Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans.

Chris T. Yohn, Zhaoshi Jiang, Sean D. McGrath, Karen E. Hayden, Philipp Khaitovich, Matthew E. Johnson, Marla Y. Eichler, John D. McPherson, Shaying Zhao, Svante Pääbo, Evan E. Eichler

Research output: Contribution to journalArticle

Abstract

Retroviral infections of the germline have the potential to episodically alter gene function and genome structure during the course of evolution. Horizontal transmissions between species have been proposed, but little evidence exists for such events in the human/great ape lineage of evolution. Based on analysis of finished BAC chimpanzee genome sequence, we characterize a retroviral element (Pan troglodytes endogenous retrovirus 1 [PTERV1]) that has become integrated in the germline of African great ape and Old World monkey species but is absent from humans and Asian ape genomes. We unambiguously map 287 retroviral integration sites and determine that approximately 95.8% of the insertions occur at non-orthologous regions between closely related species. Phylogenetic analysis of the endogenous retrovirus reveals that the gorilla and chimpanzee elements share a monophyletic origin with a subset of the Old World monkey retroviral elements, but that the average sequence divergence exceeds neutral expectation for a strictly nuclear inherited DNA molecule. Within the chimpanzee, there is a significant integration bias against genes, with only 14 of these insertions mapping within intronic regions. Six out of ten of these genes, for which there are expression data, show significant differences in transcript expression between human and chimpanzee. Our data are consistent with a retroviral infection that bombarded the genomes of chimpanzees and gorillas independently and concurrently, 3-4 million years ago. We speculate on the potential impact of such recent events on the evolution of humans and great apes.

Original languageEnglish (US)
JournalPLoS biology.
Volume3
Issue number4
StatePublished - Apr 2005
Externally publishedYes

Fingerprint

Pongo
Pongo pygmaeus
Pan troglodytes
Hominidae
Pongidae
Genes
Genome
genome
Retroviridae
Cercopithecidae
Gorilla gorilla
Endogenous Retroviruses
Gorilla
germ cells
genes
Infection
infection
Gene Expression
DNA
phylogeny

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)

Cite this

Yohn, C. T., Jiang, Z., McGrath, S. D., Hayden, K. E., Khaitovich, P., Johnson, M. E., ... Eichler, E. E. (2005). Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans. PLoS biology., 3(4).

Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans. / Yohn, Chris T.; Jiang, Zhaoshi; McGrath, Sean D.; Hayden, Karen E.; Khaitovich, Philipp; Johnson, Matthew E.; Eichler, Marla Y.; McPherson, John D.; Zhao, Shaying; Pääbo, Svante; Eichler, Evan E.

In: PLoS biology., Vol. 3, No. 4, 04.2005.

Research output: Contribution to journalArticle

Yohn, CT, Jiang, Z, McGrath, SD, Hayden, KE, Khaitovich, P, Johnson, ME, Eichler, MY, McPherson, JD, Zhao, S, Pääbo, S & Eichler, EE 2005, 'Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans.', PLoS biology., vol. 3, no. 4.
Yohn, Chris T. ; Jiang, Zhaoshi ; McGrath, Sean D. ; Hayden, Karen E. ; Khaitovich, Philipp ; Johnson, Matthew E. ; Eichler, Marla Y. ; McPherson, John D. ; Zhao, Shaying ; Pääbo, Svante ; Eichler, Evan E. / Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans. In: PLoS biology. 2005 ; Vol. 3, No. 4.
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