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The Genomics Education Partnership (GEP; https://thegep.org) began as a consortium of 16 faculty in 2006 with a goal of providing students with Course-based Undergraduate Research Experiences (CUREs) in genomics. Today, GEP has over 200 faculty from more than 180 institutions and engages more than 3,900 undergraduates in authentic genomics research annually. These faculty joined and continued to participate in the GEP for many reasons, including the collaborative nature of the research, the well-established infrastructure, and the supportive network of like-minded colleagues. Faculty implement GEP materials in diverse settings ? ranging from short modules (2-8 weeks) within a course, to a standalone full-semester course, to independent student research. GEP students show significant gains in scientific knowledge and attitudes toward science. In addition to improving their understanding of the research process and how new knowledge is created in the field, GEP students acquire desirable and transferable skills essential for future participation in the workforce, such as problem solving, independence, application of knowledge, team-work, and collaboration. Students also gain competence in the use of computational algorithms to analyze large biological datasets ? thereby preparing students for a growing need of a workforce trained at applying statistics and computational tools to analyze large datasets. In addition, GEP students and their faculty mentors are eligible to be co-authors on the scientific publications that are based on their work. In this workshop, we will provide an overview of the GEP community, a hands-on guided tour of our introductory curriculum aimed to teach gene structure, transcription, translation, and processing, and a step-by-step walkthrough that illustrates the protocol for annotating a protein-coding gene in Drosophila. Participants will receive information on how to join the GEP community and receive training and resources to enable their implementations.
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Manual annotation of Drosophila genes: a Genomics Education Partnership protocol
Annotating the genomes of multiple species allows us to analyze the evolution of their genes. While many eukaryotic genome assemblies already include computational gene predictions, these predictions can benefit from review and refinement through manual gene annotation. The Genomics Education Partnership (GEP; https://thegep.org/ ) developed a structural annotation protocol for protein-coding genes that enables undergraduate student and faculty researchers to create high-quality gene annotations that can be utilized in subsequent scientific investigations. For example, this protocol has been utilized by the GEP faculty to engage undergraduate students in the comparative annotation of genes involved in the insulin signaling pathway in 27 Drosophila species, using D. melanogaster as the reference genome. Students construct gene models using multiple lines of computational and empirical evidence including expression data (e.g., RNA-Seq), sequence similarity (e.g., BLAST and multiple sequence alignment), and computational gene predictions. Quality control measures require each gene be annotated by at least two students working independently, followed by reconciliation of the submitted gene models by a more experienced student. This article provides an overview of the annotation protocol and describes how discrepancies in student submitted gene models are resolved to produce a final, high-quality gene set suitable for subsequent analyses. The protocol can be adapted to other scientific questions (e.g., expansion of the Drosophila Muller F element) and species (e.g., parasitoid wasps) to provide additional opportunities for undergraduate students to participate in genomics research. These student annotation efforts can substantially improve the quality of gene annotations in publicly available genomic databases.
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- Award ID(s):
- 1915544
- PAR ID:
- 10464162
- Date Published:
- Journal Name:
- F1000Research
- Volume:
- 11
- ISSN:
- 2046-1402
- Page Range / eLocation ID:
- 1579
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.12688/f1000research.126839.2
