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The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. 2018
Jeramiah J Smith, and
Nataliya Timoshevskaya, and
Chengxi Ye, and
Carson Holt, and
Melissa C Keinath, and
Hugo J Parker, and
Malcolm E Cook, and
Jon E Hess, and
Shawn R Narum, and
Francesco Lamanna, and
Henrik Kaessmann, and
Vladimir A Timoshevskiy, and
Courtney K M Waterbury, and
Cody Saraceno, and
Leanne M Wiedemann, and
Sofia M C Robb, and
Carl Baker, and
Evan E Eichler, and
Dorit Hockman, and
Tatjana Sauka-Spengler, and
Mark Yandell, and
Robb Krumlauf, and
Greg Elgar, and
Chris T Amemiya
Department of Biology, University of Kentucky, Lexington, KY, USA. jjsmit3@uky.edu.
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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