Identification and analysis of unitary pseudogenes

Historic and contemporary gene losses in humans and other primates

Zhengdong Zhang, Adam Frankish, Toby Hunt, Jennifer Harrow, Mark Gerstein

Research output: Contribution to journalArticle

89 Citations (Scopus)

Abstract

Background: Unitary pseudogenes are a class of unprocessed pseudogenes without functioning counterparts in the genome. They constitute only a small fraction of annotated pseudogenes in the human genome. However, as they represent distinct functional losses over time, they shed light on the unique features of humans in primate evolution.Results: We have developed a pipeline to detect human unitary pseudogenes through analyzing the global inventory of orthologs between the human genome and its mammalian relatives. We focus on gene losses along the human lineage after the divergence from rodents about 75 million years ago. In total, we identify 76 unitary pseudogenes, including previously annotated ones, and many novel ones. By comparing each of these to its functioning ortholog in other mammals, we can approximately date the creation of each unitary pseudogene (that is, the gene 'death date') and show that for our group of 76, the functional genes appear to be disabled at a fairly uniform rate throughout primate evolution - not all at once, correlated, for instance, with the 'Alu burst'. Furthermore, we identify 11 unitary pseudogenes that are polymorphic - that is, they have both nonfunctional and functional alleles currently segregating in the human population. Comparing them with their orthologs in other primates, we find that two of them are in fact pseudogenes in non-human primates, suggesting that they represent cases of a gene being resurrected in the human lineage.Conclusions: This analysis of unitary pseudogenes provides insights into the evolutionary constraints faced by different organisms and the timescales of functional gene loss in humans.

Original languageEnglish (US)
Article numberr26
JournalGenome Biology
Volume11
Issue number3
DOIs
StatePublished - Mar 8 2010
Externally publishedYes

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Pseudogenes
pseudogenes
primate
Primates
gene
genome
Genes
genes
Human Genome
rodent
allele
mammal
divergence
loss
analysis
timescale
human population
Mammals
Rodentia
rodents

ASJC Scopus subject areas

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

Cite this

Identification and analysis of unitary pseudogenes : Historic and contemporary gene losses in humans and other primates. / Zhang, Zhengdong; Frankish, Adam; Hunt, Toby; Harrow, Jennifer; Gerstein, Mark.

In: Genome Biology, Vol. 11, No. 3, r26, 08.03.2010.

Research output: Contribution to journalArticle

Zhang, Zhengdong ; Frankish, Adam ; Hunt, Toby ; Harrow, Jennifer ; Gerstein, Mark. / Identification and analysis of unitary pseudogenes : Historic and contemporary gene losses in humans and other primates. In: Genome Biology. 2010 ; Vol. 11, No. 3.
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