Ancestral sequence reconstruction is a fundamental aspect of molecular evolution studies and can trace small-scale sequence modifications through the evolution of genomes and species. In contrast, fine-grained reconstructions of ancestral genome organizations are still in their infancy, limiting our ability to draw comprehensive views of genome and karyotype evolution. Here we reconstruct the detailed gene contents and organizations of 624 ancestral vertebrate, plant, fungi, metazoan and protist genomes, 183 of which are near-complete chromosomal gene order reconstructions. Reconstructed ancestral genomes are similar to their descendants in terms of gene content as expected and agree precisely with reference cytogenetic and in silico reconstructions when available. By comparing successive ancestral genomes along the phylogenetic tree, we estimate the intra- and interchromosomal rearrangement history of all major vertebrate clades at high resolution. This freely available resource introduces the possibility to follow evolutionary processes at genomic scales in chronological order, across multiple clades and without relying on a single extant species as reference.

祖先序列重建是分子进化研究的一个基本方面，可以通过基因组和物种的进化追踪小规模的序列修改。相比之下，祖先基因组组织的细粒度重建仍处于起步阶段，限制了我们全面了解基因组和核型进化的能力。在这里，我们重建了 624 个祖先脊椎动物、植物、真菌、后生动物和原生生物基因组的详细基因内容和组织，其中 183 个是接近完整的染色体基因顺序重建。正如预期的那样，重建的祖先基因组在基因含量方面与其后代相似，并且与参考细胞遗传学和可用的计算机重建完全一致。通过比较沿系统发育树的连续祖先基因组，我们以高分辨率估计所有主要脊椎动物进化枝的染色体内和染色体间重排历史。这种免费提供的资源引入了按时间顺序在基因组尺度上跟踪进化过程的可能性，跨越多个进化枝，而不依赖于单一现存物种作为参考。