Drosophila Genomics: Sequencing and Annotating a Genome in the Classroom

Genomics is a rapidly developing field that is proving to be relevant to many areas of biology and medicine. This course provides students with an enhanced understanding of genomics for those potentially interested in entering the field. Of the 12 Drosophila species that have been sequenced, only the fourth (\u27dot\u27) chromosome of D. melanogaster has been completed. The Genomics Education Partnership enables undergraduate students to assist in the completion of the genome sequence and annotation of the \u27dot\u27 chromosome from selected Drosophila species. Students are assigned a DNA fragment to \u27finish\u27 the DNA sequence using the resources of the genome sequencing center at Washington University at St. Louis. Students then annotate genes and the location of the gene in the dot chromosome between each species and D. melanogaster. The research contributed by students is placed into a database of genomic information, furthering scientific knowledge of comparative genomics in Drosophila

\u3ci\u3eDrosophila\u3c/i\u3e Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu