Transcriptomics

Dataset Information

3

Primate genome architecture linked with formation mechanisms and functional consequences of structural variation


ABSTRACT: 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. 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.

SUBMITTER: Omer Gokcumen   Vladimir Benes  Pavlos Pavlidis  Qihui Zhu  Jelena Tica  Rebecca Iskow  Ryan Mills  Eunjung Lee  Amy Langdon  Charles Lee  Adrian M Stütz  Jan O Korbel  Markus H Fritz  Peter Park  Verena Tischler 

PROVIDER: E-GEOD-45741 | ArrayExpress | 2013-08-10

SECONDARY ACCESSION(S): GSE45741PRJNA196636

REPOSITORIES: GEO, ArrayExpress

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