensive sampling, phylogenomic data, and rigorous statistical analysis. This sampling ill allow more accurate inference of precursors of N-fixing symbioses, gain and/or loss events, and potential transferability of the capability to crop plants not in the N-fixing clade. Novel elements of our strategy that enable geographically and taxonomically comprehensive sampling on an ambitious scale include a protocol for rapid tissue sampling of 15,000 historical specimens, a high-throughput, high-yield DNA extraction protocol specifically suited to degraded DNA, a capture kit that works across phylogenetic scales and includes key functional genes, and scaleable information management and processing using a project database.            
Our phylogenetic results are based on 100 nuclear loci sequenced for over 8,000 species from the N-fixing clade and inform our interpretation of patterns of presence/absence of ~100 nodulation genes inferred from genome screening of all species in our phylogeny. This result represents an analysis comprising more than half of our genomic and taxonomic sampling effort, which is now complete. We highlight a set of genes that may be associated with nodulation based on our preliminary results and show that these early data suggest different patterns of gene/nodulation correlation in different parts of the phylogeny. We are leveraging the total phylogenetic and comparative genomic results to discover gene candidates that potentially underlie nodule development so that these genes can be tested for function in nodulating and non-nodulating model systems.


Related Links:
Project website for DOE funded collaborative project to understand and engineer nodulation in plants


1 - University Of Florida, Florida Museum Of Natural History, Dickinson Hall, Gainesville, FL, 32611, United States
2 - University Of Florida, Florida Museum Of Natural History, Po Box 117800, Gainesville, FL, 32611, United States
3 - University of Florida, School of Forest Resources and Conservation, Gainesville, FL, 32611, United States
4 - University of Wisconsin, Department of Biostatistics & Medical Informatics, 330 North Orchard Street , Madison , WI , 53715
5 - University of Wisconsin, Departments of Bacteriology and Agronomy, 1550 Linden Drive, Madison, WI, 53715
6 - University of Florida, PO Box 117800, Gainesville, FL, 32611, United States
7 - University of Florida, Florida Museum of Natural History, PO Box 117800, Gainesville, FL, 32611, USA

Keywords:
nodulation
phylogenomics
symbioses
Herbarium Specimens
bioinformatics
nitrogen fixation.

Presentation Type: Oral Paper
Number:
Abstract ID:792
Candidate for Awards:None


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