Data for: Ancient gene linkages support ctenophores as sister to other animals

A central question in evolutionary biology is whether sponges or ctenophores (comb jellies) are the sister group to all other animals. These alternative phylogenetic hypotheses imply different scenarios for the evolution of complex neural systems and other animal-specific traits1–6. Conventional phylogenetic approaches based on morphological characters and increasingly extensive gene sequence collections have not been able to definitively answer this question7–11. Here we develop chromosome-scale gene linkage, also known as synteny, as a novel phylogenetic character for resolving this question12. We report new chromosome-scale genomes for a ctenophore and two marine sponges, and for three unicellular relatives of animals (a choanoflagellate, a filasterean amoeba, and an ichthyosporean) that serve as outgroups for phylogenetic analysis. Remarkably, we find ancient syntenies that are conserved between animals and their close unicellular relatives. Ctenophores and unicellular eukaryotes sh..., This dataset is a collection of de novo-assembled and already-published genomes, and supplementary analyses/results complementing the main and supplementary figures of this manuscript., The software necessary to perform these analyses, odp, is included in the linked Zenodo release. No proprietary software is required to open any of these files.