Literature DB >> 22722832

The bonobo genome compared with the chimpanzee and human genomes.

Kay Prüfer1, Kasper Munch, Ines Hellmann, Keiko Akagi, Jason R Miller, Brian Walenz, Sergey Koren, Granger Sutton, Chinnappa Kodira, Roger Winer, James R Knight, James C Mullikin, Stephen J Meader, Chris P Ponting, Gerton Lunter, Saneyuki Higashino, Asger Hobolth, Julien Dutheil, Emre Karakoç, Can Alkan, Saba Sajjadian, Claudia Rita Catacchio, Mario Ventura, Tomas Marques-Bonet, Evan E Eichler, Claudine André, Rebeca Atencia, Lawrence Mugisha, Jörg Junhold, Nick Patterson, Michael Siebauer, Jeffrey M Good, Anne Fischer, Susan E Ptak, Michael Lachmann, David E Symer, Thomas Mailund, Mikkel H Schierup, Aida M Andrés, Janet Kelso, Svante Pääbo.   

Abstract

Two African apes are the closest living relatives of humans: the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours, and for some of these traits they show more similarity with humans than with each other. Here we report the sequencing and assembly of the bonobo genome to study its evolutionary relationship with the chimpanzee and human genomes. We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These regions allow various aspects of the ancestry of the two ape species to be reconstructed. In addition, many of the regions that overlap genes may eventually help us understand the genetic basis of phenotypes that humans share with one of the two apes to the exclusion of the other.

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Year:  2012        PMID: 22722832      PMCID: PMC3498939          DOI: 10.1038/nature11128

Source DB:  PubMed          Journal:  Nature        ISSN: 0028-0836            Impact factor:   49.962


  26 in total

1.  Initial sequencing and analysis of the human genome.

Authors:  E S Lander; L M Linton; B Birren; C Nusbaum; M C Zody; J Baldwin; K Devon; K Dewar; M Doyle; W FitzHugh; R Funke; D Gage; K Harris; A Heaford; J Howland; L Kann; J Lehoczky; R LeVine; P McEwan; K McKernan; J Meldrim; J P Mesirov; C Miranda; W Morris; J Naylor; C Raymond; M Rosetti; R Santos; A Sheridan; C Sougnez; Y Stange-Thomann; N Stojanovic; A Subramanian; D Wyman; J Rogers; J Sulston; R Ainscough; S Beck; D Bentley; J Burton; C Clee; N Carter; A Coulson; R Deadman; P Deloukas; A Dunham; I Dunham; R Durbin; L French; D Grafham; S Gregory; T Hubbard; S Humphray; A Hunt; M Jones; C Lloyd; A McMurray; L Matthews; S Mercer; S Milne; J C Mullikin; A Mungall; R Plumb; M Ross; R Shownkeen; S Sims; R H Waterston; R K Wilson; L W Hillier; J D McPherson; M A Marra; E R Mardis; L A Fulton; A T Chinwalla; K H Pepin; W R Gish; S L Chissoe; M C Wendl; K D Delehaunty; T L Miner; A Delehaunty; J B Kramer; L L Cook; R S Fulton; D L Johnson; P J Minx; S W Clifton; T Hawkins; E Branscomb; P Predki; P Richardson; S Wenning; T Slezak; N Doggett; J F Cheng; A Olsen; S Lucas; C Elkin; E Uberbacher; M Frazier; R A Gibbs; D M Muzny; S E Scherer; J B Bouck; E J Sodergren; K C Worley; C M Rives; J H Gorrell; M L Metzker; S L Naylor; R S Kucherlapati; D L Nelson; G M Weinstock; Y Sakaki; A Fujiyama; M Hattori; T Yada; A Toyoda; T Itoh; C Kawagoe; H Watanabe; Y Totoki; T Taylor; J Weissenbach; R Heilig; W Saurin; F Artiguenave; P Brottier; T Bruls; E Pelletier; C Robert; P Wincker; D R Smith; L Doucette-Stamm; M Rubenfield; K Weinstock; H M Lee; J Dubois; A Rosenthal; M Platzer; G Nyakatura; S Taudien; A Rump; H Yang; J Yu; J Wang; G Huang; J Gu; L Hood; L Rowen; A Madan; S Qin; R W Davis; N A Federspiel; A P Abola; M J Proctor; R M Myers; J Schmutz; M Dickson; J Grimwood; D R Cox; M V Olson; R Kaul; C Raymond; N Shimizu; K Kawasaki; S Minoshima; G A Evans; M Athanasiou; R Schultz; B A Roe; F Chen; H Pan; J Ramser; H Lehrach; R Reinhardt; W R McCombie; M de la Bastide; N Dedhia; H Blöcker; K Hornischer; G Nordsiek; R Agarwala; L Aravind; J A Bailey; A Bateman; S Batzoglou; E Birney; P Bork; D G Brown; C B Burge; L Cerutti; H C Chen; D Church; M Clamp; R R Copley; T Doerks; S R Eddy; E E Eichler; T S Furey; J Galagan; J G Gilbert; C Harmon; Y Hayashizaki; D Haussler; H Hermjakob; K Hokamp; W Jang; L S Johnson; T A Jones; S Kasif; A Kaspryzk; S Kennedy; W J Kent; P Kitts; E V Koonin; I Korf; D Kulp; D Lancet; T M Lowe; A McLysaght; T Mikkelsen; J V Moran; N Mulder; V J Pollara; C P Ponting; G Schuler; J Schultz; G Slater; A F Smit; E Stupka; J Szustakowki; D Thierry-Mieg; J Thierry-Mieg; L Wagner; J Wallis; R Wheeler; A Williams; Y I Wolf; K H Wolfe; S P Yang; R F Yeh; F Collins; M S Guyer; J Peterson; A Felsenfeld; K A Wetterstrand; A Patrinos; M J Morgan; P de Jong; J J Catanese; K Osoegawa; H Shizuya; S Choi; Y J Chen; J Szustakowki
Journal:  Nature       Date:  2001-02-15       Impact factor: 49.962

Review 2.  Natural hybridization in primates: one evolutionary mechanism.

Authors:  Michael L Arnold; Axel Meyer
Journal:  Zoology (Jena)       Date:  2006-08-30       Impact factor: 2.240

3.  Global landscape of recent inferred Darwinian selection for Homo sapiens.

Authors:  Eric T Wang; Greg Kodama; Pierre Baldi; Robert K Moyzis
Journal:  Proc Natl Acad Sci U S A       Date:  2005-12-21       Impact factor: 11.205

4.  Bayesian inference of the demographic history of chimpanzees.

Authors:  Daniel Wegmann; Laurent Excoffier
Journal:  Mol Biol Evol       Date:  2010-01-29       Impact factor: 16.240

5.  Y-chromosome analysis confirms highly sex-biased dispersal and suggests a low male effective population size in bonobos (Pan paniscus).

Authors:  Jonas Eriksson; Heike Siedel; Dieter Lukas; Manfred Kayser; Axel Erler; Chie Hashimoto; Gottfried Hohmann; Christophe Boesch; Linda Vigilant
Journal:  Mol Ecol       Date:  2006-04       Impact factor: 6.185

6.  AIDS-protective HLA-B*27/B*57 and chimpanzee MHC class I molecules target analogous conserved areas of HIV-1/SIVcpz.

Authors:  Natasja G de Groot; Corrine M C Heijmans; Yvonne M Zoet; Arnoud H de Ru; Frank A Verreck; Peter A van Veelen; Jan W Drijfhout; Gaby G M Doxiadis; Edmond J Remarque; Ilias I N Doxiadis; Jon J van Rood; Frits Koning; Ronald E Bontrop
Journal:  Proc Natl Acad Sci U S A       Date:  2010-08-09       Impact factor: 11.205

7.  Bonobos fall within the genomic variation of chimpanzees.

Authors:  Anne Fischer; Kay Prüfer; Jeffrey M Good; Michel Halbwax; Victor Wiebe; Claudine André; Rebeca Atencia; Lawrence Mugisha; Susan E Ptak; Svante Pääbo
Journal:  PLoS One       Date:  2011-06-29       Impact factor: 3.240

8.  Aggressive assembly of pyrosequencing reads with mates.

Authors:  Jason R Miller; Arthur L Delcher; Sergey Koren; Eli Venter; Brian P Walenz; Anushka Brownley; Justin Johnson; Kelvin Li; Clark Mobarry; Granger Sutton
Journal:  Bioinformatics       Date:  2008-10-24       Impact factor: 6.937

9.  Analysis of chimpanzee history based on genome sequence alignments.

Authors:  Jennifer L Caswell; Swapan Mallick; Daniel J Richter; Julie Neubauer; Christine Schirmer; Sante Gnerre; David Reich
Journal:  PLoS Genet       Date:  2008-04-18       Impact factor: 5.917

Review 10.  Evaluation of the 3p21.3 tumour-suppressor gene cluster.

Authors:  L B Hesson; W N Cooper; F Latif
Journal:  Oncogene       Date:  2007-05-28       Impact factor: 9.867

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  136 in total

1.  Chimpanzees return favors at a personal cost.

Authors:  Martin Schmelz; Sebastian Grueneisen; Alihan Kabalak; Jürgen Jost; Michael Tomasello
Journal:  Proc Natl Acad Sci U S A       Date:  2017-06-19       Impact factor: 11.205

2.  Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone.

Authors:  Alison Cloutier; Timothy B Sackton; Phil Grayson; Michele Clamp; Allan J Baker; Scott V Edwards
Journal:  Syst Biol       Date:  2019-11-01       Impact factor: 15.683

3.  Finding the factors of reduced genetic diversity on X chromosomes of Macaca fascicularis: male-driven evolution, demography, and natural selection.

Authors:  Naoki Osada; Shigeki Nakagome; Shuhei Mano; Yosuke Kameoka; Ichiro Takahashi; Keiji Terao
Journal:  Genetics       Date:  2013-09-11       Impact factor: 4.562

Review 4.  The Y chromosomes of the great apes.

Authors:  Pille Hallast; Mark A Jobling
Journal:  Hum Genet       Date:  2017-03-06       Impact factor: 4.132

Review 5.  Great ape genomics.

Authors:  Jeffrey D Wall
Journal:  ILAR J       Date:  2013

6.  Primate genome architecture influences structural variation mechanisms and functional consequences.

Authors:  Omer Gokcumen; Verena Tischler; Jelena Tica; Qihui Zhu; Rebecca C Iskow; Eunjung Lee; Markus Hsi-Yang Fritz; Amy Langdon; Adrian M Stütz; Pavlos Pavlidis; Vladimir Benes; Ryan E Mills; Peter J Park; Charles Lee; Jan O Korbel
Journal:  Proc Natl Acad Sci U S A       Date:  2013-09-06       Impact factor: 11.205

7.  The core transcriptome of mammalian placentas and the divergence of expression with placental shape.

Authors:  Don L Armstrong; Michael R McGowen; Amy Weckle; Priyadarshini Pantham; Jason Caravas; Dalen Agnew; Kurt Benirschke; Sue Savage-Rumbaugh; Eviatar Nevo; Chong J Kim; Günter P Wagner; Roberto Romero; Derek E Wildman
Journal:  Placenta       Date:  2017-05-12       Impact factor: 3.481

Review 8.  Human brain evolution: transcripts, metabolites and their regulators.

Authors:  Mehmet Somel; Xiling Liu; Philipp Khaitovich
Journal:  Nat Rev Neurosci       Date:  2013-01-17       Impact factor: 34.870

9.  Thyroid autoantibodies are rare in nonhuman great apes and hypothyroidism cannot be attributed to thyroid autoimmunity.

Authors:  Holly Aliesky; Cynthia L Courtney; Basil Rapoport; Sandra M McLachlan
Journal:  Endocrinology       Date:  2013-10-03       Impact factor: 4.736

10.  Susceptibility of muridae cell lines to ecotropic murine leukemia virus and the cationic amino acid transporter 1 viral receptor sequences: implications for evolution of the viral receptor.

Authors:  Katsura Kakoki; Akio Shinohara; Mai Izumida; Yosuke Koizumi; Eri Honda; Goro Kato; Tsukasa Igawa; Hideki Sakai; Hideki Hayashi; Toshifumi Matsuyama; Tetsuo Morita; Chihiro Koshimoto; Yoshinao Kubo
Journal:  Virus Genes       Date:  2014-01-28       Impact factor: 2.332

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