Characterization of Somatically-Eliminated Genes during Development of the Sea Lamprey (Petromyzon marinus)

Stephanie A. Bryant, Joseph R. Herdy, Chris T. Amemiya, Jeramiah J. Smith

Research output: Contribution to journalArticlepeer-review

26 Scopus citations


The sea lamprey (Petromyzon marinus) is a basal vertebrate that undergoes developmentally programmed genome rearrangements (PGRs) during early development. These events facilitate the elimination of ∼20% of the genome from the somatic cell lineage, resulting in distinct somatic and germline genomes. Thus far only a handful of germline-specific genes have been definitively identified within the estimated 500 Mb of DNA that is deleted during PGR, although a few thousand germline-specific genes are thought to exist. To improve our understanding of the evolutionary/developmental logic of PGR, we generated computational predictions to identify candidate germline-specific genes within a new transcriptomic dataset derived from adult germline and the early embryonic stages during which PGR occurs. Follow-up validation studies identified 44 germline-specific genes and further characterized patterns of transcription and DNA loss during early embryogenesis. Expression analyses reveal that many of these genes are differentially expressed during early embryogenesis and presumably function in the early development of the germline. Ontology analyses indicate that many of these germline-specific genes play known roles in germline development, pluripotency, and oncogenesis (when misexpressed). These studies provide support for the theory that PGR serves to segregate molecular functions related to germline development/pluripotency in order to prevent their potential misexpression in somatic cells. This larger set of eliminated genes also allows us to extend the evolutionary/developmental breadth of this theory, as some deleted genes (or their gnathostome homologs) appear to be associated with the early development of somatic lineages, perhaps through the evolution of novel functions within gnathostome lineages.

Original languageEnglish
Pages (from-to)2337-2344
Number of pages8
JournalMolecular Biology and Evolution
Issue number9
StatePublished - Sep 1 2016

Bibliographical note

Funding Information:
We thank Brett Spear and Shirley Qui for granting access to real-time PCR resources used in this project. This study was funded by the National Institute of General Medical Sciences of the National Institutes of Health under award number R01GM104123 to J.S. and under award number R24GM095471 to C.T.A.

Publisher Copyright:
© 2016 The Author.


  • development
  • genome
  • lamprey
  • rearrangement
  • vertebrate

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics


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