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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
..., Vancouver V6T 1Z4, Canada Corresponding author: liping_ban@163.comAbstractWe present the first chromosome-level assembly of the grasshopper, Locusta migratoria, one of the largest insect s. We use coverage differences between females (XX) and males (X0) to identify the X Chromosome gene content, and find...
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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
...orthologous X Chromosome regions. (A) Alignment corresponding to ∼51–53 Mb of the human X Chromosome. The mouse X Chromosome has been rearranged within this region, and the two distant regions are shown. (B) Alignment corresponding to 154–155.6 Mb of the human X Chromosome. Genes located within the distal...
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Research: Large palindromes on the primate X Chromosome are preserved by natural selection
- Emily K. Jackson,
- Daniel W. Bellott,
- Ting-Jan Cho,
- Helen Skaletsky,
- Jennifer F. Hughes,
- Tatyana Pyntikova,
- and David C. Page
Genome Res. August 2021 31: 1337-1352; Published in Advance July 21, 2021, doi:10.1101/gr.275188.120
...Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Corresponding author: dcpage@wi.mit.eduAbstractMammalian sex chromosomes carry large palindromes that harbor protein-coding gene families with testis-biased expression. However, there are few known examples...
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Research: Quantitative analysis of Y-Chromosome gene expression across 36 human tissues
- Alexander K. Godfrey,
- Sahin Naqvi,
- Lukáš Chmátal,
- Joel M. Chick,
- Richard N. Mitchell,
- Steven P. Gygi,
- Helen Skaletsky,
- and David C. Page
Genome Res. June 2020 30: 860-873; Published in Advance May 27, 2020, doi:10.1101/gr.261248.120
..., USA Corresponding author: dcpage@wi.mit.eduAbstractLittle is known about how human Y-Chromosome gene expression directly contributes to differences between XX (female) and XY (male) individuals in nonreproductive tissues. Here, we analyzed quantitative profiles of Y-Chromosome gene expression across...
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Research: Regional epigenetic differentiation of the Z Chromosome between sexes in a female heterogametic system
- Dan Sun,
- Donna L. Maney,
- Thomas S. Layman,
- Paramita Chatterjee,
- and Soojin V. Yi
Genome Res. October 2019 29: 1673-1684; Published in Advance September 23, 2019, doi:10.1101/gr.248641.119
...Corresponding author: soojinyi@gatech.eduAbstractIn male heterogametic systems, the X Chromosome is epigenetically differentiated between males and females, to facilitate dosage compensation. For example, the X Chromosome in female mammals is largely inactivated. Relative to well-studied male heterogametic...
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Research: Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation
- Wesley A. Brashear,
- Terje Raudsepp,
- and William J. Murphy
Genome Res. December 2018 28: 1841-1851; Published in Advance October 31, 2018, doi:10.1101/gr.237586.118
...of notable events in felid Y Chromosome evolution.Three ampliconic MSY genes arose from ancestral X–Y homologs: CUL4BY, CLDN34Y, and TSPY1. No single scaffold contained the entire coding sequence of CUL4BY. Three scaffolds—Y12, Y15, and Y18—had sequences that corresponded to the first five to nine exons...
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Research: Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution
- Sahin Naqvi,
- Daniel W. Bellott,
- Kathy S. Lin,
- and David C. Page
Genome Res. April 2018 28: 474-483; Published in Advance February 15, 2018, doi:10.1101/gr.230433.117
...Institute of Technology, Cambridge, Massachusetts 02139, USA; 4Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA Corresponding author: dcpage@wi.mit.eduAbstractMammalian X and Y Chromosomes evolved from an ordinary autosomal pair. Genetic decay of the Y led to X...
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Research: Extreme heterochiasmy and high rates of sex-reversed recombination result in large yet homomorphic sex chromosomes in the Emei moustache toad
- Siyu Xie,
- Jun Li,
- Wanyan Chen,
- Lydia J.M. Fong,
- Chunhua Huang,
- Yan Feng,
- Qingbo Ai,
- Mian Zhao,
- Judith E. Mank,
- and Hua Wu
Genome Res. June 2025 35: 1325-1336; Published in Advance April 24, 2025, doi:10.1101/gr.280161.124
...of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada Corresponding author: wuhua@ccnu.edu.cnAbstractUnlike the highly degenerated sex chromosomes in birds and mammals, many amphibians possess homomorphic sex chromosomes, which may result...
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Research: Random replication of the inactive X chromosome
- Amnon Koren and
- Steven A. McCarroll
Genome Res. January 2014 24: 64-69; Published in Advance September 24, 2013, doi:10.1101/gr.161828.113
..., in fractional units, and the X chromosome evolutionary strata. (P) Pseudoautosomal region; (S) stratum. PAR1 and strata 4 and 5 showed the typical autosomal signature of allelic similarity. No other regions on the Xi appeared to have any significant replication structure at the sensitivity level of detection...
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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
..., based on previous studies of evolutionary strata on the X Chromosome (Ross et al. 2005; McLysaght 2008; Pandey et al. 2013). After excluding genes in pseudoautosomal regions (X-PARs; Ensembl v110), we found that the proportion of male-specific reproductive disease genes in the X-added region (13.07%, 23...
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