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

智力价值：基因组规模同步性，即对物种之间相对基因顺序和保守性的评估，可以提供对染色体进化动态的关键见解，可以帮助阐明遗传变异和突变的模式，并有助于识别潜在的调控基序。这个项目的总体目标是在多个硬骨基因组之间建立免疫球蛋白(Ig)基因座的共线关系。由于免疫球蛋白片段似乎出现在脊椎动物进化史的早期，可以想象是在无颌鱼类(无颌目)到有颌目动物(颌目)之间的过渡过程中，硬骨鱼在脊椎动物系统发育中占据了一个关键的分支点，以了解适应性免疫系统的出现。这个项目的具体目标是：1)利用计算方法来识别和识别三种鱼类基因组之间的相对基因顺序和Ig基因座的保守；2)通过使用从BAC文库获得和产生的DNA序列的比较分析来改进基因预测和结果基因注释；以及3)探索硬骨鱼和其他脊椎动物Ig基因座的基因组同源性。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。鱼类是整个生物学研究的重要模式系统，在基因组背景下理解免疫球蛋白基因座的多样性和变异性为基因调控的功能研究提供了一个框架。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。这个项目将为几个对生物信息学、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，并将为社区在K-12级别的科学拓展创造机会。

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.