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Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish

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Abstract

We used the classic example of the duplicated zebrafish sox11a and -b loci to test the duplication, degeneration, complementation (DDC) model of genome evolution through whole genome duplication. While recent reports have demonstrated sub-partitioning of regulatory sequences in duplicated regions, a comparison of the regulatory capabilities of extant regulatory sequences derived from ancient ancestral elements has been scarce. Consistent with the DDC model, we find that ancestral regulatory elements distributed over several hundred kb were lost in either one or the other zebrafish duplicate, leading to subpartitioning. However, regulatory sequences kept as duplicates near both sox11 co-orthologs diverged in sequence from each other and from human elements and in the regulatory patterns they drive in transgenic zebrafish. Evolutionary analysis of the loci suggested that both zebrafish protein coding sox11 orthologs have been maintained by purifying selection, and have evolved at comparable rates, indicative of non-diverged protein functions. The duplicated regulatory elements, conversely, evolved with different divergence rates and degrees of subfunctionalization. These data show that regulatory evolution of gene expression patterns occurred both through differential loss as well as through regulatory sequence evolution in zebrafish versus human genomes.

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  1. Thomas S. Becker

    Present address: Developmental Neurobiology and Genomics Laboratory, Brain and Mind Research Institute, Sydney Medical School, University of Sydney, Camperdown, NSW, 2050, Australia

  2. David Fredman

    Present address: Department for Molecular Evolution and Development, University of Vienna, 1090, Vienna, Austria

Authors and Affiliations

  1. Sars Centre for Marine Molecular Biology, University of Bergen, 5008, Bergen, Norway

    Pavla Navratilova, David Fredman, Boris Lenhard & Thomas S. Becker

  2. Computational Biology Unit, University of Bergen, 5008, Bergen, Norway

    David Fredman & Boris Lenhard

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  1. Pavla Navratilova
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  2. David Fredman
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  3. Boris Lenhard
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  4. Thomas S. Becker
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Correspondence to Thomas S. Becker.

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Communicated by S. Hohmann.

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Navratilova, P., Fredman, D., Lenhard, B. et al. Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish. Mol Genet Genomics 283, 171–184 (2010). https://doi.org/10.1007/s00438-009-0503-1

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