ANNOUNCEMENTS
Polyploidy or whole genome multiplication is a natural phenomenon that underpins plant genome evolution. The genome-wide consequences of polyploidy have been extensively studied using various model plants such as meso-hexaploid Brassica. However, the knowledge of polyploidy-driven phenomena such as differential fractionation of sub-genomes, homeolog expression bias and regulatory diversification is yet to be integrated in functional characterization of individual gene homeologs, especially those associated with crucial developmental pathways. The current study aims at understanding the impact of polyploidy-induced promoter diversification on expression and function of homeologs in Brassica. To this end, SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), a critical floral pathway integrator has been selected for study. Copy number analysis of SOC1 in Brassica revealed preservation of three homeologs in diploid Brassica genomes with strong conservation in the coding region. To investigate the presence of regulatory diversification, sequence and phylogeny of upstream regions of SOC1 homeologs have been analyzed to identify conserved and differentiating characteristics. Furthermore, a novel comparative genomics approach has been used to reliably predict functional transcription factor binding sites (TFBSs) in hitherto uncharacterized Brassica SOC1 promoters. While this analysis revealed evolutionarily conserved footprints, differential distribution of TFBSs among SOC1 homeologs was clearly observed, signifying regulatory divergence. The relative quantification of multiple SOC1 homeologs in B. juncea and B. nigra showed distinct spatio-temporal patterns of expression, indicating regulatory divergence. Reporter tagging of homeologous proximal promoters has been performed in native B. juncea background to understand the role of promoter divergence in expression differences. Our data provides compelling evidence for functional divergence of Brassica SOC1 homeologs as routed in promoter divergence. Furthermore, in order to identify and compare crucial regions of regulatory activity in homeologous SOC1 promoters, full-length and truncated proximal promoters have been tested in heterologous A. thaliana background. This experiment has highlighted other interesting aspects of homeolog-specific promoter evolution and underscores the role of divergence in transcription factors in altering the expression profiles. Lastly, crucial upstream regulators of Brassica SOC1 homeologs have been predicted based on sequence divergence, TFBS profiles, and co-expression patterns in B. rapa and B. juncea and to pinpoint most important TFs regulating SOC1 in Brassica. Overall, our study concludes that expression divergence among Brassica SOC1 homeologs is due to differential partitioning of ancestral TFBSs among promoters, signifying regulatory divergence.
