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Nat Genet. 2018 Feb;50(2):270-277. doi: 10.1038/s41588-017-0036-1. Epub 2018 Jan 22.

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

Author information

1
Department of Biology, University of Kentucky, Lexington, KY, USA. jjsmit3@uky.edu.
2
Department of Biology, University of Kentucky, Lexington, KY, USA.
3
Department of Computer Science, University of Maryland, College Park, MD, USA.
4
Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
5
Stowers Institute for Medical Research, Kansas City, MO, USA.
6
Columbia River Inter-Tribal Fish Commission, Portland, OR, USA.
7
Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
8
Department of Pathology and Laboratory Medicine, University of Kansas School of Medicine, Kansas City, KS, USA.
9
Department of Anatomy & Cell Biology, The University of Kansas School of Medicine, Kansas City, KS, USA.
10
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
11
Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
12
Radcliffe Department of Medicine, University of Oxford, Oxford, England.
13
Division of Cell Biology, Department of Anatomy, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
14
The Francis Crick Institute, London, England.
15
Benaroya Research Institute, Seattle, WA, USA.
16
School of Natural Sciences, University of California Merced, Merced, CA, USA.

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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