Genome Annotation and Comparative Genomics: Building Gene Models to Understand the Evolution of Genes, Genetic Pathways, and Genomes
Faculty Sponsor(s)
Catherine Reinke
Subject Area
Biology
Description
The Genomics Education Partnership is a nationwide crowdsourced research effort in which undergraduates use genomic data from multiple species to create gene models for comparative genomics investigations. A gene model is a representation of the coding and non-coding regions of a gene; an annotated genome is comprised of multiple gene models. Gene models are generated using bioinformatics tools to analyze computational and experimental data describing a DNA sequence. Genome annotations are used to determine how genes, genetic pathways, chromosomes, and genomes evolve.
In this project, we use the fully annotated Drosophila melanogaster genome as a reference genome; a large amount of experimental data supports the published gene models from this model organism, facilitating the generation of gene models in related species. Gene prediction algorithms (such as Genscan and Geneid) and BLAST (Basic Local Alignment Search Tool) were used to identify orthologs of D. melanogaster genes located within a contiguous region of genomic sequence from the species Drosophila ananassee. Protein sequences from D. melanogaster were compared to the D. ananassae genomic sequence, and the region of the D. ananassae genome under investigation was determined to encode an ortholog of the D. melanogaster gene MED26. Precise coordinates of each coding exon of the D. ananassee MED26 gene were determined. This work provides the first description of the MED26 transcriptional activator in D. ananassee. Additional genes are being annotated in this region of the D. ananassee genome using the genome annotation strategies described.
The practical relevance of genome annotation and comparative genomics is immediately apparent in the ongoing studies of the SARS-CoV2 viral genome; analyzing genomic changes and describing the evolution of genes and genomes has yielded insights into the spread of Covid-19 across the world. Our annotations are contributing to an analysis of the D. ananassee genome and, more specifically, an analysis of motifs necessary for gene expression.
Recommended Citation
Duey, Kylee; Steward, Lottie; and Reinke, Catherine, "Genome Annotation and Comparative Genomics: Building Gene Models to Understand the Evolution of Genes, Genetic Pathways, and Genomes" (2020). Linfield University Student Symposium: A Celebration of Scholarship and Creative Achievement. Event. Submission 30.
https://digitalcommons.linfield.edu/symposium/2020/all/30
Genome Annotation and Comparative Genomics: Building Gene Models to Understand the Evolution of Genes, Genetic Pathways, and Genomes
The Genomics Education Partnership is a nationwide crowdsourced research effort in which undergraduates use genomic data from multiple species to create gene models for comparative genomics investigations. A gene model is a representation of the coding and non-coding regions of a gene; an annotated genome is comprised of multiple gene models. Gene models are generated using bioinformatics tools to analyze computational and experimental data describing a DNA sequence. Genome annotations are used to determine how genes, genetic pathways, chromosomes, and genomes evolve.
In this project, we use the fully annotated Drosophila melanogaster genome as a reference genome; a large amount of experimental data supports the published gene models from this model organism, facilitating the generation of gene models in related species. Gene prediction algorithms (such as Genscan and Geneid) and BLAST (Basic Local Alignment Search Tool) were used to identify orthologs of D. melanogaster genes located within a contiguous region of genomic sequence from the species Drosophila ananassee. Protein sequences from D. melanogaster were compared to the D. ananassae genomic sequence, and the region of the D. ananassae genome under investigation was determined to encode an ortholog of the D. melanogaster gene MED26. Precise coordinates of each coding exon of the D. ananassee MED26 gene were determined. This work provides the first description of the MED26 transcriptional activator in D. ananassee. Additional genes are being annotated in this region of the D. ananassee genome using the genome annotation strategies described.
The practical relevance of genome annotation and comparative genomics is immediately apparent in the ongoing studies of the SARS-CoV2 viral genome; analyzing genomic changes and describing the evolution of genes and genomes has yielded insights into the spread of Covid-19 across the world. Our annotations are contributing to an analysis of the D. ananassee genome and, more specifically, an analysis of motifs necessary for gene expression.
