Undergraduate research in the Genomics Education Partnership: a comparative genomics project exploring genome organization and chromatin structure in Drosophila

In the Genomics Education Partnership (GEP), undergraduate students participate in research as they contribute to sequence improvement, engage in gene annotations, and perform comparative genomics analyses that lead to research publications. The current scientific focus of the GEP is on the largely heterochromatic Drosophila Muller F element (dot chromosome). We seek to determine whether heterochromatic and euchromatic domains can be distinguished based on sequence organization or gene characteristics. Comparative studies of D. melanogaster and D. virilis demonstrated that the dot chromosomes have higher repeat density, larger gene size, lower codon bias, and a higher rate of gene rearrangement compared to reference euchromatic domains. “Wanderer” genes that are present on the dot chromosome in one species and in a euchromatic domain on a different chromosome in the other species adopt the characteristics of the domain where they reside. Recently completed analysis of the D. mojavensis dot chromosome shows a higher level of repetitious sequence (40% due to increased simple repeats), but similar properties overall. Surveys and quizzes show that students increase their knowledge of gene and genome organization and that GEP students demonstrate personal gains comparable to students involved in a full‐time summer research experience. Funded by HHMI & NIH.