TY - JOUR
T1 - Identification and analysis of unitary pseudogenes
T2 - Historic and contemporary gene losses in humans and other primates
AU - Zhang, Zhengdong D.
AU - Frankish, Adam
AU - Hunt, Toby
AU - Harrow, Jennifer
AU - Gerstein, Mark
N1 - Funding Information:
We thank Laurens Wilming, Marie-Marthe Suner, Charles Steward, and Ifat Barnes at the Wellcome Trust Sanger Institute for annotating some of the predicted human unitary pseudogenic loci. This work was supported by an NIH grant from National Library of Medicine (1K99LM009770-01) to ZDZ. Additional funding was provided by NIH grants from National Human Genome Research Institute to MG.
PY - 2010/3/8
Y1 - 2010/3/8
N2 - 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.
AB - 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.
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U2 - 10.1186/gb-2010-11-3-r26
DO - 10.1186/gb-2010-11-3-r26
M3 - Article
C2 - 20210993
AN - SCOPUS:77952694676
SN - 1474-7596
VL - 11
JO - Genome biology
JF - Genome biology
IS - 3
M1 - r26
ER -