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Primate gene and genome evolution dr...

Case Western Reserve University.

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Primate gene and genome evolution driven by segmental duplication on chromosome 16.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Primate gene and genome evolution driven by segmental duplication on chromosome 16./
Author:	Johnson, Matthew Eric.
Description:	161 p.
Notes:	Adviser: Evan E. Eichler.
Contained By:	Dissertation Abstracts International68-08B.
Subject:	Biology, Genetics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoeng/servlet/advanced?query=3280061
ISBN:	9780549219910

Primate gene and genome evolution driven by segmental duplication on chromosome 16.
Johnson, Matthew Eric.

Primate gene and genome evolution driven by segmental duplication on chromosome 16. - 161 p.

Adviser: Evan E. Eichler.

Thesis (Ph.D.)--Case Western Reserve University, 2008.

A low copy repeat on chromosome 16a (LCR16a) was chosen to study the evolutionary roles of segmental duplications because the duplications were recent in human evolution and contained a full-length gene. To more fully understand the evolutionary significance of these events and gain insight into the mechanism underlying these changes, I have performed a detailed comparative sequencing project targeting LCR16a copies within large-insert BACs from six species: chimpanzee, gorilla, orangutan, gibbon, macaque, and baboon. Seventy-one LCR16a copies from primates and twenty-four LCR16a copies from humans (&sim;20Mb) were analyzed for genomic and gene evolution, revealing four important properties. First, a novel hominoid gene family (morpheus) contained within the LCR16a duplication has shown an extraordinary degree of amino acid divergence between humans and great apes (20%) when compared to the background rate of nucleotide substitution rate of 2%--3%. In addition, five out of seven exons have shown evidence of rapid positive selection, as determined by Ka/K s ratios. Second, LCR16a is not a lone duplication block: many of the LCR16a duplicons are associated with other LCR16 duplications as part of larger and more complex duplications, which are variable in duplicon type and number, in many different locations in primates. Phylogenetic analysis of LCR16a demonstrates a stepwise patterning of duplication centered on the LCR16a duplicon. Third, large-scale sequencing of great ape (chimpanzee, gorilla, and orangutan) BACs have revealed new (species-specific) insertions of LCR16a that do not correspond to LCR16a sites in the human genome assembly. The analysis of the sequence from these new insertion events has suggested a model where flanking repeats (SINEs) act as donors that are mediating the transposition event of LCR16a along with the coordinate deletion of large (average 19.5 kb) tracks of repeat-rich sequences at the acceptor sites. Fourth, RT-PCR expression analysis of human and primate tissues has shown a pattern of gene expression suggesting a model where a single copy of morpheus is expressed tissue-specifically in the testis of baboons while being ubiquitously expressed in all great apes. These data provide a model for the birth of a novel gene family during human evolution.

ISBN: 9780549219910Subjects--Topical Terms:

1017730
Biology, Genetics.

Primate gene and genome evolution driven by segmental duplication on chromosome 16.
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020 $a 9780549219910
035 $a (UMI)AAI3280061
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100 1 $a Johnson, Matthew Eric. $3 1023393
245 1 0 $a Primate gene and genome evolution driven by segmental duplication on chromosome 16.
300 $a 161 p.
500 $a Adviser: Evan E. Eichler.
500 $a Source: Dissertation Abstracts International, Volume: 68-08, Section: B, page: 4974.
502 $a Thesis (Ph.D.)--Case Western Reserve University, 2008.
520 $a A low copy repeat on chromosome 16a (LCR16a) was chosen to study the evolutionary roles of segmental duplications because the duplications were recent in human evolution and contained a full-length gene. To more fully understand the evolutionary significance of these events and gain insight into the mechanism underlying these changes, I have performed a detailed comparative sequencing project targeting LCR16a copies within large-insert BACs from six species: chimpanzee, gorilla, orangutan, gibbon, macaque, and baboon. Seventy-one LCR16a copies from primates and twenty-four LCR16a copies from humans (&sim;20Mb) were analyzed for genomic and gene evolution, revealing four important properties. First, a novel hominoid gene family (morpheus) contained within the LCR16a duplication has shown an extraordinary degree of amino acid divergence between humans and great apes (20%) when compared to the background rate of nucleotide substitution rate of 2%--3%. In addition, five out of seven exons have shown evidence of rapid positive selection, as determined by Ka/K s ratios. Second, LCR16a is not a lone duplication block: many of the LCR16a duplicons are associated with other LCR16 duplications as part of larger and more complex duplications, which are variable in duplicon type and number, in many different locations in primates. Phylogenetic analysis of LCR16a demonstrates a stepwise patterning of duplication centered on the LCR16a duplicon. Third, large-scale sequencing of great ape (chimpanzee, gorilla, and orangutan) BACs have revealed new (species-specific) insertions of LCR16a that do not correspond to LCR16a sites in the human genome assembly. The analysis of the sequence from these new insertion events has suggested a model where flanking repeats (SINEs) act as donors that are mediating the transposition event of LCR16a along with the coordinate deletion of large (average 19.5 kb) tracks of repeat-rich sequences at the acceptor sites. Fourth, RT-PCR expression analysis of human and primate tissues has shown a pattern of gene expression suggesting a model where a single copy of morpheus is expressed tissue-specifically in the testis of baboons while being ubiquitously expressed in all great apes. These data provide a model for the birth of a novel gene family during human evolution.
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790 1 0 $a Eichler, Evan E., $e advisor
791 $a Ph.D.
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856 4 0 $u http://pqdd.sinica.edu.tw/twdaoeng/servlet/advanced?query=3280061