Project description:Data from gorilla fibroblast cell lines described in Genome Research paper "Comparative analysis of gene expression patterns in human and African great ape cultured fibroblasts" Keywords = African Great Ape, Human Evolution, Fibroblast, Bonobo, Gorilla, Human Keywords: ordered
Project description:RNA-seq samples from 3 species across a differentiation from induced pluripotent stem cells to neural progenitor cells were generated to study gene expression evolution. Briefly, previously generated urinary stem cell derived iPSCs of 3 human (Homo sapiens) individuals (3 clones), 1 gorilla (Gorilla gorilla) individual and fibroblast derived cynomolgus macaque (Macaca fascicularis) iPSCs of 2 individuals (4 clones) (Geuder et al. 2021) were differentiated to neural progenitor cells via dual-SMAD inhibition as three-dimensional aggregation culture (Chambers et al. 2009; Ohnuki et al. 2014). Bulk RNA-seq libraries of iPSCs and NPCs were generated using prime-seq protocol (Janjic et al. 2022).
Project description:Structural variation has played an important role in the evolutionary restructuring of human and great ape genomes. We generated approximately 10-fold genomic sequence coverage from a western lowland gorilla and integrated these data into a physical and cytogenetic framework to develop a comprehensive view of structural variation. We discovered and validated over 7,665 structural changes within the gorilla lineage including sequence resolution of inversions, deletions, duplications and retrotranspositions. A comparison with human and other ape genomes shows that the gorilla genome has been subjected to the highest rate of segmental duplication. We show that both the gorilla and chimpanzee genomes have experienced independent yet parallel patterns of structural mutation that have not occurred in humans, including the formation of subtelomeric heterochromatic caps, the hyperexpansion of segmental duplications and bursts of retroviral integrations. Our analysis suggests that the chimpanzee and gorilla genomes are structurally more derived than either orangutan or human.
