E-GEOD-30352 - RNA-seq of 6 tissues from 10 species to investigate the evolution of gene expression levels in mammalian organs

Status
Released on 12 October 2011, last updated on 11 June 2014
Organism
Gallus gallus, Gorilla gorilla, Homo sapiens, Macaca mulatta, Monodelphis domestica, Mus musculus, Ornithorhynchus anatinus, Pan paniscus, Pan troglodytes, Pongo pygmaeus
Samples (131)
Protocols (2)
Description
Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. We show that the rate of gene expression evolution varies among organs, lineages and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation. Although gene expression evolution in mammals was strongly shaped by purifying selection, we identify numerous potentially selectively driven expression switches, which occurred at different rates across lineages and tissues and which probably contributed to the specific organ biology of various mammals. Our transcriptome data provide a valuable resource for functional and evolutionary analyses of mammalian genomes. To study mammalian transcriptome evolution at high resolution, we generated RNA-Seq data (∼3.2 billion Illumina Genome Analyser IIx reads of 76 base pairs) for the polyadenylated RNA fraction of brain (cerebral cortex or whole brain without cerebellum), cerebellum, heart, kidney, liver and testis (usually from one male and one female per somatic tissue and two males for testis) from nine mammalian species: placental mammals (great apes, including humans; rhesus macaque; mouse), marsupials (gray short-tailed opossum) and monotremes (platypus). Corresponding data (∼0.3 billion reads) were generated for a bird (red jungle fowl, a non-domesticated chicken) and used as an evolutionary outgroup.
Experiment type
RNA-seq of coding RNA 
Contacts
Henrik Kaessmann <geo@ncbi.nlm.nih.gov>, Anamaria Necsulea, Angelica Liechti, Ayinuer Aximu-Petri, David Brawand, Frank Grutzner, Frank W Albert, Gabor Csardi, Magali Soumillon, Manuela Weier, Martin Kircher, Patrick Harrigan, Philipp Khaitovich, Philippe Julien, Rasmus Nielsen, Svante Paabo, Sven Bergmann, Ulrich Zeller
Citation
The evolution of gene expression levels in mammalian organs. Brawand D, Soumillon M, Necsulea A, Julien P, Csárdi G, Harrigan P, Weier M, Liechti A, Aximu-Petri A, Kircher M, Albert FW, Zeller U, Khaitovich P, Grützner F, Bergmann S, Nielsen R, Pääbo S, Kaessmann H. , Europe PMC 22012392
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-GEOD-30352.idf.txt
Sample and data relationshipE-GEOD-30352.sdrf.txt
Links