A genome-wide comparison of recent chimpanzee and human segmental duplications

@article{Cheng2005AGC,
  title={A genome-wide comparison of recent chimpanzee and human segmental duplications},
  author={Ze Cheng and Mario Ventura and Xinwei She and Philipp Khaitovich and Tina Graves and Kazutoyo Osoegawa and Deanna M. Church and Pieter J. Dejong and Richard K. Wilson and Svante P{\"a}{\"a}bo and Mariano Rocchi and Evan E. Eichler},
  journal={Nature},
  year={2005},
  volume={437},
  pages={88-93}
}
We present a global comparison of differences in content of segmental duplication between human and chimpanzee, and determine that 33% of human duplications (> 94% sequence identity) are not duplicated in chimpanzee, including some human disease-causing duplications. Combining experimental and computational approaches, we estimate a genomic duplication rate of 4–5 megabases per million years since divergence. These changes have resulted in gene expression differences between the species. In… 
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References

SHOWING 1-10 OF 38 REFERENCES
Analysis of segmental duplications and genome assembly in the mouse.
TLDR
A detailed analysis of recent duplication content within the mouse genome is presented using a whole-genome assembly comparison method and a novel assembly independent method, designed to take advantage of the reduced allelic variation of the C57BL/6J strain.
Recent Segmental Duplications in the Human Genome
TLDR
A method whereby each public sequence is analyzed at the clone level for overrepresentation within a whole-genome shotgun sequence has the ability to detect duplications larger than 15 kilobases irrespective of copy number, location, or high sequence similarity.
Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements.
TLDR
Comparing the human and mouse genome sequences suggests that segmental duplications have participated in the recent evolution of the human genome, as driving forces for evolutionary rearrangements, chromosome structure polymorphisms and genomic disorders.
Lineage-Specific Gene Duplication and Loss in Human and Great Ape Evolution
TLDR
The genes identified here likely represent a significant majority of the major gene copy number changes that have occurred over the past 15 million years of human and great ape evolution and are likely to underlie some of the key phenotypic characteristics that distinguish these species.
Initial sequence of the chimpanzee genome and comparison with the human genome
TLDR
It is found that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles.
Segmental duplications: organization and impact within the current human genome project assembly.
TLDR
The above data indicate that segmental duplications represent a significant impediment to accurate human genome assembly, requiring the development of specialized techniques to finish these exceptional regions of the genome.
Patterns of segmental duplication in the human genome.
TLDR
The simulation suggests that many duplications containing genes have been selectively maintained in the genome, and the duplication frequencies in pericentromeric and subtelomeric regions are greater than the genome average by approximately threefold and fourfold.
Segmental duplications and copy-number variation in the human genome.
TLDR
This study demonstrates that segmental duplications define hotspots of chromosomal rearrangement, likely acting as mediators of normal variation as well as genomic disease, and suggests that the consideration of genomic architecture can significantly improve the ascertainment of large-scale rearrangements.
Hotspots of mammalian chromosomal evolution
TLDR
This analysis supports a nonrandom model of chromosomal evolution that implicates specific regions within the mammalian genome as having been predisposed to both recurrent small-scale duplication and large-scale evolutionary rearrangements.
Positive selection of a gene family during the emergence of humans and African apes
TLDR
The rapidity and bias for amino-acid-altering nucleotide changes suggest adaptive evolution of the morpheus gene family during the emergence of humans and African apes.
...
1
2
3
4
...