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Research: Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths
- Fangyuan Yang,
- Li-Jun Cao,
- Petr Nguyen,
- Zhong-Zheng Ma,
- Jin-Cui Chen,
- Wei Song,
- and Shu-Jun Wei
Genome Res. January 2025 35: 66-77; Published in Advance January 6, 2025, doi:10.1101/gr.279569.124
...-sex chromosomes. These fusions increase the number of sex-linked genes, which can thus evolve faster than genes on other chromosomes—a phenomenon known as the Faster-X/Z effect (Coyne 2018). Theory predicts that sex chromosome–autosome (SA) fusions should be rare when the diploid autosome count is greater than 15...
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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 Drosophila miranda, where TE accumulation has increased the level of silencing histone modifications (H3K9me3) and thus induced gene down-regulation (Zhou et al. 2013). Although the TE content of emu WS1 is comparable to that of the PAR and autosomes (9.3% vs. 7.3% and 9.8%), it has become 1.6-fold higher...
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Research: Evolution of genome structure in the Drosophila simulans species complex
- Mahul Chakraborty,
- Ching-Ho Chang,
- Danielle E. Khost,
- Jeffrey Vedanayagam,
- Jeffrey R. Adrion,
- Yi Liao,
- Kristi L. Montooth,
- Colin D. Meiklejohn,
- Amanda M. Larracuente,
- and J.J. Emerson
Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
...repetitive DNA to evolve, such as sex-chromosome meiotic drive. Such conflicts have driven the proliferation of sex-linked gene families in mammals and Drosophila (Cocquet et al. 2012; Kruger et al. 2019; for review, see Jaenike 2001). These conflicts may also impose selection pressures that trigger...
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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 whole- shotgun: release 3 of the Drosophila melanogaster euchromatic sequence. Genome Biol 3: RESEARCH0079. doi:10.1186/gb-2002-3-12-research0079 ↵Charlesworth B. 1996. The evolution of chromosomal sex determination and dosage compensation. Curr Biol 6: 149–162. doi:10.1016/S0960...
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Research: The evolution of sex-biased gene expression in the Drosophila brain
- Samuel Khodursky,
- Nicolas Svetec,
- Sylvia M. Durkin,
- and Li Zhao
Genome Res. June 2020 30: 874-884; Published in Advance June 18, 2020, doi:10.1101/gr.259069.119
...-biased autosomal genes may show a high degree of expression variability.Rates of sex-bias turnover are high and chromosome specificThese observations prompted us to look at the evolution of sex-biased genes at the expression level. First, we looked at the turnover of sex-biased genes between the three Drosophila...
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Research: Genomes of Ellobius species provide insight into the evolutionary dynamics of mammalian sex chromosomes
- Eskeatnaf Mulugeta,
- Evelyne Wassenaar,
- Esther Sleddens-Linkels,
- Wilfred F.J. van IJcken,
- Edith Heard,
- J. Anton Grootegoed,
- Walter Just,
- Joost Gribnau,
- and Willy M. Baarends
Genome Res. September 2016 26: 1202-1210; Published in Advance August 10, 2016, doi:10.1101/gr.201665.115
...across mammals. Nature 508: 488–493. Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR, et al. 2011. Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nat Genet 43...
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Research: A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster
- Ge Gao,
- Maria D. Vibranovski,
- Li Zhang,
- Zheng Li,
- Ming Liu,
- Yong E. Zhang,
- Xinmin Li,
- Wenxia Zhang,
- Qichang Fan,
- Nicholas W. VanKuren,
- Manyuan Long,
- and Liping Wei
Genome Res. April 2014 24: 629-638; Published in Advance January 9, 2014, doi:10.1101/gr.165837.113
...on Drosophila autosomes and X chromosomes and suggests that the pattern is shaped by natural selection acting on male functions. Our results contribute to a global picture of sex chromosome evolution in the Drosophila .MethodsData sourcesGenome sequence and annotations were obtained from the UCSC Genome Browser...
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Research: Age-dependent chromosomal distribution of male-biased genes in Drosophila
- Yong E. Zhang,
- Maria D. Vibranovski,
- Benjamin H. Krinsky,
- and Manyuan Long
Genome Res. November 2010 20: 1526-1533; Published in Advance August 26, 2010, doi:10.1101/gr.107334.110
...Age-dependent chromosomal distribution of male-biased genes in Drosophila Yong E. Zhang 1 , Maria D. Vibranovski 1 , Benjamin H. Krinsky 2 and Manyuan Long 1 , 2 , 3 1 Department of Ecology and Evolution, University of Chicago...
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Research: Human postmeiotic sex chromatin and its impact on sex chromosome evolution
- Ho-Su Sin,
- Yosuke Ichijima,
- Eitetsu Koh,
- Mikio Namiki,
- and Satoshi H. Namekawa
Genome Res. May 2012 22: 827-836; Published in Advance February 28, 2012, doi:10.1101/gr.135046.111
...). Compensation of gene expression by autosomal X-retrotransposed geneswas also found in a variety of organisms includingDrosophila (Vibranovski et al. 2009), suggesting that compensation by the retrotransposed copies is a common strategy among species. Of note, these classes of genes are housekeeping genes...
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Research: A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence
- Tina T. Hu,
- Michael B. Eisen,
- Kevin R. Thornton,
- and Peter Andolfatto
Genome Res. January 2013 23: 89-98; Published in Advance August 30, 2012, doi:10.1101/gr.141689.112
...reported. Specifically, we find that Drosophila melanogaster evolves faster than D. simulans at all annotated classes of sites, including putatively neutrally evolving sites found in minimal introns. While this may be partly explained by a higher mutation rate in D. melanogaster , we also find...
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