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 染色体是遗传信息可靠传递所必需的基本结构 信息.在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中令人惊讶的大部分。经常 由重复的卫星序列组成，它们被发现在不同的环境中快速进化和变化。 物种，可能是由于自私的行为。沿着着丝粒序列和位置的变化， 当一个染色体变成一个 与性别决定有关随着时间的推移，性染色体在基因组中通常会发生显著的分化。 内容、基因表达、转座因子内容和遗传变异水平。这些 染色体变化的类型可能是数量惊人的变异的根源，我们仍然 对这些变化是如何以及为什么发生的理解不足。拟议的研究是一个 对果蝇染色体进化和基因组结构的全面研究， 遗传学中最强大和最深入研究的系统。利用染色体规模的基因组 结合基因组学和生物信息学方法，这项研究将 鉴定快速进化的着丝粒卫星序列，以更好地了解 卫星周转的克里思和在核型变化中的潜在作用。此外，比较 分析将首次系统地确定全属范围的染色体进化， 对基因顺序和组织的限制。果蝇的独特之处-众多 物种，小基因组，染色体少，核型分析容易-使大规模 跟踪着丝粒卫星序列和染色体臂命运的比较分析 可能这项拟议中的研究还将调查一个具有非常年轻的性染色体的系统 其中基因含量不同的多个Y类型可能是进化的原因， 种群间的生殖不相容性。该研究将使用一个 全基因组测序和多个不同Y染色体的组装的组合， 功能特性的分歧X和Y，和人口基因组分析，以连接Y 自然种群中基因流动受限的退化。这些项目将共同 两个系统的独特属性的优势，以了解导致重大 染色体核型的变化，以及年轻性别的退化和基因调控的变化 染色体更广泛地说，这项研究将提供更深入的了解 染色体结构和功能的维持和变异 生命