RUI: Targeted Annotation and Exploration of Synteny of Immunoglobulin Loci in Teleosts using RSS Motifs

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Intellectual Merit:Genome scale synteny, the assessment of the relative gene order and conservation between species, can provide key insights into evolutionary dynamics of chromosomes, can help elucidate patterns of genetic variability and mutation, and can be useful for identifying potential regulatory motifs. The overall goal of this project is to establish syntenic relationships of immunoglobulin (Ig) loci between multiple teleost genomes. Since Ig segments appear to have emerged early during the evolutionary history of vertebrates, conceivably during the transition between jawless fishes (Agnatha) and jawed animals (Gnathostomata), teleosts occupy a critical branch point in vertebrate phylogeny for understanding the emergence of the adaptive immune system. The specific objectives of this project are to: 1) utilize computational approaches to identify and discern relative gene orders and conservation of Ig loci between three fish genomes; 2) improve gene predictions and resultant gene annotations by comparative analyses using DNA sequences derived and generated from BAC libraries; and 3) explore genomic synteny of Ig loci in teleosts with other vertebrates. Broader impacts:This work will help define the fundamental genomic architecture underlying immunoglobulin loci in teleosts. Fishes are important model systems across the spectrum of biological research, understanding diversity and variability of Ig loci in a genomic context provides a framework for functional studies of gene regulation. The College of Charleston is a public liberal arts institution with a strong history of student engagement in scientific research. This project will provide research opportunities for several students interested in pursuing bioinformatics, genomics, or molecular biology as a potential career path and will create opportunities for community outreach in science at the K-12 level.