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.
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•We report an improved assembly of the sea lamprey (Petromyzon marinus) genome•The assembly resolves at least one germline-specific chromosome•Many germline-specific genes have somatic paralogs in the sea lamprey genome•Data from other species provide insight into the timing of duplication events
Timoshevskaya et al. report an improved genome assembly for sea lamprey that aids in resolving the structure and evolution of chromosomes that are programmatically eliminated during development (germline-specific chromosomes). Using data from other species, these analyses indicate major roles of duplication and selection in the long-term evolution of germline-specific chromosomes.