Genomic Annotation of Chromosome 3L in Drosophilaananassae

Abstract

The Genomics Education Partnership (GEP) is a nationwide community of more than 100 colleges and universities dedicated to facilitating undergraduate biology education and research. GEP provides training, resources, and mentorship to provide students with experiential learning and research experiences in genomics and bioinformatics. Comparative genomics is important for understanding organismal evolution, adaptation and gene conservation. Comparative genomics also advances the understanding of gene function and homology between species.Drosophila melanogaster is one of the most commonly used model organisms in biomedical science to study fundamental genetics as well as tissue and organ development. The smallest chromosome in Drosophila melanogaster is chromosome 4, also known as the Muller F element, with an estimated size of 5.2 Mb. While the F element has maintained a similar size in many other Drosophila species, it is substantially larger in at least four Drosophila species, one of which is Drosophila ananassae. The D. ananassae Muller F element is more than 18.7 Mb in size. A portion of the D. ananassae genome was annotated for comparison to Drosophila melanogaster. Annotations were completed to generate gene models for genes in Contig 26 of the D. ananassae 3L chromosome (Muller D element) as a comparison to the Muller F element in this species. This was completed using the UCSC Genome Browser, Gene Record Finder, FlyBase, the Basic Local Alignment Search Tool (BLAST) and gene prediction software, such as GENSCAN.Models for four genes were generated from this genomic region: CG8757, Hml, Tsp68C and CG3795. These genes showed a high level of conservation when comparing Drosophila ananassae and Drosophila melanogasterorthologues. The Hml gene codes for hemolectin, which has an orthologue in humans known as the vWB factor. The CG3795 gene has orthologs in multiple species, including Drosophila melanogaster and Drosophila bipectinata, and was recently reported to be involved in proteolysis and serine‐type endopeptidase activity. CG8757, which is predicted to have dehydrogenase activity in D. melanogaster, exhibited synteny with the orthologous gene on the 3L chromosome in Drosophila melanogaster. However, the order of these in D. melanogaster was determined to be different than those annotated in D. ananassae, suggesting a genome rearrangement has occurred in this region. Interestingly, homology with another gene, CG9150, was observed as well. Synteny analysis indicated this gene is located on the X‐chromosome in D. melanogaster, and further analysis suggests a genome rearrangement in this region as well. This annotation has provided some insight to potential genome rearrangements that have occurred in the evolutionary history of these species. Further analysis will provide a greater understanding of how Drosophila genomes have changed over time.