Great ape
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA504650 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Human, Chimpanzee, Bonobo, Gorilla, Sumatran orangutan, Bornean orangutan Raw sequence reads
| PRJNA505331 | ENA
Project description:Intra-specific polymorphism in copy number is documented in many organisms, including human and chimpanzee, but very little is known for other great apes. This study aims to provide CNVs data for orangutan, gorilla, bonobo and chimpanzee, and compare the CNV patterns among these species, as well as with human CNVs and segmental duplications from public databases.
2011-08-03 | GSE30559 | GEO
Project description:Intra-specific polymorphism in copy number is documented in many organisms, including human and chimpanzee, but very little is known for other great apes. This study aims to provide CNVs data for orangutan, gorilla, bonobo and chimpanzee, and compare the CNV patterns among these species, as well as with human CNVs and segmental duplications from public databases. Each sample is hybridized against a common reference of the same species for two dye combinations (e.g. chimp1_CY5 vs chimpREF_Cy3; chimp1_CY3 vs chimpREF_Cy5; bonobo1_CY5 vs bonoboREF_Cy3; bonobo1_CY3 vs bonoboREF_Cy5;)
2011-08-02 | E-GEOD-30559 | biostudies-arrayexpress
Project description:We couple long-read sequence assembly, full-length cDNA sequencing, and a multi-platform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies where most genes are complete, gaps are closed, and novel gene models are identified. We further analyzed the overlap between structural variants in the human genome and gene expression differences in human and chimpanzee cells, including iPS-derived organoid radial glia cells.
2018-06-12 | GSE113931 | GEO
Project description:Interspecies composite cell lines (or hybrid cells) are powerful tools to study genomic divergence between species. However, to date, the only pluripotent composite lines to exist are between human and chimpanzee. In addition, while these human-chimp composite lines contain the nuclear genomes from both species, they only contain the mitochondrial genome from one: human. Here we describe the generation of multiple composite pluripotent stem cell (PSC) lines between human and all other species of great apes (chimpanzee [Pan troglodytes], bonobo [Pan paniscus], gorilla [Gorilla gorilla], and orangutan [Pongo abelii]). In addition, we utilized a strategy based on enforced mitophagy to generate human-great ape composite PSCs that contain either the human or the non-human primate (NHP) mitochondrial genomes.
2025-06-03 | GSE270085 | GEO
Project description:Wilson and King were among the first to recognize that the extent of phenotypic change between humans and great apes was dissonant with the rate of molecular change. Proteins are virtually identical; cytogenetically there are few rearrangements that distinguish ape-human chromosomes; rates of single-basepair change and retroposon activity have slowed particularly within hominid lineages when compared to rodents or monkeys. Here, we perform a systematic analysis of duplication content of four primate genomes (macaque, orangutan, chimpanzee and human) in an effort to understand the pattern and rates of genomic duplication during hominid evolution. We find that the ancestral branch leading to human and African great apes shows the most significant increase in duplication activity both in terms of basepairs and in terms of events. This duplication acceleration within the ancestral species is significant when compared to lineage-specific rate estimates even after accounting for copy-number polymorphism and homoplasy. We discover striking examples of recurrent and independent gene-containing duplications within the gorilla and chimpanzee that are absent in the human lineage. Our results suggest that the evolutionary properties of copy-number mutation differ significantly from other forms of genetic mutation and, in contrast to the hominid slowdown of single basepair mutations, there has been a genomic burst of duplication activity at this period during human evolution. A total of 3 chimpanzees, 2 bonobos, 3 gorillas, 1 orangutan and 1 macaque were hybridized against human (NA15510). Other hybridizations (other humans, and non-humans) were also used as a replicate.
2010-05-22 | E-GEOD-13884 | biostudies-arrayexpress
Project description:Wilson and King were among the first to recognize that the extent of phenotypic change between humans and great apes was dissonant with the rate of molecular change. Proteins are virtually identical; cytogenetically there are few rearrangements that distinguish ape-human chromosomes; rates of single-basepair change and retroposon activity have slowed particularly within hominid lineages when compared to rodents or monkeys. Here, we perform a systematic analysis of duplication content of four primate genomes (macaque, orangutan, chimpanzee and human) in an effort to understand the pattern and rates of genomic duplication during hominid evolution. We find that the ancestral branch leading to human and African great apes shows the most significant increase in duplication activity both in terms of basepairs and in terms of events. This duplication acceleration within the ancestral species is significant when compared to lineage-specific rate estimates even after accounting for copy-number polymorphism and homoplasy. We discover striking examples of recurrent and independent gene-containing duplications within the gorilla and chimpanzee that are absent in the human lineage. Our results suggest that the evolutionary properties of copy-number mutation differ significantly from other forms of genetic mutation and, in contrast to the hominid slowdown of single basepair mutations, there has been a genomic burst of duplication activity at this period during human evolution.
2009-03-06 | GSE13884 | GEO
Project description:Wilson and King were among the first to recognize that the extent of phenotypic change between humans and great apes was dissonant with the rate of molecular change. Proteins are virtually identical; cytogenetically there are few rearrangements that distinguish ape-human chromosomes; rates of single-basepair change and retroposon activity have slowed particularly within hominid lineages when compared to rodents or monkeys. Here, we perform a systematic analysis of duplication content of four primate genomes (macaque, orangutan, chimpanzee and human) in an effort to understand the pattern and rates of genomic duplication during hominid evolution. We find that the ancestral branch leading to human and African great apes shows the most significant increase in duplication activity both in terms of basepairs and in terms of events. This duplication acceleration within the ancestral species is significant when compared to lineage-specific rate estimates even after accounting for copy-number polymorphism and homoplasy. We discover striking examples of recurrent and independent gene-containing duplications within the gorilla and chimpanzee that are absent in the human lineage. Our results suggest that the evolutionary properties of copy-number mutation differ significantly from other forms of genetic mutation and, in contrast to the hominid slowdown of single basepair mutations, there has been a genomic burst of duplication activity at this period during human evolution.
2009-03-06 | GSE13885 | GEO
Project description:Wilson and King were among the first to recognize that the extent of phenotypic change between humans and great apes was dissonant with the rate of molecular change. Proteins are virtually identical; cytogenetically there are few rearrangements that distinguish ape-human chromosomes; rates of single-basepair change and retroposon activity have slowed particularly within hominid lineages when compared to rodents or monkeys. Here, we perform a systematic analysis of duplication content of four primate genomes (macaque, orangutan, chimpanzee and human) in an effort to understand the pattern and rates of genomic duplication during hominid evolution. We find that the ancestral branch leading to human and African great apes shows the most significant increase in duplication activity both in terms of basepairs and in terms of events. This duplication acceleration within the ancestral species is significant when compared to lineage-specific rate estimates even after accounting for copy-number polymorphism and homoplasy. We discover striking examples of recurrent and independent gene-containing duplications within the gorilla and chimpanzee that are absent in the human lineage. Our results suggest that the evolutionary properties of copy-number mutation differ significantly from other forms of genetic mutation and, in contrast to the hominid slowdown of single basepair mutations, there has been a genomic burst of duplication activity at this period during human evolution. A total of 8 humans, 8 chimpanzees and 8 orangutans were hybridized against the reference (NA15510, Clint and Susie, respectively).
2010-05-22 | E-GEOD-13885 | biostudies-arrayexpress
Project description:The orangutan (Pongo spp., Linnaeus, 1760) is the most endangered great ape, classified as critically endangered. Sperm cryopreservation is a valuable tool for banking genetic resources and solving the complexities of relocating animals; however, cryopreservation protocols remain suboptimal for this species. Due to their phylogenetic closeness, this study aimed to explore the applicability of a chimpanzee (Pan troglodytes, Blumenbach, 1775) sperm cryopreservation protocol to orangutans. To guide further modifications to the protocol, we revealed, for the first time, the comprehensive lipidomic and proteomic characterizations of orangutan ejaculates with parallel comparisons to chimpanzee ejaculates. Functional analyses of oxidative and osmotic stress responses were also conducted to provide valuable evidence of the physiological changes and defense mechanisms associated with sperm cryodamage. The cross-species multi-omic analyses showed that compared to chimpanzee, the orangutan sperm lipid profile presented significant alterations after the freezing-thawing process, notably showing significant cholesterol loss. While interspecies differences in antioxidant enzyme composition and activity were observed, insufficient evidence supported the orangutan's heightened susceptibility to oxidative stress. Conversely, orangutan sperm exhibited low tolerance to hypoosmotic conditions. To prevent cryodamage, a modified thawing protocol by implementing a serial dilution approach significantly minimized the hypoosmotic shock and improved post-thaw motility to 19%. In conclusion, this study presents the first complete proteome and lipidome analyses of chimpanzee and orangutan ejaculates, providing valuable insights into the physiological changes and defense mechanisms associated with sperm cryopreservation. This knowledge enabled a science-based approach to improving cryopreservation protocols, moving away from trial-and-error methods.
2026-03-08 | PXD073407 | Pride