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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 APGs. MHC-I genes exhibit lineage-specific duplications and signs of concerted evolution, resulting in poorly resolved phylogenies. In contrast, MHC-II genes are more conserved and exhibit extensive trans-species polymorphism. Expression and polymorphism patterns identify putative nonclassical MHC...
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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
...of birds in order to test the hypothesis that emu and other ratites have the lowest lineage-specific chromosome evolution rate among birds, therefore best representing the ancestral avian configuration. We further compared the chromatin architectures between the emu macro- and microchromosomes, and between...
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Research: Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets
- Matthew D. Pollard,
- Wynn K. Meyer,
- and Emily E. Puckett
Genome Res. December 2024 34: 2176-2189; Published in Advance November 22, 2024, doi:10.1101/gr.278930.124
...-occurred with evolution toward herbivory. The ancestral mammalian diet was insectivorous (Gill et al. 2014) and would be treated as completely carnivorous in our study. Thus, less carnivorous diets represent derived states that are likely associated with great molecular and phenotypic change as entirely new dietary...
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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
...and chromosome numbers (Montiel et al. 2016), namely, the Spiny Softshell Turtle Apalone spinifera (ZZ/ZW, 2n = 66) (Badenhorst et al. 2013) and the Northern Giant Musk Turtle Staurotypus triporcatus (XX/XY, 2n = 54) (Sites et al. 1979). To illuminate amniote evolution, we not only test for changes to the linear...
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Research: The life history of retrocopies illuminates the evolution of new mammalian genes
- Francesco Nicola Carelli,
- Takashi Hayakawa,
- Yasuhiro Go,
- Hiroo Imai,
- Maria Warnefors,
- and Henrik Kaessmann
Genome Res. March 2016 26: 301-314; Published in Advance January 4, 2016, doi:10.1101/gr.198473.115
...Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan New genes contribute substantially to adaptive evolutionary innovation, but the functional evolution of new mammalian genes has been little explored at a broad scale. Previous work...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...a broader conservation across the class, with the exception of the Lepidoptera (Pease and Hahn 2012).Previous work has documented convergent gene content on the mammalian Y, avian W, and snake W Chromosomes (Bellott and Page 2021) and convergent evolution of mammalian X and avian Z Chromosome gene content...
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Resource: The pig X and Y Chromosomes: structure, sequence, and evolution
- Benjamin M. Skinner,
- Carole A. Sargent,
- Carol Churcher,
- Toby Hunt,
- Javier Herrero,
- Jane E. Loveland,
- Matt Dunn,
- Sandra Louzada,
- Beiyuan Fu,
- William Chow,
- James Gilbert,
- Siobhan Austin-Guest,
- Kathryn Beal,
- Denise Carvalho-Silva,
- William Cheng,
- Daria Gordon,
- Darren Grafham,
- Matt Hardy,
- Jo Harley,
- Heidi Hauser,
- Philip Howden,
- Kerstin Howe,
- Kim Lachani,
- Peter J.I. Ellis,
- Daniel Kelly,
- Giselle Kerry,
- James Kerwin,
- Bee Ling Ng,
- Glen Threadgold,
- Thomas Wileman,
- Jonathan M.D. Wood,
- Fengtang Yang,
- Jen Harrow,
- Nabeel A. Affara,
- and Chris Tyler-Smith
Genome Res. January 2016 26: 130-139; Published in Advance November 11, 2015, doi:10.1101/gr.188839.114
...substantially increased and brings the porcine X closer in gene content to other well-sequenced mammalian X Chromosomes (e.g., human and mouse). Skinner et al. 132 Genome Research www..org identifying those pig homologs present. Many of the ancestral Xrelated genes previously reported in other mammalian Y...
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Research: The evolution of duplicate gene expression in mammalian organs
- Katerina Guschanski,
- Maria Warnefors,
- and Henrik Kaessmann
Genome Res. September 2017 27: 1461-1474; Published in Advance July 25, 2017, doi:10.1101/gr.215566.116
...-specific functions during more recent mammalian evolution. Lineage-specific and young duplications also contained higher than expected proportions of genes specifically expressed in the liver (Fig. 4B,C; Supplemental Figs. S7, S8). However, in contrast to the testis, liver-specific genes tend to be highly expressed...
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Research: Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals
- Daniel W. Bellott and
- David C. Page
Genome Res. February 2021 31: 198-210; Published in Advance January 21, 2021, doi:10.1101/gr.268516.120
...Tables S1–S6; Supplemental Methods). Previous reconstructions of caenophidian sex chromosome evolution used lizard Chromosome 6 as a proxy for the ancestral autosomes and identified 1135 ancestral Z genes (Vicoso et al. 2013a; Yin et al. 2016). We began our search for ancestral Z-linked genes...
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Method: A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y
- Marta Tomaszkiewicz,
- Samarth Rangavittal,
- Monika Cechova,
- Rebeca Campos Sanchez,
- Howard W. Fescemyer,
- Robert Harris,
- Danling Ye,
- Patricia C.M. O'Brien,
- Rayan Chikhi,
- Oliver A. Ryder,
- Malcolm A. Ferguson-Smith,
- Paul Medvedev,
- and Kateryna D. Makova
Genome Res. April 2016 26: 530-540; Published in Advance March 2, 2016, doi:10.1101/gr.199448.115
...(Rozen et al. 2003; Graves 2010). Even when the Y is targeted, its unusual highly repetitive structure makes it the most challenging mammalian chromosome to sequence and assemble. Indeed, although the X has largely retained the ancestral autosomal structure and gene content (Graves 2010), the Y has...
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