The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution

TLDR

The sea lamprey (Petromyzon marinus) serves as a comparative model for reconstructing vertebrate evolution. The authors developed a new lamprey germline genome assembly integrating multiple data sets to facilitate informed analyses and support diverse studies of lamprey biology and vertebrate evolution. They assembled a highly contiguous, chromosome‑scale germline genome by integrating several complementary data sets. The assembly reveals extensive chromosomal and whole‑genome duplications, including chromosomes carrying six HOX clusters, identifies hundreds of genes consistently eliminated from somatic cells, and shows that gnathostome homologs of these genes are marked by PRCs, indicating shared regulatory mechanisms of DNA elimination and embryonic PRC‑mediated bivalency.

Abstract

The sea lamprey (Petromyzon marinus) serves as a comparative model for reconstructing vertebrate evolution. To enable more informed analyses, we developed a new assembly of the lamprey germline genome that integrates several complementary data sets. Analysis of this highly contiguous (chromosome-scale) assembly shows that both chromosomal and whole-genome duplications have played significant roles in the evolution of ancestral vertebrate and lamprey genomes, including chromosomes that carry the six lamprey HOX clusters. The assembly also contains several hundred genes that are reproducibly eliminated from somatic cells during early development in lamprey. Comparative analyses show that gnathostome (mouse) homologs of these genes are frequently marked by polycomb repressive complexes (PRCs) in embryonic stem cells, suggesting overlaps in the regulatory logic of somatic DNA elimination and bivalent states that are regulated by early embryonic PRCs. This new assembly will enhance diverse studies that are informed by lampreys' unique biology and evolutionary/comparative perspective.