The Puerto Rican Parrot Project of the Genomics Education Partnership (GEP; thegep.org) is a conservation-based bioinformatics Classroom Undergraduate Research Experience (CURE). The Puerto Rican Parrot (Amazona vittata), the only parrot native to a U.S. jurisdiction, has been listed as critically endangered since 1967; by 1975, only 13 individuals remained. Conservation efforts have been hampered by a weak egg-shell phenotype, likely due to the increase or fixation of deleterious alleles during the population bottleneck. This project trains students in bioinformatics while they perform comparative gene annotations and search for candidate mutations in the coding sequences of ~1,512 genes expressed in the uterus. Students use a standard set of practices to construct gene models that satisfy basic biological constraints; start/stop codons and compatible splice donor and acceptor sites to maintain the open reading frame. In order to construct these gene models, students learn how to interpret multiple lines of experimental
(RNA-Seq data) and computational (transcript and protein sequence alignments against chicken and other avian species, gene predictions) evidence that are potentially contradictory. To ensure gene models are high quality, each gene is annotated by at least two students working independently at different institutions, before being reconciled by a third individual. Students identify potentially deleterious mutations using SIFT and Polyphen-2. The phenotypic effect of these mutations might be tested in vivo using CRISPR editing in chicken embryos. The expansion of this CURE from a single course (University of Puerto Rico at Mayagu??ez), to a second course (Saint Mary???s College), to current beta-testing with a larger group of GEP members in preparation for release to a wider public audience, has identified implementation challenges. I am particularly interested in connecting with others who are interested in expanding access to CUREs/CUR-like experiences to students in introductory-level and non-science major courses.
Keywords: CURE, Genomics, Bioinformatics, Conservation, Puerto Rican Parrot, Cross-Institutional
University of Manitoba (2025)
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