During eukaryotic cell division, the sister chromatids of duplicated chromosomes are pulled apart by microtubules, which connect via kinetochores. The kinetochore is a multiprotein structure that links centromeres to microtubules, and that emits molecular signals in order to safeguard the equal distribution of duplicated chromosomes over daughter cells. Although microtubule‐mediated chromosome segregation is evolutionary conserved, kinetochore compositions seem to have diverged. To systematically inventory kinetochore diversity and to reconstruct its evolution, we determined orthologs of 70 kinetochore proteins in 90 phylogenetically diverse eukaryotes. The resulting ortholog sets imply that the last eukaryotic common ancestor (LECA) possessed a complex kinetochore and highlight that current‐day kinetochores differ substantially. These kinetochores diverged through gene loss, duplication, and, less frequently, invention and displacement. Various kinetochore components co‐evolved with one another, albeit in different manners. These co‐evolutionary patterns improve our understanding of kinetochore function and evolution, which we illustrated with the RZZ complex, TRIP13, the MCC, and some nuclear pore proteins. The extensive diversity of kinetochore compositions in eukaryotes poses numerous questions regarding evolutionary flexibility of essential cellular functions.

Eukaryogenesis is one of the most enigmatic evolutionary transitions, during which simple prokaryotic cells gave rise to complex eukaryotic cells. While evolutionary intermediates are lacking, gene duplications provide information on the order of events by which eukaryotes originated. Here we use a phylogenomics approach to reconstruct successive steps during eukaryogenesis. We found that gene duplications roughly doubled the proto-eukaryotic gene repertoire, with families inherited from the Asgard archaea-related host being duplicated most. By relatively timing events using phylogenetic distances we inferred that duplications in cytoskeletal and membrane trafficking families were among the earliest events, whereas most other families expanded predominantly after mitochondrial endosymbiosis. Altogether, we infer that the host that engulfed the proto-mitochondrion had some eukaryote-like complexity, which drastically increased upon mitochondrial acquisition. This scenario bridges the signs of complexity observed in Asgard archaeal genomes to the proposed role of mitochondria in triggering eukaryogenesis.

Eukaryotic Protein Kinases (ePKs) are essential for eukaryotic cell signalling. Several phylogenetic trees of the ePK repertoire of single eukaryotes have been published, including the human kinome tree. However, a eukaryote-wide kinome tree was missing due to the large number of kinases in eukaryotes. Using a pipeline that overcomes this problem, we present here the first eukaryotic kinome tree. The tree reveals that the Last Eukaryotic Common Ancestor (LECA) possessed at least 92 ePKs, much more than previously thought. The retention of these LECA ePKs in present-day species is highly variable. Fourteen human kinases with unresolved placement in the human kinome tree were found to originate from three known ePK superfamilies. Further analysis of ePK superfamilies shows that they exhibit markedly diverse evolutionary dynamics between the LECA and present-day eukaryotes. The eukaryotic kinome tree thus unveils the evolutionary history of ePKs, but the tree also enables the transfer of functional information between related kinases.perspective, there is one substantial hurdle: the large number of kinases in eukaryotes. Only the human kinome tree consists already of 491 ePK domains 7 , and in a collection of nearly 100 eukaryotes, this number increases to over 36,000 ePK domains. Such a number of sequences precludes the use of state-of-the-art alignment as well as tree building software. Moreover, it is a Sisyphean task to analyse a phylogenetic tree that consists of over 36,000 leaves.A more general problem of gene trees is the negative impact of rapidly evolving sequences on statistic support. A commonly used strategy to improve statistic support in species trees is to select slowly evolving genes or positions 17 . For gene trees, an equivalent of this strategy has been proposed: the Scrollsaw method 18 . The Scrollsaw method systematically selects only slowly evolving sequences for generating a gene tree. As a result, both the number of sequences is reduced, and rapidly evolving sequences are excluded. This makes the Scrollsaw method perfectly suitable to handle the large number of ePKs and generate a well-supported eukaryotic kinome tree.Here we present the first eukaryotic kinome tree, generated with a modified and extended version of the Scrollsaw method. The tree reveals ePK superfamily membership for several ePKs that have been labelled as Unaffiliated in the human kinome tree, most notably CAMKK1 and CAMKK2. The tree furthermore unveils that the LECA had much more ePKs than was thought before: at least 92.These 92 ePKs include some surprising examples of ePKs that were previously believed to be specific for certain eukaryotic supergroups, like human CHK1 and the plant CIPKs. The number of LECA ePKs retained in present-day species varies enormously within and between eukaryotic supergroups. The expansion of LECA ePKs since the common ancestor of eukaryotes also differs within and between ePK superfamilies. This variation in LECA ePK dispensability and duplicability is

Eukaryogenesis is one of the most enigmatic evolutionary transitions, during which simple prokaryotic cells gave rise to complex eukaryotic cells 1,2 . The last eukaryotic common ancestor (LECA) harboured intracellular compartments, including mitochondria. In addition to mitochondrial endosymbiosis, eukaryogenesis was driven by numerous gene acquisitions 3 , inventions and duplications 4 , which shaped the ancestral eukaryotic traits. While evolutionary intermediates are lacking, gene duplications allow us to elucidate the order of events by which eukaryotes originated. Here we reconstruct successive steps during eukaryogenesis using phylogenomics and show that mitochondrial endosymbiosis was an intermediate episode. We found that gene duplications roughly doubled the proto-eukaryotic genome, with families inherited from the Asgard archaea-related host being duplicated most. Importantly, by relatively timing events using branch lengths we inferred that duplications of archaeal families occurred throughout eukaryogenesis, both before and after the acquisition of bacterial genes. Duplications in cytoskeletal and membrane trafficking families were among the earliest events, whereas most other families expanded primarily after mitochondrial endosymbiosis. Altogether, we demonstrate that the host that engulfed the protomitochondrion had some eukaryote-like complexity, which further increased drastically upon mitochondrial acquisition. This scenario bridges the signs of complexity observed in Asgard archaeal genomes 5,6 to the proposed role of mitochondria in triggering eukaryogenesis 7,8 .