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

TitleLineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans.
Publication TypeJournal Article
Year of Publication2005
AuthorsYohn, CT, Jiang, Z, McGrath, SD, Hayden, KE, Khaitovich, P, Johnson, ME, Eichler, MY, McPherson, JD, Zhao, S, Pääbo, S, Eichler, EE
JournalPLoS Biol
Volume3
Issue4
Paginatione110
Date Published2005 Apr
ISSN1545-7885
KeywordsAnimals, Chromosome Mapping, Endogenous Retroviruses, Gorilla gorilla, Hominidae, Humans, Introns, Molecular Sequence Data, Pan troglodytes, Pongo pygmaeus, Protein Biosynthesis, Retroelements, Species Specificity, Transcription, Genetic
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.

DOI10.1371/journal.pbio.0030110
Alternate JournalPLoS Biol.
PubMed ID15737067
PubMed Central IDPMC1054887
Grant ListHD-07104-26 / HD / NICHD NIH HHS / United States
GM58815 / GM / NIGMS NIH HHS / United States
P51-RR013986 / RR / NCRR NIH HHS / United States
P51 RR013986 / RR / NCRR NIH HHS / United States
T32 HD007104 / HD / NICHD NIH HHS / United States