TY - JOUR
T1 - An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes
AU - Timoshevskaya, Nataliya
AU - Eşkut, Kaan
AU - Timoshevskiy, Vladimir A.
AU - Robb, Sofia M.C.
AU - Holt, Carson
AU - Hess, Jon E.
AU - Parker, Hugo J.
AU - Baker, Cindy F.
AU - Miller, Allison K.
AU - Saraceno, Cody
AU - Yandell, Mark
AU - Krumlauf, Robb
AU - Narum, Shawn R.
AU - Lampman, Ralph T.
AU - Gemmell, Neil J.
AU - Mountcastle, Jacquelyn
AU - Haase, Bettina
AU - Balacco, Jennifer R.
AU - Formenti, Giulio
AU - Pelan, Sarah
AU - Sims, Ying
AU - Howe, Kerstin
AU - Fedrigo, Olivier
AU - Jarvis, Erich D.
AU - Smith, Jeramiah J.
N1 - Publisher Copyright:
© 2023 The Authors
PY - 2023/3/28
Y1 - 2023/3/28
N2 - 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.
AB - 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.
KW - CP: Molecular biology
KW - assembly
KW - chromatin diminution
KW - chromosome
KW - evolution
KW - genome
KW - germline
KW - lamprey
KW - programmed DNA loss
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U2 - 10.1016/j.celrep.2023.112263
DO - 10.1016/j.celrep.2023.112263
M3 - Article
C2 - 36930644
AN - SCOPUS:85150029905
SN - 2211-1247
VL - 42
JO - Cell Reports
JF - Cell Reports
IS - 3
M1 - 112263
ER -