Chromosome evolution and rapid Y chromosome degeneration

项目总结 染色体是基因忠实传递所必需的基本结构 信息。染色体形成和分离的中心是着丝粒，其 潜在的DNA序列通常占基因组的一大部分，令人惊讶。经常 它们由重复的卫星序列组成，被发现在 物种，很可能是由于自私的行为。随着着丝粒在序列和位置上的变化， 最戏剧性的基因组变化之一就是当一条染色体变成 参与性别决定。随着时间的推移，性染色体在基因上通常会发生显著的分化 含量、基因表达、转座元件含量和遗传变异水平。这些 各种类型的染色体变化可能是数量惊人的变异的根源，我们仍然 对这些变化是如何发生的以及为什么会发生的理解很差。拟议的研究是一项 果蝇染色体进化和基因组结构的综合研究 是遗传学中最强大和最深入研究的系统之一。使用染色体规模的基因组 结合基因组学和生物信息学的方法，这项研究将 识别集团内快速进化的着丝粒卫星序列，以更好地了解 卫星周转的速度和在核型变化中的潜在作用。此外，比较 分析将首次系统地识别全属范围的染色体进化和 对基因顺序和组织的限制。果蝇的独特特征--数量众多 物种、小基因组、少染色体、易于核型分析--使大规模 着丝粒卫星序列和染色体臂命运追踪的比较分析 有可能。这项拟议的研究还将调查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类型可能是导致 种群间的生殖不亲和性。拟议的研究将使用一种 全基因组测序与多条发散Y染色体组装相结合， 分离的X和Y的功能特征，以及与Y连锁的群体基因组分析 自然种群中基因流动受限的退化。这些项目加在一起，将需要 利用两个系统的独特属性来了解导致主要 年轻性别的核型变化、变性变异和基因调控 染色体。更广泛地说，这项研究将提供对 我们在树上看到的染色体结构和功能的维持和变异 生活的一部分。

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.