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Resource: Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution
- Flavia Angela Maria Maggiolini,
- Ashley D. Sanders,
- Colin James Shew,
- Arvis Sulovari,
- Yafei Mao,
- Marta Puig,
- Claudia Rita Catacchio,
- Maria Dellino,
- Donato Palmisano,
- Ludovica Mercuri,
- Miriana Bitonto,
- David Porubský,
- Mario Cáceres,
- Evan E. Eichler,
- Mario Ventura,
- Megan Y. Dennis,
- Jan O. Korbel,
- and Francesca Antonacci
Genome Res. November 2020 30: 1680-1693; Published in Advance October 22, 2020, doi:10.1101/gr.265322.120
...class of SVs, first identified by Sturtevant in 1917 (Sturtevant 1917), that play a key dual role in primate evolution and predisposition to disease. Chromosome inversions are the most common rearrangements differentiating humans and the great ape species at the karyotypic level (Yunis et al. 1980...
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Research: Single-cell sequencing deciphers a convergent evolution of copy number alterations from primary to circulating tumor cells
- Yan Gao,
- Xiaohui Ni,
- Hua Guo,
- Zhe Su,
- Yi Ba,
- Zhongsheng Tong,
- Zhi Guo,
- Xin Yao,
- Xixi Chen,
- Jian Yin,
- Zhao Yan,
- Lin Guo,
- Ying Liu,
- Fan Bai,
- X. Sunney Xie,
- and Ning Zhang
Genome Res. August 2017 27: 1312-1322; Published in Advance May 9, 2017, doi:10.1101/gr.216788.116
...- sequencing. (C) A two-step model to elucidate the CNAs involving four regions on Chromosome 8 containing theMYC gene. Sequential FoSTeS events first caused the CNA regions to be duplicated, after which homologous recombination further amplified these duplicated regions to extreme copy numbers. Convergent...
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Research: Primate segmental duplication creates novel promoters for the LRRC37 gene family within the 17q21.31 inversion polymorphism region
- Cemalettin Bekpen,
- Ibrahim Tastekin,
- Priscillia Siswara,
- Cezmi A. Akdis,
- and Evan E. Eichler
Genome Res. June 2012 22: 1050-1058; Published in Advance March 14, 2012, doi:10.1101/gr.134098.111
...for this article.] Gene duplication events are one of the primary sources for the evolution of novel gene functions and are, thus, important in our understanding of the evolution of species (Ohno 1970). The human shows a complex pattern of interspersed segmental duplication typified by a mosaic pattern...
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LETTER: Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice
- Jianxin Ma and
- Scott A. Jackson
Genome Res. February 2006 16: 251-259; Published in Advance December 14, 2005, doi:10.1101/gr.4583106
...-1479. ↵ Horvath, J.E., Gulden, C.L., Vallente, R.U., Eichler, M.Y., Ventura, M., McPherson, J.D., Graves, T.A., Wilson, R.K., Schwartz, S., Rocchi, M., et al. 2005 . Punctuated duplication seeding events during the evolution of human chromosome 2p11. Genome Res. 15 : 914 -927. ↵ International Rice...
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LETTER: Dynamic evolution at pericentromeres
- Anne E. Hall,
- Gregory C. Kettler,
- and Daphne Preuss
Genome Res. March 2006 16: 355-364; Published in Advance February 6, 2006, doi:10.1101/gr.4399206
...comparative FISH in primates has revealed that initial “seeding” pericentromere duplications occurred as a punctuated event prior to the divergence of humans and great apes 10–20 million years ago (Mya), with subsequent secondary dispersal duplications during the radiation of humans, chimps, and gorillas...
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Research: Evolutionary dynamism of the primate LRRC37 gene family
- Giuliana Giannuzzi,
- Priscillia Siswara,
- Maika Malig,
- Tomas Marques-Bonet,
- NISC Comparative Sequencing Program,
- James C. Mullikin,
- Mario Ventura,
- and Evan E. Eichler
Genome Res. January 2013 23: 46-59; Published in Advance October 11, 2012, doi:10.1101/gr.138842.112
...organization of LRRC37 copies. (C ) FISH results of representative lemur BAC clones confirm a single cluster of tandem duplicated copies on lemur chromosome 17. Primate LRRC37 gene family evolution Genome Research 51 www..org various sources (Fig. 7; Supplemental Note) revealing extensive alternative splicing...
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LETTER: Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions
- Stefan Kirsch,
- Claudia Münch,
- Zhaoshi Jiang,
- Ze Cheng,
- Lin Chen,
- Christiane Batz,
- Evan E. Eichler,
- and Werner Schempp
Genome Res. July 2008 18: 1030-1042; Published in Advance April 29, 2008, doi:10.1101/gr.076711.108
...to the pericentromeric regions in chimpanzee and human. This suggests an evolutionary shift in the direction of duplicative transposition events from subtelomeric in Old World monkeys to pericentromeric in the human/ape lineage. Extensive chromosomal relocation of autosomal-duplicated sequences from euchromatin...
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Research: Allelic diversification after transposable element exaptation promoted gsdf as the master sex determining gene of sablefish
- Amaury Herpin,
- Manfred Schartl,
- Alexandra Depincé,
- Yann Guiguen,
- Julien Bobe,
- Aurélie Hua-Van,
- Edward S. Hayman,
- Anna Octavera,
- Goro Yoshizaki,
- Krista M. Nichols,
- Giles W. Goetz,
- and J. Adam Luckenbach
Genome Res. August 2021 31: 1366-1380; Published in Advance June 28, 2021, doi:10.1101/gr.274266.120
...may occur by rare punctual but rather large changes, or by more steady and gradual transformations. It can therefore be asked whether genetic changes underlying morphological, physiological, and/or behavioral innovations during evolution occur in a punctual manner, whereby a single mutational event...
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Research: Single worm transcriptomics identifies a developmental core network of oscillating genes with deep conservation across nematodes
- Shuai Sun,
- Christian Rödelsperger,
- and Ralf J. Sommer
Genome Res. September 2021 31: 1590-1601; Published in Advance July 22, 2021, doi:10.1101/gr.275303.121
...of oscillatory gene expression between the two model organisms P. pacificus and C. elegans and associated evolutionary dynamics.The evolution of novelty and phenotypic divergence depends on two major molecular processes. First, the emergence of new genes through gene duplication, divergence, and de novo...
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RESOURCE: DupMasker: A tool for annotating primate segmental duplications
- Zhaoshi Jiang,
- Robert Hubley,
- Arian Smit,
- and Evan E. Eichler
Genome Res. August 2008 18: 1362-1368; Published in Advance May 23, 2008, doi:10.1101/gr.078477.108
...comparison between sequences from a chimpanzee BAC clone (AC097264.4) and its orthologous locus on human chromosome 17 predicts a large (∼80 kbp) chimpanzee-specific insertion. DupMasker analysis suggests that the insertion is the result of a duplicative transposition event composed of segmental duplications...

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