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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...the formation of unfit MHC-I–APG recombinants. This theory, based on research in chicken and rat, assumes a single dominantly expressed MHC-I gene that coevolves with APGs (Kaufman 1999, 2015). Such a state has been suggested as ancestral for jawed vertebrates, with a “lucky” accident of a genomic rearrangement...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...−16) (Supplemental Table S8). To understand the enrichment pattern of disease phenotypes for young and old genes, we introduced a metric of the disease phenotype enrichment index (PEI), which quantifies the range of phenotypes across multiple systems (for details, see Methods). Our findings revealed that the most...
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Research: Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages
- Jennifer F. Hughes,
- Helen Skaletsky,
- Tatyana Pyntikova,
- Natalia Koutseva,
- Terje Raudsepp,
- Laura G. Brown,
- Daniel W. Bellott,
- Ting-Jan Cho,
- Shannon Dugan-Rocha,
- Ziad Khan,
- Colin Kremitzki,
- Catrina Fronick,
- Tina A. Graves-Lindsay,
- Lucinda Fulton,
- Wesley C. Warren,
- Richard K. Wilson,
- Elaine Owens,
- James E. Womack,
- William J. Murphy,
- Donna M. Muzny,
- Kim C. Worley,
- Bhanu P. Chowdhary,
- Richard A. Gibbs,
- and David C. Page
Genome Res. December 2020 30: 1716-1726; Published in Advance November 18, 2020, doi:10.1101/gr.269902.120
...–Y coevolution through gene amplification, and the selfish forces underlying this phenomenon, were dominatingly powerful among diverse mammalian lineages. Together with Y gene decay, X–Y arms races molded mammalian sex chromosomes and influenced the course of mammalian evolution.Mammalian sex chromosomes evolved...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...). Recombination rate usually varies considerably across chromosomes and genomic regions, and mapping this variation may shed light on the mechanistic control of where recombination is initiated. The reasons for such regional recombination rate variation have been studied in detail in a few organism groups...
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Research: Birth, evolution, and transmission of satellite-free mammalian centromeric domains
- Solomon G. Nergadze,
- Francesca M. Piras,
- Riccardo Gamba,
- Marco Corbo,
- Federico Cerutti,
- Joseph G.W. McCarter,
- Eleonora Cappelletti,
- Francesco Gozzo,
- Rebecca M. Harman,
- Douglas F. Antczak,
- Donald Miller,
- Maren Scharfe,
- Giulio Pavesi,
- Elena Raimondi,
- Kevin F. Sullivan,
- and Elena Giulotto
Genome Res. June 2018 28: 789-799; Published in Advance April 30, 2018, doi:10.1101/gr.231159.117
...that has not acquired repetitive sequences. Satellite-free centromeres were subsequently observed in chicken (Shang et al. 2010), orangutan (Locke et al. 2011), and potato (Gong et al. 2012).Examination of the centromere of horse Chromosome 11 in several individuals revealed that the satellite...
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Resource: Recovering genome rearrangements in the mammalian phylogeny
- Hao Zhao and
- Guillaume Bourque
Genome Res. May 2009 19: 934-942; doi:10.1101/gr.086009.108
...reveal highly variable rates of genomic rearrangements across different lineages. Genome Res. 15: 98–110. Bourque, G., Tesler, G., and Pevzner, P.A. 2006. The convergence of cytogenetics and rearrangement-based models for ancestral reconstruction. Genome Res. 16: 311–313. Cosner, M.E., Jansen, R...
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Research: An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
- Ignacio Maeso,
- Manuel Irimia,
- Juan J. Tena,
- Esther González-Pérez,
- David Tran,
- Vydianathan Ravi,
- Byrappa Venkatesh,
- Sonsoles Campuzano,
- José Luis Gómez-Skarmeta,
- and Jordi Garcia-Fernàndez
Genome Res. April 2012 22: 642-655; Published in Advance January 10, 2012, doi:10.1101/gr.132233.111
...: Highly divergent, pseudogenized exonic remnants are detectable in the chicken, anole lizard, and several mammalian s, including human (blue circles in Supplemental Fig. S12). The presence of Sowah2 ‘‘pseudoexons’’ across deeply diverged tetrapod lineages was surprising, since nonfunctional pseudogenic...
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PERSPECTIVE: Chicken genome: Current status and future opportunities
- David W. Burt
Genome Res. December 2005 15: 1692-1698; doi:10.1101/gr.4141805
....T., Tickle, C., Brown, W.R., Wilson, S.A., and Hubbard, S.J. 2002 . A comprehensive collection of chicken cDNAs. Curr. Biol. 12 : 1965 -1969. ↵ Bourque, G., Zdobnov, E.M., Bork, P., Pevzner, P.A., and Tesler, G. 2005 . Comparative architectures of mammalian and chicken s reveal highly variable rates...
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Forum: Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?
- Lutz Froenicke,
- Montserrat Garcia Caldés,
- Alexander Graphodatsky,
- Stefan Müller,
- Leslie A. Lyons,
- Terence J. Robinson,
- Marianne Volleth,
- Fengtang Yang,
- and Johannes Wienberg
Genome Res. March 2006 16: 306-310; doi:10.1101/gr.3955206
...and chicken s reveal highly variable rates of genomic rearrangements across different lineages. Genome Res. 15 : 98 –110. ↵ Chowdhary, B.P., Raudsepp, T., Fronicke, L., and Scherthan, H. 1998 . Emerging patterns of comparative organization in some mammalian species as revealed by Zoo-FISH. Genome Res. 8 : 577...
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Chicken Special/Letters: Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes
- Erik Axelsson,
- Matthew T. Webster,
- Nick G.C. Smith,
- David W. Burt,
- and Hans Ellegren
Genome Res. January 2005 15: 120-125; Published in Advance December 8, 2004, doi:10.1101/gr.3021305
...: 555 -556. ↵ Zhao, Z. and Boerwinkle, E. 2002 . Neighboring-nucleotide effects on single nucleotide polymorphisms: A study of 2.6 million polymorphisms across the human . Genome Res. 12 : 1679 -1686. Comparison of the chicken and turkey s reveals a higher rate of nucleotide divergence...

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