An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes.

Autor:	Timoshevskaya N; Department of Biology, University of Kentucky, Lexington, KY 40506, USA., Eşkut KI; Department of Biology, University of Kentucky, Lexington, KY 40506, USA., Timoshevskiy VA; Department of Biology, University of Kentucky, Lexington, KY 40506, USA., Robb SMC; Stowers Institute for Medical Research, Kansas City, MO 64110, USA., Holt C; Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA., Hess JE; Columbia River Inter-Tribal Fish Commission, Portland, OR 97232, USA., Parker HJ; Stowers Institute for Medical Research, Kansas City, MO 64110, USA., Baker CF; National Institute of Water and Atmospheric Research Limited (NIWA), Hamilton, Waikato 3261, New Zealand., Miller AK; Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, Otago 9054, New Zealand., Saraceno C; Department of Biology, University of Kentucky, Lexington, KY 40506, USA., Yandell M; Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA., Krumlauf R; Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Anatomy & Cell Biology, The University of Kansas School of Medicine, Kansas City, KS 66160, USA., Narum SR; Columbia River Inter-Tribal Fish Commission, Hagerman, ID 83332, USA., Lampman RT; Yakama Nation Fisheries Resource Management Program, Pacific Lamprey Project, Toppenish, WA 98948, USA., Gemmell NJ; Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, Otago 9054, New Zealand., Mountcastle J; Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA., Haase B; Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA., Balacco JR; Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA., Formenti G; Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA; Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA., Pelan S; Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK., Sims Y; Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK., Howe K; Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK., Fedrigo O; Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA., Jarvis ED; Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA; Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA., Smith JJ; Department of Biology, University of Kentucky, Lexington, KY 40506, USA. Electronic address: jjsmit3@uky.edu.
Jazyk:	angličtina
Zdroj:	Cell reports [Cell Rep] 2023 Mar 28; Vol. 42 (3), pp. 112263. Date of Electronic Publication: 2023 Mar 15.
DOI:	10.1016/j.celrep.2023.112263
Abstrakt:	Programmed DNA loss is a gene silencing mechanism that is employed by several vertebrate and nonvertebrate lineages, including all living jawless vertebrates and songbirds. Reconstructing the evolution of somatically eliminated (germline-specific) sequences in these species has proven challenging due to a high content of repeats and gene duplications in eliminated sequences and a corresponding lack of highly accurate and contiguous assemblies for these regions. Here, we present an improved assembly of the sea lamprey (Petromyzon marinus) genome that was generated using recently standardized methods that increase the contiguity and accuracy of vertebrate genome assemblies. This assembly resolves highly contiguous, somatically retained chromosomes and at least one germline-specific chromosome, permitting new analyses that reconstruct the timing, mode, and repercussions of recruitment of genes to the germline-specific fraction. These analyses reveal major roles of interchromosomal segmental duplication, intrachromosomal duplication, and positive selection for germline functions in the long-term evolution of germline-specific chromosomes. Competing Interests: Declaration of interests The authors declare no competing interests. (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)
Databáze:	MEDLINE
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