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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
...Matthew Naish and Ian R. Henderson Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom Corresponding author: irh25@cam.ac.ukAbstractCentromeres are essential regions of eukaryotic chromosomes responsible for the formation of kinetochore complexes, which connect...
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Research: Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution
- Chris Papadopoulos,
- Isabelle Callebaut,
- Jean-Christophe Gelly,
- Isabelle Hatin,
- Olivier Namy,
- Maxime Renard,
- Olivier Lespinet,
- and Anne Lopes
Genome Res. December 2021 31: 2303-2315; Published in Advance November 22, 2021, doi:10.1101/gr.275638.121
...the birth of novel genes and shape the evolution and the structural diversity of proteins remains unclear. Therefore, by combining different bioinformatic approaches, we characterized the fold potential diversity of the amino acid sequences encoded by all intergenic open reading frames (ORFs) of S...
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Research: Recruitment of histone modifications to assist mRNA dosage maintenance after degeneration of cytosine DNA methylation during animal evolution
- Andrew Ying-Fei Chang and
- Ben-Yang Liao
Genome Res. September 2017 27: 1513-1524; Published in Advance July 18, 2017, doi:10.1101/gr.221739.117
...were found to be largely organism specific. Thus, it appears that many of the histone marks that maintain mRNA dosage were independently recruited during the evolution of worms and flies to compensate for the loss of cytosine DNA methylation machinery from their s. [Supplemental material is available...
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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
...constitute a principal driver of evolution, shaping its architecture and regulatory networks. In this context, Tuberaceae can become an important model system to study their genomic impact; however, the family lacks high-quality assemblies. Here, we investigate the interplay between TEs and Tuberaceae...
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Research: Phylogenetic relatedness rather than aquatic habitat fosters horizontal transfer of transposable elements in animals
- Héloïse Muller,
- Rosina Savisaar,
- Jean Peccoud,
- Sylvain Charlat,
- and Clément Gilbert
Genome Res. September 2025 35: 2011-2022; Published in Advance August 8, 2025, doi:10.1101/gr.280432.125
...evolutionary time (Schaack et al. 2010). This process, therefore, deeply influences evolution, given that TEs compose a major fraction of the chromosomes of most eukaryotic taxa (Gilbert and Feschotte 2018). Whereas their evolutionary impacts are well identified, the mechanisms by which TEs circulate between...
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Research: Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza
- Chenbo Gong,
- Yicheng Huang,
- Mengmeng Liu,
- Yong Zhou,
- Yinwei Xu,
- Nahed Mohammed,
- Xintong Qiao,
- Andrea Zuccolo,
- Weibo Xie,
- Rod A. Wing,
- Jianwei Zhang,
- Fei Zhou,
- and Yongjun Lin
Genome Res. June 2025 35: 1349-1363; Published in Advance April 25, 2025, doi:10.1101/gr.279609.124
.../or mitochondrial DNA with each other. In summary, this work provides novel insights into the process of endosymbiotic DNA transfer and its role in reshaping variation and plant evolution.The observation of “promiscuous DNA,” which is defined as a nucleotide sequence occurring in more than one of the three membrane...
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Review: Origins, evolution, and phenotypic impact of new genes
- Henrik Kaessmann
Genome Res. October 2010 20: 1313-1326; Published in Advance July 22, 2010, doi:10.1101/gr.101386.109
...considered to be a major contributor to adaptive evolutionary innovation. Here, I review the origin and evolution of new genes and their functions in eukaryotes, an area of research that has made rapid progress in the past decade thanks to the genomics revolution. Indeed, recent work has provided initial...
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Research: The human phosphotyrosine signaling network: Evolution and hotspots of hijacking in cancer
- Lei Li,
- Chabane Tibiche,
- Cong Fu,
- Tomonori Kaneko,
- Michael F. Moran,
- Martin R. Schiller,
- Shawn Shun-Cheng Li,
- and Edwin Wang
Genome Res. July 2012 22: 1222-1230; Published in Advance December 22, 2011, doi:10.1101/gr.128819.111
...The human phosphotyrosine signaling network: Evolution and hotspots of hijacking in cancer Lei Li 1 , 2 , 9 , Chabane Tibiche 3 , 9 , Cong Fu 3 , 9 , 10 , Tomonori Kaneko 1 , Michael F. Moran 2 , 4 , 5 , Martin R. Schiller...
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Research: Semiconservative transmission of DNA N⁶-adenine methylation in a unicellular eukaryote
- Yalan Sheng,
- Yuanyuan Wang,
- Wentao Yang,
- Xue Qing Wang,
- Jiuwei Lu,
- Bo Pan,
- Bei Nan,
- Yongqiang Liu,
- Fei Ye,
- Chun Li,
- Jikui Song,
- Yali Dou,
- Shan Gao,
- and Yifan Liu
Genome Res. May 2024 34: 740-756; Published in Advance May 14, 2024, doi:10.1101/gr.277843.123
...Yalan Sheng1,2,6,7, Yuanyuan Wang1,2,6, Wentao Yang3,6, Xue Qing Wang3, Jiuwei Lu4, Bo Pan1,2, Bei Nan1,2, Yongqiang Liu1,2, Fei Ye1,2, Chun Li5, Jikui Song4, Yali Dou3, Shan Gao1,2 and Yifan Liu3 1MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine...
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Research: Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth
- Clarence Zheng,
- Sherwood R. Casjens,
- Alan R. Davidson,
- Susan K. Amundsen,
- and Gerald R. Smith
Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
...on their recombination functions and their Chi content. The analysis of these phages and their encoded proteins provides broad perspective and allows discussion of the complex evolution of these phages and their interaction with RecBCD and Chi.Results and DiscussionFour lambdoid phages aided by RecBCDIn our search...
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