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Research: Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
- Shaoqiang Hu,
- Xiangguo Zeng,
- Yuguo Liu,
- Yongping Li,
- Minghao Qu,
- Wen-Biao Jiao,
- Yongchao Han,
- and Chunying Kang
Genome Res. October 2024 34: 1582-1594; Published in Advance October 15, 2024, doi:10.1101/gr.279378.124
..., and the mutation frequency varies among the subs. Our study has systematically characterized the genetic and epigenetic variants in regenerated woodland strawberry plants and different individuals of the same strawberry cultivar, providing an accurate assessment of somatic mutations at the genomic scale...
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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
...chromosomes over large genomic regions.The evolution of sex chromosomes represents one of the major innovations of inheritance and plays a core role in sexual evolution in the animal kingdom (Charlesworth 1991; Wright et al. 2016). In species with genetic sex determination mechanisms, sex chromosomes carry...
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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
...for Systems Genetics, West China University Hospital, Chengdu 610041, China; 3Department of Pathology, The University of Chicago, Chicago, Illinois 60637, USA; 4Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois 60637, USA; 5Key Laboratory of Zoological...
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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
...–driven evolution for more than a century. Despite strong efforts, knowledge on genomic organization and molecular differentiation of the sex chromosome pair remains unsatisfactory and partly contradictory with respect to regions of reduced recombination. Especially the border between pseudoautosomal and male...
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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
...as macrosynteny, is seen between bilaterian phyla as divergent as Chordata, Echinodermata, Mollusca, and Nemertea. Here, we report a unique pattern of evolution in Bryozoa, an understudied phylum of colonial invertebrates. Using comparative genomics, we reconstruct the chromosomal evolutionary history of five...
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Research: Resetting of the 24-nt siRNA landscape in rice zygotes
- Chenxin Li,
- Jonathan I. Gent,
- Hengping Xu,
- Hong Fu,
- Scott D. Russell,
- and Venkatesan Sundaresan
Genome Res. February 2022 32: 309-323; Published in Advance December 23, 2021, doi:10.1101/gr.275981.121
...challenges, the epigenetic changes that accompany the transition from differentiated gametes to totipotent zygote are poorly understood. Because siRNAs serve as both regulators and outputs of the epi, we characterized small RNA transcriptomes of zygotes from rice. Zygote small RNAs exhibit extensive maternal...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...and Schnittger 2017), INCENP (Komaki et al. 2020), and BOREALIN RELATED (BORR) (Komaki et al. 2020). (B) Representative cytological image of the A. thaliana chromosomes during segregation at metaphase (Naish et al. 2021). The DNA is stained with DAPI (white), together with FISH for the CEN178 centromere...
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Research: Transposable element accumulation drives size differences among polymorphic Y Chromosomes in Drosophila
- Alison H. Nguyen,
- Weixiang Wang,
- Emily Chong,
- Kamalakar Chatla,
- and Doris Bachtrog
Genome Res. June 2022 32: 1074-1088; Published in Advance May 2, 2022, doi:10.1101/gr.275996.121
...are a fascinating part of the in species with heteromorphic sex chromosomes (Bachtrog 2020). Not only do Y Chromosomes determine maleness in many taxa (Bull 1983; Bachtrog et al. 2014), but their clonal and male-limited transmission is responsible for several unique evolutionary processes that shape their genomic...
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Research: Genome-wide mapping reveals R-loops associated with centromeric repeats in maize
- Yang Liu,
- Qian Liu,
- Handong Su,
- Kunpeng Liu,
- Xue Xiao,
- Wei Li,
- Qianwen Sun,
- James A. Birchler,
- and Fangpu Han
Genome Res. August 2021 31: 1409-1418; Published in Advance July 9, 2021, doi:10.1101/gr.275270.121
...are favorable for R-loop formationCentromeres are defined by the presence of CENH3, a variant of histone H3. Genome-wide mapping of sequences associated with CENH3 nucleosomes revealed CENH3-enriched and CENH3-depleted subdomains in the centromeres of rice, maize, and other species (Yan et al. 2008; Su et al...
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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
...recovered the 13.6-Mb D. melanogaster-specific 3R inversion (In(3R)84F1; 93F6–7; 3R:8,049,180–21,735,108) that was initially characterized cytologically (Sturtevant and Plunkett 1926) and confirmed by breakpoint cloning (Fig. 2; Ranz et al. 2007). Among nine inversions shared in all sim-complex species...
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