Genomic mechanisms of asexual reproduction

项目摘要 真核生物通过有性和重组实现基因多样化的创新提供了重要的 适应性优势。尽管如此，一些动物能够无性繁殖的认识可以追溯到 至少在公元1740年，无性恋已经在整个动物界独立出现了多次。这 过渡通常伴随着修饰的减数分裂和基因组结构。因为减数分裂的缺陷是 与年龄相关的人类生育力下降和基因组不稳定是细胞老化的标志，研究如何 成功的无性血统可以在对这些核心细胞程序进行重大修改的情况下蓬勃发展 为衰老和不孕不育的机制提供新的分子见解。 为了描述无性繁殖的基因组特征，我们之前对基因组和 Pachys线虫的转录组，一种来自异常持久的无性世系的线虫，估计 起源于1800万年前。这项工作表明，玉米草缺乏关键的减数分裂基因，第一个 减数分裂，不需要受精就能在卵母细胞中重建二倍体基因组。 令人惊讶的是，它的核基因组正好包装成一对染色体，我们展示了它们的来源 来自所有祖先染色体的完全融合。然而，基因组组装仍然包含许多空白 这限制了我们回答有关D。pachys进化的关键问题的能力：如何以及何时基因组融合和 如何在没有基因重组的情况下保持高水平的序列多样性， 以及是哪些分子变化推动了向无性繁殖的转变，这仍然是一个谜。 我们建议使用长阅读测序和比较基因组学的力量来解决这些问题。 在目标1中，我们将生成一个高度连续的、染色体水平的粗毛虫基因组组装。这将是 揭示祖先染色体融合的模式，主要的基因组重排是否可能排除 减数分裂交叉，以及染色体融合部位和端粒的性质。在目标2中，我们将生产 另外四个单性生殖基因及其已知性近亲的染色体水平基因组组合 在相同的系统发育分支中。这将允许对基因组结构进行比较分析，并使 与无性生殖相关的分子遗传变化的进化重建。在《目标3》中，我们将 分析所有五个物种中染色质的可及性以及调控序列和编码区的变化 揭示基因和/或表观遗传机制是否导致两种基因表达水平的差异 等位基因，如在D。pachys中看到的，这可能使这些动物能够克服潜在的高负荷 有害的等位基因。总之，这项研究为探索无性恋者的进化提供了一个独特的机会 动物繁殖，生物学上一个数百年的谜团，其分子基础可能提供新的 对人类衰老潜在的分子过程的洞察。

Project Summary The eukaryotic innovation of genetic diversification through sex and recombination provides significant adaptive advantages. Still, the recognition that some animals are capable of asexual reproduction dates back to at least 1740 CE, and asexuality has arisen independently multiple times across the animal kingdom. This transition is often accompanied by modified meiosis and genome organization. Since meiotic defects underlie age-related decline in human fertility, and genomic instability is a hallmark of aging cells, studying how successful asexual lineages can thrive in light of major modifications to these core cellular programs can provide new molecular insights into the mechanisms of aging and infertility. To characterize genomic signatures of asexual reproduction, we previously sequenced the genome and transcriptome of Diploscapter pachys, a nematode from an unusually persistent asexual lineage estimated to have originated 18 million years ago. This work showed that D. pachys lacks key meiotic genes and the first (reductional) meiotic division, enabling reconstitution of a diploid genome in the oocyte without fertilization. Strikingly, its nuclear genome is packaged into exactly one pair of chromosomes, which we showed derives from the full fusion of all ancestral chromosomes. However, the genome assembly still contains many gaps that limit our ability to answer key questions about D. pachys evolution: how and when genome fusions and abridged meiosis arose, how a high level of sequence diversity is maintained without genetic recombination, and which molecular changes drove the transition to asexual reproduction remain a mystery. We propose to use the power of long-read sequencing and comparative genomics to address these questions. In Aim 1, we will generate a highly contiguous, chromosome-level genome assembly for D. pachys. This will reveal the pattern of ancestral chromosome fusions, whether major genome rearrangements likely preclude meiotic crossovers, and the nature of chromosome fusion sites and telomeres. In Aim 2, we will produce chromosome-level genome assemblies of four additional parthenogens and their closest known sexual relative in the same phylogenetic clade. This will allow a comparative analyses of genome architecture and enable evolutionary reconstruction of molecular genetic changes linked to asexual reproduction. In Aim 3, we will analyze chromatin accessibility and changes in regulatory sequences and coding regions in all five species to uncover whether genetic and/or epigenetic mechanisms underlie differences in expression levels between alleles, as seen in D. pachys, which may enable these animals to overcome potentially high loads of deleterious alleles. In summary, this study presents a unique opportunity to explore the evolution of asexual reproduction in animals, a centuries-old mystery in biology, whose molecular underpinning may provide new insights into molecular processes underlying aging in humans.