Presentation Title

DNA Annotation of Contig 33 on Drosophila ficusphila 3L Chromosome

Format of Presentation

Poster to be presented Friday March 31, 2017

Abstract

Utilizing comparative genomics is essential in the DNA annotation of Drosophila genomes. As a part of the Genomics Education Partnership (GEP), we have manually annotated 40 000 bp of DNA sequence on contig 33 of the Drosophila ficusphila 3L chromosome. The GEP UCSC Genome Browser was used to provide a visualization of the genomic region with evidence tracks. Putative orthologs compared to D. melanogaster were identified using NCBI blastx. Information of the putative ortholog was obtained from FlyBase and NCBI. Comparative data for gene and isoform structure in D. melanogaster was gathered from Gene Record Finder. Gene Model Checker was used to identify any obvious annotation errors. A final gene model was constructed to compare the annotated genes of D. ficusphila with blastx alignment of D. melanogaster proteins and various gene predictors. Contig 33 was determined to contain seven orthologs with D. melanogaster; SLC22A-PA, DNApol-eta-PA, CG14562-PA, CG14562-PB, CG7458-PA, CS-2-PC, CS-2-PD. The identity between the protein alignments of the orthologs is 91.2%, 80.3%, 91.1%, 91.1%, 87.1%, 91.2%, 91.2%, respectively. Custom gene models were constructed for all annotated genes and isoforms in D. ficusphila.

Department

Biological Sciences

Faculty Advisor

James Bedard

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DNA Annotation of Contig 33 on Drosophila ficusphila 3L Chromosome

Utilizing comparative genomics is essential in the DNA annotation of Drosophila genomes. As a part of the Genomics Education Partnership (GEP), we have manually annotated 40 000 bp of DNA sequence on contig 33 of the Drosophila ficusphila 3L chromosome. The GEP UCSC Genome Browser was used to provide a visualization of the genomic region with evidence tracks. Putative orthologs compared to D. melanogaster were identified using NCBI blastx. Information of the putative ortholog was obtained from FlyBase and NCBI. Comparative data for gene and isoform structure in D. melanogaster was gathered from Gene Record Finder. Gene Model Checker was used to identify any obvious annotation errors. A final gene model was constructed to compare the annotated genes of D. ficusphila with blastx alignment of D. melanogaster proteins and various gene predictors. Contig 33 was determined to contain seven orthologs with D. melanogaster; SLC22A-PA, DNApol-eta-PA, CG14562-PA, CG14562-PB, CG7458-PA, CS-2-PC, CS-2-PD. The identity between the protein alignments of the orthologs is 91.2%, 80.3%, 91.1%, 91.1%, 87.1%, 91.2%, 91.2%, respectively. Custom gene models were constructed for all annotated genes and isoforms in D. ficusphila.