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Abstract
Duplication of DNA is one of the prime drivers of diversification, speciation, and adaptation for life on earth. Plants are highly tolerant of polyploidy or whole-genome duplication (WGD) - indeed, all characterized plant genomes show traces of a history of polyploidy. Duplicated genes often diverge in their function post-duplication, and can assume subsets of their old functions, take on new functions, or be deleted altogether. Studying how these processes have affected crop plants can illuminate their evolution and show how they might be improved through breeding in the future. Legumes, and especially soybean (Glycine max L.), offer a valuable system to study this. For this work, first, the soybean genome was aligned to itself, which showed that gene pairs from the most recent duplication event in soybean have maintained similar expression profiles within tissues and have maintained their methylation status more consistently than older duplicate pairs. Next, an algorithm (TetrAssign) was developed to reconstruct and phase ancient soybean subgenomes post-WGD, and comparison of these reconstructions with maize showed that soybeans ancient subgenome sets were less divergent in their gene deletion, expression, and methylation profiles than maizes. Then, a set of gene families (orthogroups) for soybean and several other sequenced legume genomes was analyzed to reveal that rates of stochastic gene duplication were low, while gene deletion (death) rates were higher but variable among the legume branches, and furthermore found that the Glycine-specific duplication event had a much higher retention of gene duplicates post-WGD than the Faboideae duplication. Lastly, resequencing of elite and wild (Glycine soja) soybean accessions determined that while duplicated genes dominate the gene set of soybean, orphan genes and dispensable genes are overrepresented among genes most strongly selected for during the domestication of soybean. The results of this work indicate that soybeans genome is unusually duplicated for a diploidized paleotetraploid, that its subgenomes 8-13 My ago were less diverged than was initially thought, and that the evolution of duplicate genes is ongoing in soybean and has probably impacted the transformation of soybean from a wild, vine-like plant into the dependable economic powerhouse it is today.