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.

项目摘要 染色体是忠实传播通用的基本结构 信息。在染色体形成和隔离的中心是Centromeres，谁 基础DNA序列通常构成基因组的大部分。经常 由重复的卫星序列组成，发现它们会迅速发展和变化 物种，可能是由于自私的行为。以及序列和位置的丝粒变化， 可能发生的最戏剧性的基因组变化之一是染色体变成 参与性别决定。随着时间的流逝，性别染色体通常在基因中显着差异 含量，基因表达，可转座元素含量和遗传变异水平。这些 染色体变化的类型可能是令人惊讶的变化的根源，我们仍然 对这些变化的发生方式和为什么的了解不足。拟议的研究是 果蝇中染色体进化和基因组结构的全面检查，一个 遗传学中最强大，最重的系统。使用染色体规模的基因组 组合以及基因组学和基于生物信息学方法的方法，这项研究将 确定整个组的快速发展的中心颗粒卫星序列，以更好地理解 卫星周转率的节奏和核型变化中的潜在作用。另外，比较 分析将首次系统地确定整个属染色体的演化和 基因顺序和组织的限制。果蝇的独特功能 - 许多 物种，小基因组，很少的染色体，易于核分型 - 大规模做 比较分析跟踪着丝粒卫星序列和染色体臂的命运 可能的。拟议的研究还将调查一个非常年轻的性染色体的系统 其中多种y类型的基因含量可能导致 人群之间的生殖不相容。拟议的研究将使用 多个发散Y染色体的整个基因组测序和组装的组合， 分歧X和Y以及种群基因组分析的功能表征，以链接Y 自然种群中基因流量受限的变性。这些项目将在一起 两个系统的独特属性的优势，以了解导致主要的过程 核型的变化以及年轻性别的变性和基因调节的变化 染色体。从更广泛的角度来看，这项研究将为您提供更深入的了解 我们在树上看到的染色体结构和功能的维护和变化 生活。