Department of Biology, University of Oxford, Oxford OX1 3RB, UK; cE3c, Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculty of Sciences, University of Lisbon, Lisbon 1749-016, Portugal; Department of Animal Biology, Faculty of Sciences, University of Lisbon, Lisbon 1749-016, Portugal.
School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
Curr Biol. 2024 Oct 7;34(19):4412-4423.e5. doi: 10.1016/j.cub.2024.08.009. Epub 2024 Sep 10.
Oxford ragwort (Senecio squalidus) is one of only two homoploid hybrid species known to have originated very recently, so it is a unique model for determining genomic changes and stabilization following homoploid hybrid speciation. Here, we provide a chromosome-level genome assembly of S. squalidus with 95% of the assembly contained in the 10 longest scaffolds, corresponding to its haploid chromosome number. We annotated 30,249 protein-coding genes and estimated that ∼62% of the genome consists of repetitive elements. We then characterized genome-wide patterns of linkage disequilibrium, polymorphism, and divergence in S. squalidus and its two parental species, finding that (1) linkage disequilibrium is highly heterogeneous, with a region on chromosome 4 showing increased values across all three species but especially in S. squalidus; (2) regions harboring genetic incompatibilities between the two parental species tend to be large, show reduced recombination, and have lower polymorphism in S. squalidus; (3) the two parental species have an unequal contribution (70:30) to the genome of S. squalidus, with long blocks of parent-specific ancestry supporting a very rapid stabilization of the hybrid lineage after hybrid formation; and (4) genomic regions with major parent ancestry exhibit an overrepresentation of loci with evidence for divergent selection occurring between the two parental species on Mount Etna. Our results show that both genetic incompatibilities and natural selection play a role in determining genome-wide reorganization following hybrid speciation and that patterns associated with homoploid hybrid speciation-typically seen in much older systems-can evolve very quickly following hybridization.
牛津千里光（Senecio squalidus）是仅有的两种同源多倍体杂种物种之一，其起源非常近，因此它是一个独特的模型，可以确定同源多倍体杂种形成后基因组的变化和稳定。在这里，我们提供了 S. squalidus 的染色体水平基因组组装，其中 95%的组装包含在 10 个最长的支架中，对应于其单倍体染色体数。我们注释了 30,249 个蛋白质编码基因，并估计约 62%的基因组由重复元件组成。然后，我们在 S. squalidus 及其两个亲本物种中表征了全基因组连锁不平衡、多态性和分化的模式，发现：（1）连锁不平衡高度异质，第 4 号染色体上的一个区域在所有三个物种中都表现出增加的值，但在 S. squalidus 中尤其明显；（2）在两个亲本物种之间存在遗传不相容性的区域往往较大，重组减少，S. squalidus 中的多态性较低；（3）两个亲本物种对 S. squalidus 基因组的贡献不均等（70:30），长的亲本特异性起源块支持杂种形成后杂种谱系的快速稳定；（4）具有主要亲本遗传背景的基因组区域表现出较高的代表性，表明在埃特纳火山上两个亲本物种之间存在分歧选择的位点。我们的研究结果表明，遗传不相容性和自然选择都在决定同源多倍体杂种形成后全基因组的重排中起作用，并且与同源多倍体杂种形成相关的模式-通常在更古老的系统中看到-可以在杂交后非常迅速地进化。
