Abstract

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.

Document Type

Article

Publication Date

3-2023

Notes/Citation Information

© 2023 The Authors. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Digital Object Identifier (DOI)

https://doi.org/10.1016/j.celrep.2023.112263

Funding Information

This work was funded by grants from the National Institutes of Health (NIH) (R35GM130349) and the National Science Foundation (NSF) (MCB1818012) to J.J.S., a grant from the Great Lakes Fishery Commission to J.J.S. and E.D.J., HHMI funds to E.D.J., and New Zealand Ministry of Business Innovation and Employment (MBIE) contract C01X1615 to C.F.B. A.K.M. and N.J.G. are supported by the University of Otago and a subcontract from C01X1615.

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