Evidence for a unique DNA-dependent RNA polymerase in cereal crops

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2018-02-28
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Trujillo, Joshua
Hufford, Matthew
Beilstein, Mark
Mosher, Rebecca
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Seetharam, Arun
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Ecology, Evolution and Organismal Biology

The Department of Ecology, Evolution, and Organismal Biology seeks to teach the studies of ecology (organisms and their environment), evolutionary theory (the origin and interrelationships of organisms), and organismal biology (the structure, function, and biodiversity of organisms). In doing this, it offers several majors which are codirected with other departments, including biology, genetics, and environmental sciences.

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The Department of Ecology, Evolution, and Organismal Biology was founded in 2003 as a merger of the Department of Botany, the Department of Microbiology, and the Department of Zoology and Genetics.

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2003–present

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Genome Informatics Facility
The Genome Informatics Facility serves as a centralized resource of expertise on the application of emerging sequencing technologies and open source software as applied to biological systems. Its mission is to integrate this knowledge into pipelines that are easy to understand and use by faculty, staff and students to enable the transformation of ‘big data’ into data that dramatically accelerates our understanding of biology and evolutionary processes.
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Gene duplication is an important driver for the evolution of new genes and protein functions. Duplication of DNA-dependent RNA polymerase (Pol) II subunits within plants led to the emergence of RNA Pol IV and V complexes, each of which possess unique functions necessary for RNA-directed DNA Methylation. Comprehensive identification of Pol V subunit orthologs across the monocot radiation revealed a duplication of the largest two subunits within the grasses (Poaceae), including critical cereal crops. These paralogous Pol subunits display sequence conservation within catalytic domains, but their carboxy terminal domains differ in length and character of the Ago-binding platform, suggesting unique functional interactions. Phylogenetic analysis of the catalytic region indicates positive selection on one paralog following duplication, consistent with retention via neofunctionalization. Positive selection on residue pairs that are predicted to interact between subunits suggests that paralogous subunits have evolved specific assembly partners. Additional Pol subunits as well as Pol-interacting proteins also possess grass-specific paralogs, supporting the hypothesis that a novel Pol complex with distinct function has evolved in the grass family, Poaceae.

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This is a pre-print of the article Trujillo, Joshua T., Arun S. Seetharam, Matthew B. Hufford, Mark A. Beilstein, and Rebecca A. Mosher. "Evidence for a unique DNA-dependent RNA polymerase in cereal crops." bioRxiv (2018): 272708. DOI: 10.1101/272708. Posted with permission.

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Mon Jan 01 00:00:00 UTC 2018
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