High-resolution comparative analysis of great ape genomes
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens Pan troglodytes
PROVIDER: GSE113931 | GEO | 2018/06/12
REPOSITORIES: GEO
Similar Datasets
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:Human, Chimpanzee, Bonobo, Gorilla, Sumatran orangutan, Bornean orangutan Raw sequence reads
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Project description:Human, Chimpanzee, Bonobo, Gorilla, Sumatran orangutan, Bornean orangutan Raw sequence reads
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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: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:Genetic studies of human evolution require high-quality contiguous ape genome assemblies that are not guided by the human reference. We coupled long-read sequence assembly and full-length complementary DNA sequencing with a multiplatform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies. By comparing these with two long-read de novo human genome assemblies and a gorilla genome assembly, we characterized lineage-specific and shared great ape genetic variation ranging from single- to mega-base pair-sized variants. We identified ~17,000 fixed human-specific structural variants identifying genic and putative regulatory changes that have emerged in humans since divergence from nonhuman apes. Interestingly, these variants are enriched near genes that are down-regulated in human compared to chimpanzee cerebral organoids, particularly in cells analogous to radial glial neural progenitors.
| S-EPMC6178954 | biostudies-literature
Project description:The human brain has changed dramatically from other primate species, but the genetic and developmental mechanisms behind the differences remains unclear. Here we used single cell RNA sequencing based on 10X technology to explore temporal transcriptomic dynamics and cellular heterogeneity in cerebral organoids derived from human and non-human primates chimpanzee and rhesus macaque stem cells. Using cerebral organoids as a proxy of early brain development, we detect a delayed pace of human brain development relative to the other two primate species. Additional human-specific gene expression patterns resolved to different cell states through progenitors to neurons are also found. Our data provide a transcriptomic cell atlas of primate early brain development, and illustrate features that are unique to humans.
2019-12-30 | E-MTAB-7552 | biostudies-arrayexpress