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author Mao, Yafei
Catacchio, Claudia R.
Hillier, LaDeana W.
Porubsky, David
Li, Ruiyang
Sulovari, Arvis
Fernandes, Jason D.
Montinaro, Francesco
Gordon, David S.
Storer, Jessica M.
Haukness, Marina
Fiddes, Ian T.
Murali, Shwetha Canchi
Dishuck, Philip C.
Hsieh, PingHsun
Harvey, William T.
Audano, Peter A.
Mercuri, Ludovica
Piccolo, Ilaria
Antonacci, Francesca
Munson, Katherine M.
Lewis, Alexandra P.
Baker, Carl
Underwood, Jason G.
Hoekzema, Kendra
Huang, Tzu-Hsueh
Sorensen, Melanie
Walker, Jerilyn A.
Hoffman, Jinna
Thibaud-Nissen, Françoise
Salama, Sofie R.
Pang, Andy W. C.
Lee, Joyce
Hastie, Alex R.
Paten, Benedict
Batzer, Mark A.
Diekhans, Mark
Ventura, Mario
Eichler, Evan E.
author_facet Mao, Yafei
Catacchio, Claudia R.
Hillier, LaDeana W.
Porubsky, David
Li, Ruiyang
Sulovari, Arvis
Fernandes, Jason D.
Montinaro, Francesco
Gordon, David S.
Storer, Jessica M.
Haukness, Marina
Fiddes, Ian T.
Murali, Shwetha Canchi
Dishuck, Philip C.
Hsieh, PingHsun
Harvey, William T.
Audano, Peter A.
Mercuri, Ludovica
Piccolo, Ilaria
Antonacci, Francesca
Munson, Katherine M.
Lewis, Alexandra P.
Baker, Carl
Underwood, Jason G.
Hoekzema, Kendra
Huang, Tzu-Hsueh
Sorensen, Melanie
Walker, Jerilyn A.
Hoffman, Jinna
Thibaud-Nissen, Françoise
Salama, Sofie R.
Pang, Andy W. C.
Lee, Joyce
Hastie, Alex R.
Paten, Benedict
Batzer, Mark A.
Diekhans, Mark
Ventura, Mario
Eichler, Evan E.
author_sort Mao, Yafei
collection PubMed
description The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation(1,2). Here we describe a fully annotated, high-quality bonobo genome assembly, which was constructed without guidance from reference genomes by applying a multiplatform genomics approach. We generate a bonobo genome assembly in which more than 98% of genes are completely annotated and 99% of the gaps are closed, including the resolution of about half of the segmental duplications and almost all of the full-length mobile elements. We compare the bonobo genome to those of other great apes(1,3–5) and identify more than 5,569 fixed structural variants that specifically distinguish the bonobo and chimpanzee lineages. We focus on genes that have been lost, changed in structure or expanded in the last few million years of bonobo evolution. We produce a high-resolution map of incomplete lineage sorting and estimate that around 5.1% of the human genome is genetically closer to chimpanzee or bonobo and that more than 36.5% of the genome shows incomplete lineage sorting if we consider a deeper phylogeny including gorilla and orangutan. We also show that 26% of the segments of incomplete lineage sorting between human and chimpanzee or human and bonobo are non-randomly distributed and that genes within these clustered segments show significant excess of amino acid replacement compared to the rest of the genome.
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spelling pubmed-81723812021-06-17 A high-quality bonobo genome refines the analysis of hominid evolution Mao, Yafei Catacchio, Claudia R. Hillier, LaDeana W. Porubsky, David Li, Ruiyang Sulovari, Arvis Fernandes, Jason D. Montinaro, Francesco Gordon, David S. Storer, Jessica M. Haukness, Marina Fiddes, Ian T. Murali, Shwetha Canchi Dishuck, Philip C. Hsieh, PingHsun Harvey, William T. Audano, Peter A. Mercuri, Ludovica Piccolo, Ilaria Antonacci, Francesca Munson, Katherine M. Lewis, Alexandra P. Baker, Carl Underwood, Jason G. Hoekzema, Kendra Huang, Tzu-Hsueh Sorensen, Melanie Walker, Jerilyn A. Hoffman, Jinna Thibaud-Nissen, Françoise Salama, Sofie R. Pang, Andy W. C. Lee, Joyce Hastie, Alex R. Paten, Benedict Batzer, Mark A. Diekhans, Mark Ventura, Mario Eichler, Evan E. Nature Article The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation(1,2). Here we describe a fully annotated, high-quality bonobo genome assembly, which was constructed without guidance from reference genomes by applying a multiplatform genomics approach. We generate a bonobo genome assembly in which more than 98% of genes are completely annotated and 99% of the gaps are closed, including the resolution of about half of the segmental duplications and almost all of the full-length mobile elements. We compare the bonobo genome to those of other great apes(1,3–5) and identify more than 5,569 fixed structural variants that specifically distinguish the bonobo and chimpanzee lineages. We focus on genes that have been lost, changed in structure or expanded in the last few million years of bonobo evolution. We produce a high-resolution map of incomplete lineage sorting and estimate that around 5.1% of the human genome is genetically closer to chimpanzee or bonobo and that more than 36.5% of the genome shows incomplete lineage sorting if we consider a deeper phylogeny including gorilla and orangutan. We also show that 26% of the segments of incomplete lineage sorting between human and chimpanzee or human and bonobo are non-randomly distributed and that genes within these clustered segments show significant excess of amino acid replacement compared to the rest of the genome. Nature Publishing Group UK 2021-05-05 2021 /pmc/articles/PMC8172381/ /pubmed/33953399 http://dx.doi.org/10.1038/s41586-021-03519-x Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Mao, Yafei
Catacchio, Claudia R.
Hillier, LaDeana W.
Porubsky, David
Li, Ruiyang
Sulovari, Arvis
Fernandes, Jason D.
Montinaro, Francesco
Gordon, David S.
Storer, Jessica M.
Haukness, Marina
Fiddes, Ian T.
Murali, Shwetha Canchi
Dishuck, Philip C.
Hsieh, PingHsun
Harvey, William T.
Audano, Peter A.
Mercuri, Ludovica
Piccolo, Ilaria
Antonacci, Francesca
Munson, Katherine M.
Lewis, Alexandra P.
Baker, Carl
Underwood, Jason G.
Hoekzema, Kendra
Huang, Tzu-Hsueh
Sorensen, Melanie
Walker, Jerilyn A.
Hoffman, Jinna
Thibaud-Nissen, Françoise
Salama, Sofie R.
Pang, Andy W. C.
Lee, Joyce
Hastie, Alex R.
Paten, Benedict
Batzer, Mark A.
Diekhans, Mark
Ventura, Mario
Eichler, Evan E.
A high-quality bonobo genome refines the analysis of hominid evolution
title A high-quality bonobo genome refines the analysis of hominid evolution
title_full A high-quality bonobo genome refines the analysis of hominid evolution
title_fullStr A high-quality bonobo genome refines the analysis of hominid evolution
title_full_unstemmed A high-quality bonobo genome refines the analysis of hominid evolution
title_short A high-quality bonobo genome refines the analysis of hominid evolution
title_sort high-quality bonobo genome refines the analysis of hominid evolution
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8172381/
https://www.ncbi.nlm.nih.gov/pubmed/33953399
http://dx.doi.org/10.1038/s41586-021-03519-x
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