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The Sea Lamprey Germline Genome Provides Insights into Programmed Genome Rearrangement and Vertebrate Evolution

Jun 28, 2018


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.


Jeramiah Smith, Nataliya Timoshevskaya, Chengxi Ye, Carson Holt, Melissa Keinath, Hugo Parker, Malcolm Cook, Jon Hess, Shawn Narum, Francesco Lamanna, Henrik Kaessmann, Vladimir Timoshevskiy, Courtney Waterbury, Cody Saraceno, Leanne Wiedemann, Sofia Robb, Carl Baker, Evan Eichler, Dorit Hockman, Tatjana Sauka-Spengler, Mark Yandell, Robb Krumlauf, Greg Elgar, and Chris Amemiya


Smith,J.J., N. Timoshevskaya, C. Ye, C. Holt, M.C. Keinath, H.J. Parker, M.E. Cook, J.E. Hess, S.R. Narum, F. Lamanna, H. Kaessmann, V.A. Timoshevskiy, C.K.M. Waterbury, C. Saraceno, L.M. Wiedemann, S.M.C. Robb, C. Baker, E.E. Eichler, D. Hockman, T. Sauka-Spengler, M. Yandell, R. Krumlauf, G. Elgar, and C.T. Amemiya. 2018. The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nature Genetics 50:270–277.  Online at Online at



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Journal Article