Abstract
Ancient polyploidization events have had a lasting impact on vertebrate genome structure, organization and function. Some key questions regarding the number of ancient polyploidization events and their timing in relation to the cyclostome-gnathostome divergence have remained contentious. Here we generate de novo long-read-based chromosome-scale genome assemblies for the Japanese lamprey and elephant shark. Using these and other representative genomes and developing algorithms for the probabilistic macrosynteny model, we reconstruct high-resolution proto-vertebrate, proto-cyclostome and proto-gnathostome genomes. Our reconstructions resolve key questions regarding the early evolutionary history of vertebrates. First, cyclostomes diverged from the lineage leading to gnathostomes after a shared tetraploidization (1R) but before a gnathostome-specific tetraploidization (2R). Second, the cyclostome lineage experienced an additional hexaploidization. Third, 2R in the gnathostome lineage was an allotetraploidization event, and biased gene loss from one of the subgenomes shaped the gnathostome genome by giving rise to remarkably conserved microchromosomes. Thus, our reconstructions reveal the major evolutionary events and offer new insights into the origin and evolution of vertebrate genomes.
Highlights
Ancient polyploidization events have had a lasting impact on vertebrate genome structure, organization and function
The timing of 1R and 2R relative to the cyclostome–gnathostome divergence has remained contentious— a significant gap in our knowledge considering the important implications for the genetic basis of the shared and derived features of these two lineages
We generated de novo chromosome-scale genome assemblies for elephant shark and Japanese lamprey using a combination of PacBio singlemolecule real-time (SMRT) sequencing (68- and 87-fold coverage, respectively), and ‘Chicago’[35] and Hi-C data aided scaffolding
Summary
Ancient polyploidization events have had a lasting impact on vertebrate genome structure, organization and function. Previous studies have produced conflicting results supporting each of the three possibilities[18,19,20,21,22,23,24,25,26], i.e. divergence occurring prior to 1R, between 1R and 2R, and after 2R (Fig. 1) This uncertainty has been further compounded by the discovery of six Hox clusters in both lampreys and hagfish[19,22,27] compared to four clusters in most gnathostome lineages, suggesting the possibility of an additional tetraploidization or chromosome-scale segmental duplications in the cyclostome ancestor[18,19,22]. This strategy has the potential to reveal chromosome fusion/fission events that occurred in the interval between 1R and 2R and/or after 2R13,15
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