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

智力优势：基因组尺度的同质性，评估物种之间的相对基因顺序和保守性，可以提供对染色体进化动力学的关键见解，可以帮助阐明遗传变异和突变的模式，并且可以用于识别潜在的调控基序。本项目的总体目标是在多个硬骨鱼基因组之间建立免疫球蛋白（Ig）位点的合成关系。由于Ig片段似乎在脊椎动物进化史的早期就出现了，可以想象，在无颌鱼类（Agnatha）和有颌动物（Gnathostomata）之间的过渡期间，硬骨鱼在脊椎动物系统发育中占据了一个关键的分支点，可以理解适应性免疫系统的出现。该项目的具体目标是：1)利用计算方法识别和辨别三种鱼类基因组之间的相对基因顺序和Ig位点的保守性；2)通过对比分析从BAC文库中导出和生成的DNA序列，改进基因预测和最终基因注释；3)探索硬骨鱼Ig基因座与其他脊椎动物的基因组同源性。更广泛的影响：这项工作将有助于确定硬骨鱼免疫球蛋白基因座的基本基因组结构。鱼类是生物学研究中重要的模型系统，了解基因组背景下Ig基因座的多样性和可变性为基因调控的功能研究提供了框架。查尔斯顿学院是一所公立文科院校，在学生参与科学研究方面有着悠久的历史。该项目将为一些对生物信息学、基因组学或分子生物学感兴趣的学生提供研究机会，作为潜在的职业道路，并将为K-12级别的科学社区推广创造机会。

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.