|
| Status |
Public on Aug 10, 2013 |
| Title |
Primate genome architecture linked with formation mechanisms and functional consequences of structural variation |
| Platform organisms |
Macaca mulatta; Pan troglodytes; Pongo pygmaeus |
| Sample organisms |
Macaca mulatta; Pan troglodytes; Pongo abelii |
| Experiment type |
Genome variation profiling by genome tiling array
|
| Summary |
While nucleotide-resolution maps of genomic structural variants (SVs) have provided insights into the origin and impact on phenotypic diversity in humans, comparable maps in nonhuman primates have thus far been lacking. Using massively parallel DNA sequencing we constructed fine-resolution, species-specific structural variation and segmental duplication maps for five chimpanzees, five orang-utans, and five rhesus macaques. The SV maps, comprising thousands of deletions, duplications, and mobile element insertions, revealed a high activity of retrotransposition in macaques. Non-allelic homologous recombination, linked with genomic architecture, primarily shaped the genomes of great apes resulting in different SV formation mechanism landscapes across species, with distinct functional consequences. Transcriptome analyses across nonhuman primates and humans revealed significant effects of species-specific gene duplications on gene expression, with these effects displaying remarkable diversity in direction and magnitude. Thirteen inter-species gene duplications coincided with the species-specific gain of expression in a new tissue, implicating these duplications in function acquisition.
|
| |
|
| Overall design |
Agilent arrays were custom designed for probes to be relatively evenly spaced across the reference genomes of chimpanzee, orang-utan, and rhesus macaque. For each species 9 one million probe arrays were used to cover the autosomes and a single 400k probe array was used for the sex chromosomes.
|
| |
|
| Contributor(s) |
Gokcumen O, Tischler V, Tica J, Zhu Q, Iskow R, Lee E, Fritz MH, Langdon A, Stütz AM, Pavlidis P, Benes V, Mills R, Park P, Lee C, Korbel JO |
| Citation(s) |
24014587 |
| |
| Submission date |
Apr 03, 2013 |
| Last update date |
Oct 18, 2013 |
| Contact name |
Charles Lee |
| E-mail(s) |
clee@rics.bwh.harvard.edu
|
| Organization name |
Brigham and Women's Hospital/Harvard Medical School
|
| Department |
Pathology
|
| Lab |
Lee Lab--Molecular Genetic Research Unit
|
| Street address |
221 Longwood Ave., EBRC-422
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platforms (30)
|
| GPL16903 |
Agilent-034032 PanTro2_HD_1M_4 |
| GPL16904 |
Agilent-034033 PanTro2_HD_1M_5 |
| GPL16905 |
Agilent-034034 PanTro2_HD_1M_6 |
| GPL16906 |
Agilent-034035 PanTro2_HD_1M_7 |
| GPL16907 |
Agilent-034036 PanTro2_HD_1M_8 |
| GPL16908 |
Agilent-034037 PanTro2_HD_1M_9 |
| GPL16909 |
Agilent-034038 RheMac2_HD_1M_1 |
| GPL16910 |
Agilent-034039 RheMac2_HD_1M_2 |
| GPL16911 |
Agilent-034040 PanTro2_HD_1M_10 |
| GPL16912 |
Agilent-034041 RheMac2_HD_1M_3 |
| GPL16913 |
Agilent-034042 RheMac2_HD_1M_4 |
| GPL16914 |
Agilent-034043 RheMac2_HD_1M_5 |
| GPL16915 |
Agilent-034044 RheMac2_HD_1M_6 |
| GPL16916 |
Agilent-034045 RheMac2_HD_1M_7 |
| GPL16917 |
Agilent-034046 RheMac2_HD_1M_9 |
| GPL16918 |
Agilent-034047 RheMac2_HD_400K_10 |
| GPL16919 |
Agilent-034048 RheMac2_HD_1M_8 |
| GPL16920 |
Agilent-035944 ponAbe2_HD_1M_5 |
| GPL16921 |
Agilent-035950 ponAbe2_HD_400K_10 |
| GPL16922 |
Agilent-035952 ponAbe2_HD_1M_4 |
| GPL16923 |
Agilent-035954 ponAbe2_HD_1M_6 |
| GPL16924 |
Agilent-035955 ponAbe2_HD_1M_7 |
| GPL16925 |
Agilent-035956 ponAbe2_HD_1M_8 |
| GPL16926 |
Agilent-035957 ponAbe2_HD_1M_9 |
| GPL16927 |
Agilent-035978 ponAbe2_HD_1M_1 |
| GPL16928 |
Agilent-035979 ponAbe2_HD_1M_2 |
| GPL16929 |
Agilent-035980 ponAbe2_HD_1M_3 |
|
| Samples (30)
|
|
| Relations |
| BioProject |
PRJNA196636 |
Less...
More...