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Pie chart of the Annotation Errors for the Pathways Project Reconciliation Statistics during Summer 2021 Synteny 61.6% Splice site boundaries 4.8% Extra/missing exon(s) 2.1% Mislabeled/missing 6.8% Gene model missing 1.4% Off By 1 2.7% Submission error 19.9%

2021 Pathways GEP Summer Research Fellows

  • October 11, 2021
During Summer 2021, nine Summer Fellows from The University of Alabama and Oklahoma Christian University reconciled coding region annotation projects from the Pathways Project. The Summer Fellows—James O’Brien, Ryan Dufur, Aidan Long, Cole A. Kiser, Ashley Morgan, Alyssa Koehler, Annie Backlund, Jhilam Dasgupta, and Rachael Cowan—were mentored by Dr. Laura K. Reed with support from Chinmay P. Rele both of which are at The University of Alabama.

Collectively, the Summer Fellows reconciled 102 gene models. Approximately 10% of the submitted gene models were in congruence with the final gene models. The most common annotation error in the submitted gene models was improperly assigning synteny (62%). The image above illustrates the preliminary reconciliation statistics for the types of annotation errors for the Pathways Project in Summer 2021.

Reconcilers primarily focused on a single gene each, so that they could perform deeper analysis on the evolution of that gene within our selected clade. Presentations summarizing each of their work are publicly available on Box.

The Summer Fellows also generated microPublication documents. Multiple models of four genes (Tor, Ilp3, raptor, and Dsor1) will be sent to microPublication for review by the end of September 2021. Five of the reconcilers will continue to work with the Pathways Project team to reconcile gene models and send them for publication.

GEP Student Wins 1st Place at Research Conference

  • May 13, 2021May 11, 2021

The University of Alabama’s 14th annual Undergraduate Research and Creative Activity Conference (URCA) was held on March 31, 2021. 

Six GEP students (mentored by Dr. Laura Reed) presented at URCA 2021 one of which, Samantha Hoffman, won 1st place in her division. 

click to enlarge

Analyzing the evolutionary rate of wrd in connection to its position in the insulin signaling pathway

Abstract: The insulin signaling pathway is a metabolic pathway involved in glucose regulation and has been linked to cell growth, fat and protein metabolism, and disease. Insulin and its pathways can lead to Type II Diabetes, Cardiovascular Disease, and cancers in humans, which are some of the most common and fatal diseases in the United States. Since this pathway is well conserved across phyla, we are using Drosophila melanogaster to analyze the rate of evolution in the gene wrd, a negative regulator of the insulin receptor and TORC1 signaling pathways. The goal of this study is to use gene annotation to compare wrd across six different species of Drosophila and analyze the evolutionary differences and conservation patterns of this negative regulator.

New microPublication Alert

GEP’s Prototype microPublication is Published

  • February 19, 2021November 15, 2021

GEP’s first/prototype microPublication has been published! Now that we have made it all the way through the process with the first one we will be moving quickly to submit the additional manuscripts that are ready to go.

Rele, CP; Williams, J; Reed, LK; Youngblom, JJ; Leung, W (2021). Drosophila grimshawi – Rheb. microPublication Biology. 10.17912/micropub.biology.000371.

GEP Annotation Protocol
Preprint

  • December 15, 2020August 19, 2021

We’re excited to announce this preprint as it moves us one step closer to rolling out microPublications for the Pathways Project!

Abstract: Annotating the genomes of multiple organisms allows us to study their genes as well as the evolution of those 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; thegep.org) has developed an annotation protocol for protein-coding genes that enables undergraduate students and other 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 28 Drosophila species, using D. melanogaster as the informant genome. Students construct gene models using multiple lines of computational and experimental evidence including expression data (e.g., RNA-Seq), sequence similarity (e.g., BLAST, multiple sequence alignments), and computational gene predictions. For quality control, each gene is 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. This annotation protocol can be adapted to other scientific questions (e.g., expansion of the Drosophila Muller F element) and other 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.

Final gene model for Akt1 in D. arizonae, along with the submitted student models, and RNA-Seq data aligning to the region. The final model shows that despite there being only a single isoform prediction for a protein coding gene by RefSeq, there are likely two protein coding isoforms for this gene, which were annotated using multiple lines of evidence. The second isoform has a larger coding region in the reconciled gene model that is missed by the RefSeq genome predictor.

Rele CP, Sandlin KM, Leung W, Reed LK. Manual Annotation of Genes within Drosophila Species: the Genomics Education Partnership protocol. bioRxiv 2020.12.10.420521; doi: https://doi.org/10.1101/2020.12.10.420521.

Beta Version of Pathways Project Walkthrough is Live

  • January 28, 2020February 19, 2021

We are very excited to release the beta version of the newest piece of GEP curriculum, the Drosophila Pathways Project: Annotation Walkthrough! Katie has been working really hard to bring this into being. We appreciate the indispensable help from the GEP members who shared with us their own curriculum and personal observations and piloted our earlier drafts. In particular, we would like to acknowledge the contributions by Andy Arsham, Indi Bose, John Braverman, Amy Hark, Shan Hays, Jennifer Kennell, Lindsey Long, Juan Carlos Martinez-Cruzado, Mollie Manier, Chinmay Rele, Joyce Stamm, Jeff Thompson, Jacqueline Wittke-Thompson, and Jim Youngblom (and others we apologize if we missed). An extra special thanks goes out to Alexa Sawa and her students who gave extensive feedback on the penultimate version of this curriculum by using it in Alexa’s January term research course. Also, as always, Wilson was of critical help in shaping the walkthrough and its contents, and in the development of the supporting tools.

This walkthrough illustrates how to apply the GEP annotation strategy for the Pathways Project to construct a gene model for the Ras homolog enriched in brain (Rheb) gene in Drosophila yakuba.

Visit the Drosophila Pathways Project page for more information.