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

Jeramiah J. Smith(University of Kentucky), Nataliya Timoshevskaya(University of Kentucky), Chengxi Ye(University of Maryland, College Park), Carson Holt(University of Utah), Melissa C. Keinath(University of Kentucky), Hugo J. Parker(Stowers Institute for Medical Research), Malcolm Cook(Stowers Institute for Medical Research), Jon E. Hess(Columbia River Inter-Tribal Fish Commission), Shawn R. Narum(Columbia River Inter-Tribal Fish Commission), Francesco Lamanna(Heidelberg University), Henrik Kaessmann(Heidelberg University), Vladimir A. Timoshevskiy(University of Kentucky), Courtney K. M. Waterbury(University of Kentucky), Cody Saraceno(University of Kentucky), Leanne M. Wiedemann(Stowers Institute for Medical Research), Sofia Robb(Stowers Institute for Medical Research), Carl Baker(University of Washington), Evan E. Eichler(Howard Hughes Medical Institute), Dorit Hockman(University of Cape Town), Tatjana Sauka‐Spengler(University of Oxford), Mark Yandell(University of Utah), Robb Krumlauf(Stowers Institute for Medical Research), Greg Elgar(The Francis Crick Institute), Chris T. Amemiya(University of California, Merced)
Nature Genetics
January 19, 2018
10.1038/s41588-017-0036-1
Cited by 323Open Access
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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.

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