Chromosome evolution and rapid Y chromosome degeneration

染色体进化和 Y 染色体快速退化

• 批准号: 10713635
• 负责人: Ryan Bracewell
• 金额: $ 38.83万
• 依托单位: TRUSTEES OF INDIANA UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-08-01 至 2028-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10713635
• 关键词: Behavior; Bioinformatics; Biological Models; Centromere; Chromosome Arm; Chromosome Structures; Chromosomes; Coupled; DNA Sequence; DNA Transposable Elements; Drosophila genus; Evolution; Gene Expression; Gene Expression Regulation; Gene Order; Gene Structure; Genes; Genetic; Genetic Variation; Genome; Genomics; Karyotype; Karyotype determination procedure; Life; Link; Maintenance; Modeling; Order Coleoptera; Pattern; Population; Positioning Attribute; Process; Research; Role; Satellite DNA; Sex Chromosomes; Shapes; Structure; System; Time; Trees; Variant; Y Chromosome; comparative; genetic information; genome sequencing; genome-wide; reproductive; segregation; sex determination; transmission process; whole genome

PROJECT SUMMARY Chromosomes are a fundamental structure necessary for the faithful transmission of genetic information. At the center of chromosome formation and segregation are centromeres, whose underlying DNA sequence often make up a surprisingly large portion of a genome. Often composed of repetitive satellite sequences, they are found to evolve and change quickly across species, likely due to selfish behavior. Along with centromeric changes in sequence and position, one of the most dramatic genomic changes that can occur is when a chromosome becomes involved in sex determination. Over time, sex chromosomes typically diverge dramatically in gene content, gene expression, transposable element content, and levels of genetic variation. These types of chromosomal changes can be the root of a surprising amount of variation, and we still have a poor understanding of how and why these changes occur. The proposed research is a comprehensive examination of chromosome evolution and genome structure in Drosophila, one of the most powerful and heavily studied systems in genetics. Using chromosome-scale genome assemblies coupled with genomics and bioinformatics-based approaches, this research will identify rapidly evolving centromeric satellite sequences across the group to better understand the tempo of satellite turnover and potential role in karyotypic changes. Additionally, comparative analyses will for the first time systematically identify genus-wide chromosome evolution and constraints on gene order and organization. The unique features of Drosophila – numerous species, small genomes, few chromosomes, ease of karyotyping – make a large-scale comparative analysis tracking the fates of centromeric satellite sequence and chromosome arms possible. The proposed research will also investigate a system with very young sex chromosomes where multiple Y types that vary in their gene content are likely responsible for the evolution of reproductive incompatibilities between populations. The proposed research will use a combination of whole genome sequencing and assembly of multiple divergent Y chromosomes, functional characterization of the diverging X and Y, and population genomic analyses, to link Y degeneration with restricted gene flow in natural populations. Together, these projects will take advantage of the unique attributes of two systems to understand the processes that lead to major changes in karyotype, and variation in degeneration and gene regulation of young sex chromosomes. More broadly, this research will provide a deeper understanding of the maintenance of, and variation in, chromosome structure and function that we see across the tree of life.

项目概要 染色体是遗传忠实传递所必需的基本结构 染色体形成和分离的中心是着丝粒。 潜在的 DNA 序列通常构成基因组的很大一部分。 由重复的卫星序列组成，它们被发现在各个领域快速发展和变化 物种，可能是由于自私行为以及着丝粒序列和位置的变化， 可能发生的最显着的基因组变化之一是染色体变成 随着时间的推移，性染色体的基因通常会发生巨大的分化。 含量、基因表达、转座元件含量和遗传变异水平。 染色体变化的类型可能是数量惊人的变异的根源，而且我们仍然 对这些变化如何以及为何发生的了解甚少。 果蝇染色体进化和基因组结构的综合检查，之一 使用染色体规模基因组的最强大且经过深入研究的系统。 组装与基因组学和基于生物信息学的方法相结合，这项研究将 识别整个群体中快速进化的着丝粒卫星序列，以更好地理解 卫星周转的速度以及在核型变化中的潜在作用。 分析将首次系统地识别属范围的染色体进化和 果蝇的基因顺序和组织的独特特征——众多。 物种少，基因组小，染色体少，易于核型分析——大规模生产 跟踪着丝粒卫星序列和染色体臂命运的比较分析 拟议的研究还将研究具有非常年轻的性染色体的系统。 其中基因含量不同的多种 Y 类型可能是导致进化的原因 拟议的研究将使用人口之间的生殖不相容性。 全基因组测序和多个不同 Y 染色体的组装相结合， 潜水 X 和 Y 的功能表征以及群体基因组分析，以将 Y 联系起来 这些项目将共同解决自然种群中基因流动受限的退化问题。 利用两个系统的独特属性来了解导致重大事件的过程 年轻性别核型的变化、退化和基因调控的变化 更广泛地说，这项研究将提供对染色体的更深入的了解。 我们在树上看到的染色体结构和功能的维持和变化 的生活。