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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
..., and size, we reconstructed the ancestral state of young TE insertions. The results showed that A. spatula has the lowest insertion rate among examined vertebrates (Fig. 3A; Supplemental Fig. S11). Additionally, we analyzed the copy number distribution of young TE families, revealing that gars exhibit...
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Research: Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization
- Kazuaki Yamaguchi,
- Yoshinobu Uno,
- Mitsutaka Kadota,
- Osamu Nishimura,
- Ryo Nozu,
- Kiyomi Murakumo,
- Rui Matsumoto,
- Keiichi Sato,
- and Shigehiro Kuraku
Genome Res. September 2023 33: 1527-1540; Published in Advance August 17, 2023, doi:10.1101/gr.276840.122
...Elasmobranch sequencing reveals evolutionary trends of vertebrate karyotype organization Kazuaki Yamaguchi1,6, Yoshinobu Uno1,7, Mitsutaka Kadota1, Osamu Nishimura1, Ryo Nozu2,8, Kiyomi Murakumo3, Rui Matsumoto3, Keiichi Sato2,3 and Shigehiro Kuraku1,4,5 1Laboratory for Phyloinformatics, RIKEN...
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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
..., revealing how the ancestral teleost became tetraploid.ResultsConstruction of TGD-aware teleost gene treesWe collected a data set of 101 vertebrate s, including 74 teleost fish, two nonteleost fish (bowfin and spotted gar, which did not undergo the teleost duplication or TGD), 20 other vertebrates of which...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...identified in this study between Apalone, Staurotypus, and Trachemys (chromosome nomenclature and homology as in B).Whole- comparisons between chicken and turtles reveal several -reshuffling eventsWe next explored the dynamics of karyotype evolution and reshuffling in turtles through comparative genomics...
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Research: Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus
- Nikolaos Vakirlis,
- Véronique Sarilar,
- Guénola Drillon,
- Aubin Fleiss,
- Nicolas Agier,
- Jean-Philippe Meyniel,
- Lou Blanpain,
- Alessandra Carbone,
- Hugo Devillers,
- Kenny Dubois,
- Alexandre Gillet-Markowska,
- Stéphane Graziani,
- Nguyen Huu-Vang,
- Marion Poirel,
- Cyrielle Reisser,
- Jonathan Schott,
- Joseph Schacherer,
- Ingrid Lafontaine,
- Bertrand Llorente,
- Cécile Neuvéglise,
- and Gilles Fischer
Genome Res. July 2016 26: 918-932; Published in Advance May 31, 2016, doi:10.1101/gr.204420.116
...Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus Nikolaos Vakirlis 1 , 6 , Véronique Sarilar 2 , 6 , Guénola Drillon 1 , 6 , Aubin Fleiss 1 , Nicolas Agier...
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Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
- Charles Plessy,
- Michael J. Mansfield,
- Aleksandra Bliznina,
- Aki Masunaga,
- Charlotte West,
- Yongkai Tan,
- Andrew W. Liu,
- Jan Grašič,
- María Sara del Río Pisula,
- Gaspar Sánchez-Serna,
- Marc Fabrega-Torrus,
- Alfonso Ferrández-Roldán,
- Vittoria Roncalli,
- Pavla Navratilova,
- Eric M. Thompson,
- Takeshi Onuma,
- Hiroki Nishida,
- Cristian Cañestro,
- and Nicholas M. Luscombe
Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
...al. 2020) and the Nextflow workflow system (Di Tommaso et al. 2017). The all-by-all pairwise alignments revealed an unexpected level of genomic rearrangement, and the most extreme case of scrambling was observed in the OKI–OSA (Fig. 1B) and OKI–BAR (Supplemental Fig. S2) comparisons. The line plot...
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Resource: A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes
- Jing Liu,
- Zongji Wang,
- Jing Li,
- Luohao Xu,
- Jiaqi Liu,
- Shaohong Feng,
- Chunxue Guo,
- Shengchan Chen,
- Zhanjun Ren,
- Jinpeng Rao,
- Kai Wei,
- Yuezhou Chen,
- Erich D. Jarvis,
- Guojie Zhang,
- and Qi Zhou
Genome Res. March 2021 31: 497-511; Published in Advance January 6, 2021, doi:10.1101/gr.271569.120
...that microchromosomes represent archaic linkage groups of ancestral vertebrates (Ohno et al. 1969; Tegelström and Ryttman 1981; Burt 2002; Uno et al. 2012). This was implicated by reconstruction of the ancestral vertebrate karyotype, first using the s of a few (Nakatani et al. 2007), and recently many more available...
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Research: The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications
- Jeramiah J. Smith and
- Melissa C. Keinath
Genome Res. August 2015 25: 1081-1090; Published in Advance June 5, 2015, doi:10.1101/gr.184135.114
...not explicitly test alternative evolutionary models. Unfortunately, existing lamprey assemblies do not permit the resolution of chromosome-scale patterns of homology or the robust reconstruction of ancestral vertebrate chromosomes, which are necessary to test assumptions of the 2R hypothesis.View larger version...
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Research: Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes
- Stephen R. Voss,
- D. Kevin Kump,
- Srikrishna Putta,
- Nathan Pauly,
- Anna Reynolds,
- Rema J. Henry,
- Saritha Basa,
- John A. Walker,
- and Jeramiah J. Smith
Genome Res. August 2011 21: 1306-1312; Published in Advance April 11, 2011, doi:10.1101/gr.116491.110
..., Morishita S. 2007. Reconstruction of the vertebrate ancestral reveals dynamic reorganization in early vertebrates. Genome Res 17: 1254–1265. Nanda I, Benisch P, Fetting D, Haaf T, Schmid M. 2011. Synteny conservation of chicken macrochromosomes 1-10 in different avian lineages revealed by cross...
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Resource: Cactus: Algorithms for genome multiple sequence alignment
- Benedict Paten,
- Dent Earl,
- Ngan Nguyen,
- Mark Diekhans,
- Daniel Zerbino,
- and David Haussler
Genome Res. September 2011 21: 1512-1528; Published in Advance June 10, 2011, doi:10.1101/gr.123356.111
...of the changes that separate ancestral sequences from their derived versions. Evolver therefore starts from a single root sequence. The root sequence and its annotations were taken from an actual human genomic loci (see Methods). We simulated forward evolution from the root for a total phylogenetic distance of 1...
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