Discipline: Biological Sciences
Chrysten Brown - Bowie State University
Co-Author(s): Alusine Bangura, Myron Jackson, Venatus Chieze, George Ude, Aditi Das, and George Acquaah, Natural Science Department, Bowie State University Cecille Aninweze, Obih Chosen, Christabel Ene, and James Ogbonna, Godfrey Okoye University, Enugu, Nigeria Michael Okoro, Godfrey Okoye University, Enugu, Nigeria and DNA Learning Center, Cold Spring Harbor, NYC David Igwe, International Institute for Tropical Agriculture, Ibadan, Nigeria Dave Micklos, DNA Learning Center, Cold Spring Harbor, NYC
The increasing population of West African immigrants in the United States is causing a surge in the demand and importation of dried fish from Africa. Moreover, the imported dried fish products sometimes are a mixture of improperly identified fish types which raises concern about food safety and import sustainability. Our project aims to study the indigenous species of fish in South Eastern Nigeria with the goal to identify unique DNA sequence markers or single nucleotide polymorphisms that accurately identify and classify the species. A short 600-700 base-pair DNA fragment from the cytochrome c oxidase I (COI) gene in the mitochondria was amplified by PCR in all 92 fish samples collected from three separate water bodies in Nigeria: Nike Lake, Ugwuomu Lake, and Ezu River. The PCR amplicons were then sent to Genewiz LLC for sequencing, and the resulting sequences were analyzed using the DNA Subway. DNA Subway, is an intuitive interface for genome informatics developed by the iPlant Collaborative. Only thirty-five fish samples (38%) yielded good and reliable sequences. Clustering analysis using the neighbor joining and the maximum likelihood methods showed five distinct clusters in the phylogenetic trees indicating abundant genetic diversity within the South Eastern Nigeria fishes. Catfish cluster (group C) represented by two main species – Clarias gariepinus and Clarias gabonensis were dominant in Enugu State, Nigeria. Groups A, B, D and E clustered around Synodontis obesus, Clarotes laticeps, Hepsetus odoe, and Hemichromis fasciatus, respectively. Group F showed a mixture of different species not identified properly because of poor sequence quality. SNP’s were identified that separated between the various fish groups in the dendrogram. Overall, this project has generated species specific DNA barcodes for the purpose of authenticating and tracking dry fish types imported for consumption in the United States of America.
Funder Acknowledgement(s): Acknowledgements go to the National Science Foundation (NSF) for funding this project as well as Bowie State University Summer Undergraduate Research Institute (SURI) for supporting our trip to Africa. George Ude and Aditi Das (Research Mentors)
Faculty Advisor: George Ude, firstname.lastname@example.org
Role: I participated in sample collection, DNA extraction, DNA amplification, gel electrophoresis, amplicon sequencing, as well as sequence data analysis.