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Comparative and demographic analysis of orang-utan genomes.

Locke DP | Hillier LW | Warren WC | Worley KC | Nazareth LV | Muzny DM | Yang SP | Wang Z | Chinwalla AT | Minx P | Mitreva M | Cook L | Delehaunty KD | Fronick C | Schmidt H | Fulton LA | Fulton RS | Nelson JO | Magrini V | Pohl C | Graves TA | Markovic C | Cree A | Dinh HH | Hume J | Kovar CL | Fowler GR | Lunter G | Meader S | Heger A | Ponting CP | Marques-Bonet T | Alkan C | Chen L | Cheng Z | Kidd JM | Eichler EE | White S | Searle S | Vilella AJ | Chen Y | Flicek P | Ma J | Raney B | Suh B | Burhans R | Herrero J | Haussler D | Faria R | Fernando O | Darré F | Farré D | Gazave E | Oliva M | Navarro A | Roberto R | Capozzi O | Archidiacono N | Della Valle G | Purgato S | Rocchi M | Konkel MK | Walker JA | Ullmer B | Batzer MA | Smit AF | Hubley R | Casola C | Schrider DR | Hahn MW | Quesada V | Puente XS | Ordoñez GR | López-Otín C | Vinar T | Brejova B | Ratan A | Harris RS | Miller W | Kosiol C | Lawson HA | Taliwal V | Martins AL | Siepel A | Roychoudhury A | Ma X | Degenhardt J | Bustamante CD | Gutenkunst RN | Mailund T | Dutheil JY | Hobolth A | Schierup MH | Ryder OA | Yoshinaga Y | de Jong PJ | Weinstock GM | Rogers J | Mardis ER | Gibbs RA | Wilson RK
Nature | Jan 27, 2011

'Orang-utan' is derived from a Malay term meaning 'man of the forest' and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (N(e)) expanded exponentially relative to the ancestral N(e) after the split, while Bornean N(e) declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.

Pubmed ID: 21270892 RIS Download

Mesh terms: Animals | Centromere | Cerebrosides | Chromosomes | Evolution, Molecular | Female | Gene Rearrangement | Genetic Speciation | Genetic Variation | Genetics, Population | Genome | Humans | Male | Phylogeny | Pongo abelii | Pongo pygmaeus | Population Density | Population Dynamics | Species Specificity

Research resources used in this publication

None found

Data used in this publication

None found

Associated grants

  • Agency: Medical Research Council, Id: G0501331
  • Agency: Medical Research Council, Id: MC_U137761446
  • Agency: Medical Research Council, Id: U54 HG003273
  • Agency: NHGRI NIH HHS, Id: P01 AG022064
  • Agency: NIA NIH HHS, Id: HG002385
  • Agency: NHGRI NIH HHS, Id: R01 HG002939
  • Agency: NHGRI NIH HHS, Id: U54 HG003079-08
  • Agency: NHGRI NIH HHS, Id: R01 GM59290
  • Agency: NIGMS NIH HHS, Id: R01 GM059290
  • Agency: NIGMS NIH HHS, Id: U54 HG003079
  • Agency: NHGRI NIH HHS, Id: R01 HG002385
  • Agency: NHGRI NIH HHS, Id: R01 HG002238
  • Agency: NHGRI NIH HHS, Id: HG002238
  • Agency: NHGRI NIH HHS, Id:

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Ensembl

A collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. The goal of Ensembl is to automatically annotate the genome, integrate this annotation with other available biological data and make the data publicly available via the web. The range of available data has also expanded to include comparative genomics, variation and regulatory data. Ensembl allows users to: upload and analyze data and save it to an Ensembl account; search for a DNA or protein sequence using BLAST or BLAT; fetch desired data from the public database, using the Perl API; download the databases via FTP in FASTA, MySQL and other formats; and mine Ensembl with BioMart and export sequences or tables in text, HTML, or Excel format. The DNA sequences and assemblies used in the Ensembl genebuild are provided by various projects around the world. Ensembl has entered into an agreement with UCSC and NCBI with regard to sequence identifiers in order to improve consistency between the data provided by different genome browsers. The site also links to the Ensembl blog with updates on new species and sequences as they are added to the database.

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GenomeNet

GenomeNet is a Japanese network of database and computational services for genome research and related research areas in biomedical sciences, operated by the Kyoto University Bioinformatics Center. GenomeNet was established in September 1991 under the Human Genome Program of the then Ministry of Education, Science and Culture (Monbusho). The GenomeNet service has been developed by the Kanehisa Laboratory in Kyoto University as part of the research projects. GenomeNet is operated using the Supercomputer System of the Institute for Chemical Research, Kyoto University. LinkDB is supported by the National Bioscience Database Center of the Japan Science and Technology Agency.

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NCBI Sequence Read Archive

Repository of raw sequencing data from the next generation of sequencing platforms including including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, Complete Genomics, and Pacific Biosciences SMRT. In addition to raw sequence data, SRA now stores alignment information in the form of read placements on a reference sequence. Data submissions are welcome. SRA is NIH''''s primary archive of high-throughput sequencing data and is part of the international partnership of archives (INSDC) at the NCBI, the European Bioinformatics Institute and the DNA Database of Japan. Data submitted to any of the three organizations are shared among them. NCBI announced that due to budget constraints, it would be discontinuing SRA but NIH has since committed interim funding for SRA in its current form until October 1, 2011. In addition, NCBI has been working with staff from other NIH Institutes and NIH grantees to develop an approach to continue archiving a widely used subset of next generation sequencing data after October 1, 2011.

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UCSC Genome Browser

A collection of genomes which include reference sequences and working draft assemblies, as well as a variety of tools to explore these sequences. The Genome Browser zooms and scrolls over chromosomes, showing the work of annotators worldwide. The Gene Sorter shows expression, homology and other information on groups of genes that can be related in many ways. Blat quickly maps your sequence to the genome. The Table Browser provides access to the underlying database. VisiGene lets you browse through a large collection of in situ mouse and frog images to examine expression patterns. Genome Graphs allows you to upload and display genome-wide data sets. Also provided is a portal to the Encyclopedia of DNA Elements (ENCODE) and Neandertal projects.

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NCBI

A portal to biomedical and genomic information. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information for the better understanding of molecular processes affecting human health and disease.

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Genome Institue at Wahington University Genomes

Genome databases housed at the Genome Institute at Washington University. Included are genome databases from Humans/Primates, other vertebrates, microorganisms, plants and invertebrates.

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