Molecular evidence for functional divergence and decay of a transcription factor derived from whole genome duplication in XXXX .

@entity71134 @entity958 @entity40408 @entity36008 @entity4334
UNASSIGNED: Functional divergence between duplicate transcription factors (TFs) has been linked to critical events in the evolution of land plants and can result from changes in patterns of expression, binding site divergence and/or interactions with other proteins. Although plant TFs tend to be retained post polyploidization, many are lost within tens to hundreds of million years. Thus it can be hypothesized that some TFs in plant genomes are in the process of becoming pseudogenes. Here we use a pair of salt tolerance-conferring transcription factors, DWARF AND DELAYED FLOWERING1 ( @entity40408 ) and @entity71134 , that duplicated through paleopolyploidy 50-65 million years ago, as examples to illustrate potential mechanisms leading to duplicate retention and loss. We found that the expression patterns of @entity958 (At) @entity40408 and @entity71134 have diverged in a highly asymmetric manner, and @entity71134 has lost most inferred ancestral stress responses. Consistent with disablement, the @entity71134 promoter has fewer predicted cis-elements and a methylated repetitive element. Through comparisons of @entity40408 , @entity71134 , and their @entity36008 orthologs, we identified significant differences in binding affinities and binding site preference. In particular, an @entity71134 -specific substitution within the DNA binding domain significantly reduces binding affinity. Cross-species analyses indicate that both @entity40408 and @entity71134 are under selective constraint, but among A. thaliana accessions, @entity71134 has a higher level of nonsynonymous @entity4334 diversity compared to @entity40408 . This may be the result of selection in different environments, or may point towards the possibility of ongoing functional decay despite retention for millions of years after gene duplication.
