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Annotation of the Gene Ci on Contig 3 Dot Chromosome of Drosophila Eugracilis Open Access

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In many Drosophila species, the fourth chromosome is very small and bears relatively few genes. This "dot" chromosome is mostly heterochromatic, has low rates of meiotic recombination, and replicates late in the S phase of mitosis. Despite these hallmarks of suppressed gene expression, genes on the dot chromosome are expressed at normal rates. This unusual pattern piqued the interest of the Genomics Education Partnership (GEP), a research consortium centered in the Biology Department and the McDonnel Genome Institute of Washington University in St. Louis. GEP's mission is to allow undergraduates to participate in genomics research through course curricula and includes consortium members at over 150 universities. GW students in BISC 2208 Genetics Laboratory learn to annotate genes to improve genomic resources for non-model species, facilitating genomic analysis and leading to a publication. My annotation was focused on the gene cubitus interruptus (ci), which encodes for zinc-finger proteins in the Hedgehog (Hh) signaling pathway. This gene is involved in integumentary system development (cuticle pattern and epidermis formation) and organ formation (eye, heart, and nerves). I began by identifying the correct D. melanogaster ortholog and confirming this in D. eugracilis using BLAST and RNA-seq evidence. Then, specific isoforms of ci were identified, and their exon coordinates, frame, and phases were recorded for all existing unique exons. The corrected exon coordinates were then processed through the Gene Model Checker and assessed for similarity with D. melanogaster. Isoform ci-PA had small gaps in exons 2, 3, 4, and 6, and ci-PB presented small gaps in exons 2, 3, and 5. Isoform ci-PC presented gaps in exons 2, 3, 4, and no match in exons 5 and 6. All the exon mismatch corresponds the respective protein alignments. There were mismatches within and at the end of exons, especially in exons 5 and 6. I found substantial evolutionary divergence between D. melanogaster and D. eugracilis lineages in these exons, accounting for only 77% amino acid similarity overall. These results suggested relaxed selection and lower functional significance in this portion of the protein.

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