Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution

Yoichiro Nakatani, Prashant Shingate, Vydianathan Ravi, Nisha E. Pillai, Aravind Prasad, Aoife McLysaght () and Byrappa Venkatesh ()
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Yoichiro Nakatani: University of Dublin
Prashant Shingate: Institute of Molecular and Cell Biology, A*STAR, Biopolis
Vydianathan Ravi: Institute of Molecular and Cell Biology, A*STAR, Biopolis
Nisha E. Pillai: Institute of Molecular and Cell Biology, A*STAR, Biopolis
Aravind Prasad: Institute of Molecular and Cell Biology, A*STAR, Biopolis
Aoife McLysaght: University of Dublin
Byrappa Venkatesh: Institute of Molecular and Cell Biology, A*STAR, Biopolis

Nature Communications, 2021, vol. 12, issue 1, 1-14

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41467-021-24573-z

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