Searching journal content for articles similar to Cui et al. 16 (6): 738.

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Research: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
- Thomas D. Lewin,
- Isabel Jiah-Yih Liao,
- Mu-En Chen,
- John D.D. Bishop,
- Peter W.H. Holland,
- and Yi-Jyun Luo
Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
...= 0.0001, respectively) (Supplemental Fig. S13). Therefore, the physical separation of Hox cluster genes by rearrangements is associated with differences in expression levels.DiscussionOur study reveals widespread rearrangements to bryozoan chromosomes that have extensively fragmented the 24 ALGs...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...(TEs) and other repetitive sequences are known to be one of the major causes of structural variations within individuals and species, promoting expansion, gene duplication, gene loss, genomic rearrangements, and reshaping of the overall genomic regulatory network (Bourque et al. 2018). Among fungi...
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Research: Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence
- Scott Ferguson,
- Ashley Jones,
- Kevin Murray,
- Rose Andrew,
- Benjamin Schwessinger,
- and Justin Borevitz
Genome Res. April 2024 34: 606-619; Published in Advance April 8, 2024, doi:10.1101/gr.277999.123
...of rearrangements within each species could be assessed. This would provide insight into the functional significance of the widespread genomic rearrangements we have found and would potentially identify rearrangements conferring adaptive traits across the landscape.Eucalyptus contains more than 800 species...
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Research: Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants
- Kazumasa Shirai,
- Mitsuhiko P. Sato,
- Ranko Nishi,
- Masahide Seki,
- Yutaka Suzuki,
- and Kousuke Hanada
Genome Res. June 2021 31: 1060-1068; Published in Advance May 18, 2021, doi:10.1101/gr.271726.120
.... Bioinformatics 30: 2114–2120. doi:10.1093/bioinformatics/btu170 ↵Bouyer D, Kramdi A, Kassam M, Heese M, Schnittger A, Roudier F, Colot V. 2017. DNA methylation dynamics during early plant life. Genome Biol 18: 179. doi:10.1186/s13059-017-1313-0 ↵Carreno-Quintero N, Bouwmeester HJ, Keurentjes JJB. 2013. Genetic...
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Research: Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary
- Kevin Vanneste,
- Guy Baele,
- Steven Maere,
- and Yves Van de Peer
Genome Res. August 2014 24: 1334-1347; Published in Advance May 16, 2014, doi:10.1101/gr.168997.113
...://www..org/cgi/doi/10.1101/gr.168997.113. Freely available online through the Genome Research Open Access option. 1334 Genome Research www..org 24:1334–1347 Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/14; www..org an estimated 15% and 31% of speciations in flowering plants and ferns, respectively...
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Research: The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize
- Thomas E. Hughes,
- Jane A. Langdale,
- and Steven Kelly
Genome Res. August 2014 24: 1348-1355; Published in Advance April 30, 2014, doi:10.1101/gr.172684.114
...are a widespread feature of plant evolution, having been detected in all flowering plant lineages. Despite the prevalence of these events, the extent to which duplicated genes (homeolog gene pairs) functionally diverge (neofunctionalization) is unclear. We present a -wide analysis of molecular evolution...
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Resource: The western redcedar genome reveals low genetic diversity in a self-compatible conifer
- Tal J. Shalev,
- Omnia Gamal El-Dien,
- Macaire M.S. Yuen,
- Shu Shengqiang,
- Shaun D. Jackman,
- René L. Warren,
- Lauren Coombe,
- Lise van der Merwe,
- Ada Stewart,
- Lori B. Boston,
- Christopher Plott,
- Jerry Jenkins,
- Guifen He,
- Juying Yan,
- Mi Yan,
- Jie Guo,
- Jesse W. Breinholt,
- Leandro G. Neves,
- Jane Grimwood,
- Loren H. Rieseberg,
- Jeremy Schmutz,
- Inanc Birol,
- Matias Kirst,
- Alvin D. Yanchuk,
- Carol Ritland,
- John H. Russell,
- and Joerg Bohlmann
Genome Res. October 2022 32: 1952-1964; Published in Advance September 15, 2022, doi:10.1101/gr.276358.121
...-fertilization (selfing), was determined to be 86% complete by BUSCO analysis, one of the most complete assemblies for a conifer. Population genomic analysis revealed WRC to be one of the most genetically depauperate wild plant species, with an effective population size of approximately 300 and no significant genetic...
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Research: Global deceleration of gene evolution following recent genome hybridizations in fungi
- Sira Sriswasdi,
- Masako Takashima,
- Ri-ichiroh Manabe,
- Moriya Ohkuma,
- Takashi Sugita,
- and Wataru Iwasaki
Genome Res. August 2016 26: 1081-1090; Published in Advance July 20, 2016, doi:10.1101/gr.205948.116
...-8568, Japan; 6Atmosphere and Ocean Research Institute, University of Tokyo, Kashiwa, Chiba 277-8564, Japan Corresponding authors: sirasris@bs.s.u-tokyo.ac.jp , iwasaki@bs.s.u-tokyo.ac.jp Abstract Polyploidization events such as whole-genome duplication and inter...
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PERSPECTIVE: Genome-wide analyses of alternative splicing in plants: Opportunities and challenges
- W. Brad Barbazuk,
- Yan Fu,
- and Karen M. McGinnis
Genome Res. September 2008 18: 1381-1392; Published in Advance July 30, 2008, doi:10.1101/gr.053678.106
...; Rosenfeld et al. 1982 ), it was characterized at the single gene level and thought to occur in &lt;5% of human genes ( Sharp 1994 ). However, analysis of sequence data has demonstrated that AS is widespread in metazoans ( Ast 2004 ; Sorek et al. 2004 ; Blencowe 2006 ; Kim et al. 2007 ). AS can affect...
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ARTICLE: A Recent Polyploidy Superimposed on Older Large-Scale Duplications in the Arabidopsis Genome
- Guillaume Blanc,
- Karsten Hokamp,
- and Kenneth H. Wolfe
Genome Res. February 1, 2003 13: 137-144; doi:10.1101/gr.751803
...from large-scale events. This would not be very surprising, as polyploidy is known to be very widespread in the plant kingdom, with at least 50%–70% of plant species being estimated to have experienced polyploidy in their ancestry ( Wendel 2000 ) and 2%–4% of plant speciation events being attributed...

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