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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
...via gene acquisition (Bellott et al. 2017). It remains unclear whether the conservation in gene content in Insecta reflects conservation of the sex chromosome itself, repeated origin of X Chromosomes from the same underlying syntenic regions, or repeated movement of the same gene content to the sex...
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Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
..., a fundamental component of dosage compensation mechanisms studied to date is the up-regulation of genes on the X Chromosome to compensate for gene dosage imbalances in the heterogametic sex (Deng et al. 2011; Larsson et al. 2019; Lentini et al. 2022). In eutherian mammals, up-regulation of genes on the single...
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Research: Accumulation and ineffective silencing of transposable elements on an avian W Chromosome
- Vera M. Warmuth,
- Matthias H. Weissensteiner,
- and Jochen B.W. Wolf
Genome Res. April 2022 32: 671-681; Published in Advance February 11, 2022, doi:10.1101/gr.275465.121
...that incomplete TE silencing may reflect a pervasive trade-off between epigenetic TE silencing and host function, as the former can interfere with the expression of nearby genes (for review, see Choi and Lee 2020). If occurring on sex-limited chromosomes, such trade-offs have important consequences...
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Research: Specific down-regulation of spermatogenesis genes targeted by 22G RNAs in hybrid sterile males associated with an X-Chromosome introgression
- Runsheng Li,
- Xiaoliang Ren,
- Yu Bi,
- Vincy Wing Sze Ho,
- Chia-Ling Hsieh,
- Amanda Young,
- Zhihong Zhang,
- Tingting Lin,
- Yanmei Zhao,
- Long Miao,
- Peter Sarkies,
- and Zhongying Zhao
Genome Res. September 2016 26: 1219-1232; Published in Advance May 18, 2016, doi:10.1101/gr.204479.116
...explanation for this is the dominance theory,whichproposes that if alleles causingHI are recessive and sex-linked, the heterogametic hybrid progeny will manifest full effects because of hemizygosity, whereas homogametic hybrid progeny will not, owing to compensation by a second copy of a wild-type allele...
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Research: Epigenetic modification and inheritance in sexual reversal of fish
- Changwei Shao,
- Qiye Li,
- Songlin Chen,
- Pei Zhang,
- Jinmin Lian,
- Qiaomu Hu,
- Bing Sun,
- Lijun Jin,
- Shanshan Liu,
- Zongji Wang,
- Hongmei Zhao,
- Zonghui Jin,
- Zhuo Liang,
- Yangzhen Li,
- Qiumei Zheng,
- Yong Zhang,
- Jun Wang,
- and Guojie Zhang
Genome Res. April 2014 24: 604-615; Published in Advance February 2, 2014, doi:10.1101/gr.162172.113
...conclude that epigenetic regulation plays multiple crucial roles in sexual reversal of tongue sole fish. We also offer the first clues on the mechanisms behind gene dosage balancing in an organism that undergoes sexual reversal. Finally, we suggest a causal link between the bias sex chromosome assortment...
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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
...of the softshell turtles R. swinhoei (Ren et al. 2022) and P. cantorii (Liu et al. 2023), also produced by long-read sequencing (Supplemental Fig. S1B). Likewise, GC-rich microchromosomic regions were underrepresented in the Staurotypus and Apalone assemblies, which include portions of the sex chromosomes...
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Research: The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes
- Drew R. Schield,
- Daren C. Card,
- Nicole R. Hales,
- Blair W. Perry,
- Giulia M. Pasquesi,
- Heath Blackmon,
- Richard H. Adams,
- Andrew B. Corbin,
- Cara F. Smith,
- Balan Ramesh,
- Jeffery P. Demuth,
- Esther Betrán,
- Marc Tollis,
- Jesse M. Meik,
- Stephen P. Mackessy,
- and Todd A. Castoe
Genome Res. April 2019 29: 590-601; Published in Advance March 21, 2019, doi:10.1101/gr.240952.118
...differences between classes of chromosomes and distinctions from patterns observed in mammalian data sets. Rattlesnakes have highly differentiated ZW sex chromosomes (Matsubara et al. 2006), and we use our and additional resequenced s to identify the Z Chromosome, the pseudoautosomal region of Z and W...
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Research: Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage
- Ray Marin,
- Diego Cortez,
- Francesco Lamanna,
- Madapura M. Pradeepa,
- Evgeny Leushkin,
- Philippe Julien,
- Angélica Liechti,
- Jean Halbert,
- Thoomke Brüning,
- Katharina Mössinger,
- Timo Trefzer,
- Christian Conrad,
- Halie N. Kerver,
- Juli Wade,
- Patrick Tschopp,
- and Henrik Kaessmann
Genome Res. December 2017 27: 1974-1987; Published in Advance November 13, 2017, doi:10.1101/gr.223727.117
...) (Fig. 1; Alfoldi et al. 2011). This opened the opportunity to study the functional evolution of an amniote male heterogametic sex chromosome system outside of mammals. The distribution and karyotypic patterns of this XY system within the large Anolis genus and its presence in other (pleurodont) lizards...
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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...-ligation-based haplotype phasing and scaffolding, and adds support for multiple long-read data types. These enhancements allow Verkko2 to assemble all regions of a diploid human , including the short arms of the acrocentric chromosomes and both sex chromosomes. Together, these changes increase the number of telomere...
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Review: k-mer approaches for biodiversity genomics
- Katharine M. Jenike,
- Lucía Campos-Domínguez,
- Marilou Boddé,
- José Cerca,
- Christina N. Hodson,
- Michael C. Schatz,
- and Kamil S. Jaron
Genome Res. February 2025 35: 219-230; Published in Advance January 31, 2025, doi:10.1101/gr.279452.124
...Chromosome.View larger version: In this window In a new window Figure 3. k-mer comparison of multiple sequencing libraries. Examples of two 2D k-mer spectra for species with the following: (A) A XO sex determination system (Orchesella cincta; data from Anderson et al. 2022) and (B) a ZW (female heterogametic...
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