Presentation Title

Annotation of Contig47 from the Dot Chromososme of Drosophila ficusphila

Format of Presentation

Poster to be presented Friday March 31, 2017

Abstract

Gene annotation of an organism can provide a wealth of information for future study and an understanding of species evolution. Annotation primarily uncovers the identity and/or presence of genes in a given area of the genome. The specific region investigated in this study was contig 47 in chromosome 3L of Drosophila ficusphila. Using comparative genomics and various bioinformatics tools accessible through the Genomics Education Partnership, including the GEP genome browser, small exon finder, gene record finder, and gene model checker, the entire contig of 33,000 bp was annotated for all possible protein coding genes. By using D. melanogaster as the reference genome it was possible to find the intron splice acceptor and donor regions, which helped to determine the exon boundaries of a gene along with other evidence. Six genes and twenty-two isoforms were determined in this region with all passing the gene model checker. Furthermore, all but three of the isoforms, M6-PE, M6-PF, and M6-PF had an amino acid sequence similarity of at least 80% to D. melanogaster. M6-PE and M6-PF both share the same initial protein coding exon, which was found to be dramatically shortened causing a significant shift in the dot plot. Likewise, the terminal exon in M6-PG was found to be lacking a stop codon at the predicted site, also causing a large shift in the dot plot. Transcription start sites were also investigated in D. ficusphila, but the exact coordinates could not be determined.

Department

Biological Sciences

Faculty Advisor

James E. J. Bedard

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Annotation of Contig47 from the Dot Chromososme of Drosophila ficusphila

Gene annotation of an organism can provide a wealth of information for future study and an understanding of species evolution. Annotation primarily uncovers the identity and/or presence of genes in a given area of the genome. The specific region investigated in this study was contig 47 in chromosome 3L of Drosophila ficusphila. Using comparative genomics and various bioinformatics tools accessible through the Genomics Education Partnership, including the GEP genome browser, small exon finder, gene record finder, and gene model checker, the entire contig of 33,000 bp was annotated for all possible protein coding genes. By using D. melanogaster as the reference genome it was possible to find the intron splice acceptor and donor regions, which helped to determine the exon boundaries of a gene along with other evidence. Six genes and twenty-two isoforms were determined in this region with all passing the gene model checker. Furthermore, all but three of the isoforms, M6-PE, M6-PF, and M6-PF had an amino acid sequence similarity of at least 80% to D. melanogaster. M6-PE and M6-PF both share the same initial protein coding exon, which was found to be dramatically shortened causing a significant shift in the dot plot. Likewise, the terminal exon in M6-PG was found to be lacking a stop codon at the predicted site, also causing a large shift in the dot plot. Transcription start sites were also investigated in D. ficusphila, but the exact coordinates could not be determined.