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Undergraduate independent research

Annotation of Ac/Ds distribution in B73 and W22 maize inbred lines via undergraduate independent research

Five undergraduates earned independent research credits in Fall 2009 and Spring 2010 by assisting M.S. student Andrew Hoffman in the annotation of Ac/Ds transposable elements in the B73 genome and in the analysis of the subset shared by W22.  The results of this analysis are being prepared for publication.  Using an algorithm to search through the maize pseudomolecules, about 1000 Ds-like elements were located and annotated.  There are 367 type 1 Ds1 elements and 635 type 2 Ac deletion derivatives.  Among the type 2 Ds elements, 36 are related to the 1.3-kb Ds2, 36 have homology to the internal transposase of Ac, 352 are composed of only truncated subterminal regions of Ac, and the rest share similarity with only the 3’ end of Ac.  Forty-six type 1 and one hundred seventy-three type 2 Ds elements appear to have inserted into genes. The size of the type 2 elements ranges from 600 bp to 20 kb. Helitrons, LTR retrotransposons, and full-length cDNAs can be found embedded in the larger elements.  We are also using next-generation sequencing technology to characterize the spectrum of Ds-like elements in W22.