Drosophila Genomics: A Novel Research Experience in the Classroom

Through support of the Genomics Education Partnership (GEP), students are provided an opportunity to experience genomics research and its applications in a classroom setting. The majority of the genomes from many Drosophila species have been sequenced, except for the dot chromosome, which is composed of highly repetitive DNA sequence much like the human genome. We are currently working towards improving the DNA sequence of the 4th (dot) chromosome in D. ananassae. Large DNA fragments were identified that cover the dot chromosome, and using the resources established by the GEP, students finished the DNA sequence to high quality using Consed . After finishing DNA sequence of 1 fosmid, students annotate DNA contigs from the dot chromosomes of D. mojavensis or D. grimshawi to determine how the dot chromosome structure changes between species. The results contributed by students are placed into the GEP database, 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