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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...studies have sought to catalog driver events occurring in hundreds of cancer genes across different tumor types (Martincorena and Campbell 2015; Chung et al. 2016; Tokheim and Karchin 2019; Dietlein et al. 2020; Kumar et al. 2020; The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020...
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Research: Evidence for selfing in a vertebrate from whole-genome sequencing
- Astrid Böhne,
- Zeynep Oğuzhan,
- Ioannis Chrysostomakis,
- Simon Vitt,
- Denis Meuthen,
- Sebastian Martin,
- Sandra Kukowka,
- and Timo Thünken
Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
...of sister chromatids, this leads to offspring being homozygous (Lampert 2008). Offspring production by an aborted meiosis II and gamete duplication has the same genetic consequences (see Fig. 1; Asher 1970). In automixis with central fusion, products of meiosis I fuse and give rise to offspring s, which...
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Research: An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
- Elise Parey,
- Alexandra Louis,
- Jérôme Montfort,
- Yann Guiguen,
- Hugues Roest Crollius,
- and Camille Berthelot
Genome Res. September 2022 32: 1685-1697; Published in Advance August 12, 2022, doi:10.1101/gr.276953.122
...duplicated regions maintained tetraploidy for more than 60 million years, with three chromosome pairs diverging genetically only after the separation of major teleost families. This evidence suggests that the teleost ancestor was an autopolyploid. Further, we find evidence for biased gene retention along...
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Letter: Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates
- Karin S. Kassahn,
- Vinh T. Dang,
- Simon J. Wilkins,
- Andrew C. Perkins,
- and Mark A. Ragan
Genome Res. August 2009 19: 1404-1418; Published in Advance May 13, 2009, doi:10.1101/gr.086827.108
...Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates Karin S. Kassahn 1 , Vinh T. Dang 1 , Simon J. Wilkins 2 , Andrew C. Perkins 2 and Mark A. Ragan 1 , 3 1...
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RESOURCE: The zebrafish gene map defines ancestral vertebrate chromosomes
- Ian G. Woods,
- Catherine Wilson,
- Brian Friedlander,
- Patricia Chang,
- Daengnoy K. Reyes,
- Rebecca Nix,
- Peter D. Kelly,
- Felicia Chu,
- John H. Postlethwait,
- and William S. Talbot
Genome Res. September 2005 15: 1307-1314; Published in Advance August 18, 2005, doi:10.1101/gr.4134305
..., although similar overall numbers of duplicated genes may have been retained in these two species. These differences in retention of duplicated genes are consistent with the proposal that divergent resolution may have facilitated the vast species radiation observed in teleosts. Finally, our three...
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Research: Global deceleration of gene evolution following recent genome hybridizations in fungi
- Sira Sriswasdi,
- Masako Takashima,
- Ri-ichiroh Manabe,
- Moriya Ohkuma,
- Takashi Sugita,
- and Wataru Iwasaki
Genome Res. August 2016 26: 1081-1090; Published in Advance July 20, 2016, doi:10.1101/gr.205948.116
...-8568, Japan; 6Atmosphere and Ocean Research Institute, University of Tokyo, Kashiwa, Chiba 277-8564, Japan Corresponding authors: sirasris@bs.s.u-tokyo.ac.jp , iwasaki@bs.s.u-tokyo.ac.jp Abstract Polyploidization events such as whole-genome duplication and inter...
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Methods: Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes
- Antoine Barrière,
- Shiaw-Pyng Yang,
- Elizabeth Pekarek,
- Cristel G. Thomas,
- Eric S. Haag,
- and Ilya Ruvinsky
Genome Res. March 2009 19: 470-480; Published in Advance February 9, 2009, doi:10.1101/gr.081851.108
.... Here we show that despite this inbreeding, the heterozygous fraction of the whole genome shotgun assemblies of three gonochoristic Caenorhabditis species, C. brenneri , C. remanei , and C. japonica , is considerable. We first demonstrate experimentally that independently assembled sequence...
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ARTICLE: Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
- Hiroshi Kikuta,
- Mary Laplante,
- Pavla Navratilova,
- Anna Z. Komisarczuk,
- Pär G. Engström,
- David Fredman,
- Altuna Akalin,
- Mario Caccamo,
- Ian Sealy,
- Kerstin Howe,
- Julien Ghislain,
- Guillaume Pezeron,
- Philippe Mourrain,
- Staale Ellingsen,
- Andrew C. Oates,
- Christine Thisse,
- Bernard Thisse,
- Isabelle Foucher,
- Birgit Adolf,
- Andrea Geling,
- Boris Lenhard,
- and Thomas S. Becker
Genome Res. May 2007 17: 545-555; Published in Advance March 26, 2007, doi:10.1101/gr.6086307
...into and beyond adjacent transcriptional units. We termed these chromosomal segments genomic regulatory blocks (GRBs). After whole genome duplication in teleosts, GRBs, including HCNEs and target genes, were often maintained in both copies, while bystander genes were typically lost from one GRB, strongly...
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LETTER: Uneven chromosome contraction and expansion in the maize genome
- Rémy Bruggmann,
- Arvind K. Bharti,
- Heidrun Gundlach,
- Jinsheng Lai,
- Sarah Young,
- Ana C. Pontaroli,
- Fusheng Wei,
- Georg Haberer,
- Galina Fuks,
- Chunguang Du,
- Christina Raymond,
- Matt C. Estep,
- Renyi Liu,
- Jeffrey L. Bennetzen,
- Agnes P. Chan,
- Pablo D. Rabinowicz,
- John Quackenbush,
- W. Brad Barbazuk,
- Rod A. Wing,
- Bruce Birren,
- Chad Nusbaum,
- Steve Rounsley,
- Klaus F.X. Mayer,
- and Joachim Messing
Genome Res. October 2006 16: 1241-1251; Published in Advance August 10, 2006, doi:10.1101/gr.5338906
...a similar whole genome duplication event, has only one orthologous region (4.9 Mb) on the short arm of chromosome 3, and can be used as reference for the maize homoeologous regions. Alignment of the three regions allowed identification of syntenic blocks, and indicated that the maize regions have undergone...
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Research: Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal
- Pille Hallast,
- Pierpaolo Maisano Delser,
- Chiara Batini,
- Daniel Zadik,
- Mariano Rocchi,
- Werner Schempp,
- Chris Tyler-Smith,
- and Mark A. Jobling
Genome Res. April 2016 26: 427-439; Published in Advance February 16, 2016, doi:10.1101/gr.198754.115
...in the species phylogenies (Supplemental Table S2) suggests that hidden structural variants such as duplications are not leading to a high number of errors. A more serious potential problem is differential capture of nonhuman sequences, depending on their degree of divergence from the human reference...
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