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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
.... 2017; Xu et al. 2019), including a high-resolution reference assembly of its 20 chromosomes from the S. polyrhiza 9509 (Sp9509) and 7498 (Sp7498) clones (Michael et al. 2017; Hoang et al. 2018; Harkess et al. 2021). For our study, we retrieved Sp9509 from the Landolt duckweed collection, now managed...
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Research: Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
- Kristine Bilgrav Saether,
- Angelo Salazar Mantero,
- Marlene Ek,
- Maria Pettersson,
- Elisabeth Syk Lundberg,
- Christopher M. Grochowski,
- Claudia M.B. Carvalho,
- Jesper Eisfeldt,
- and Anna Lindstrand
Genome Res. April 2026 36: 661-670; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
...on a single chromosome (RD_P276, RD_P278, RD_P273, RD_P166, RD_P550, RD_P275), and three were complex rearrangements involving either more than three BPJs (RD_P272, RD_P586) or more than one chromosome (RD_P328) (Table 2). In traditional cytogenetics, a simple sSMC is defined as a continuous DNA fragment...
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Method: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
- Sergey Koren,
- Zhigui Bao,
- Andrea Guarracino,
- Shujun Ou,
- Sara Goodwin,
- Katharine M. Jenike,
- Julian Lucas,
- Brandy McNulty,
- Jimin Park,
- Mikko Rautiainen,
- Arang Rhie,
- Dick Roelofs,
- Harrie Schneiders,
- Ilse Vrijenhoek,
- Koen Nijbroek,
- Olle Nordesjo,
- Sergey Nurk,
- Mike Vella,
- Katherine R. Lawrence,
- Doreen Ware,
- Michael C. Schatz,
- Erik Garrison,
- Sanwen Huang,
- William Richard McCombie,
- Karen H. Miga,
- Alexander H.J. Wittenberg,
- and Adam M. Phillippy
Genome Res. November 2024 34: 1919-1930; Published in Advance November 6, 2024, doi:10.1101/gr.279334.124
...as scaffolds (four as gapless contigs) by the Pore-C assembly. The remaining nonacrocentric chromosomes had coverage gaps that were resolved by higher Duplex coverage, with the exception of Chromosome 9, which was fragmented into multiple components in all assemblies. We found that Duplex coverage dropped...
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Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
- Marlies E. Oomen,
- A. Nicole Fox,
- Inma Gonzalez,
- Amandine Molliex,
- Thaleia Papadopoulou,
- Pablo Navarro,
- and Job Dekker
Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
..., Germany Corresponding authors: pnavarro@pasteur.fr, job.dekker@umassmed.eduAbstractMitotic chromosomes are considered to be universally folded as loop arrays across species and cell types. However, some studies suggest that features of mitotic chromosomes might be cell type– or species-specific. We...
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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
...mammals and crocodilians, that only possess large (macro) chromosomes, turtles (like birds) exhibit larger (macro) and tiny (micro) chromosomes, and vary widely in their diploid number between 2n = 28 and 2n = 68 (Montiel et al. 2016), likely as the result of fusions and fissions over >210 million years...
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Method: RAmbler resolves complex repeats in human Chromosomes 8, 19, and X
- Sakshar Chakravarty,
- Glennis Logsdon,
- and Stefano Lonardi
Genome Res. April 2025 35: 863-876; Published in Advance March 4, 2025, doi:10.1101/gr.279308.124
...coverage, nonuniform sequencing errors, and chimeric reads. Repetitive regions (or segmental duplications) are the primary reasons for which de novo assemblies are often fragmented and incomplete. A large fraction of eukaryotic s is made of repetitive elements, including satellite DNA, minisatellites...
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Research: Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths
- Fangyuan Yang,
- Li-Jun Cao,
- Petr Nguyen,
- Zhong-Zheng Ma,
- Jin-Cui Chen,
- Wei Song,
- and Shu-Jun Wei
Genome Res. January 2025 35: 66-77; Published in Advance January 6, 2025, doi:10.1101/gr.279569.124
...into contigs using NextDenovo v2.5.0 (Hu et al. 2024). Redundant fragments were removed using Purge_dups v1.2.6 (Guan et al. 2020). The Hi-C reads were then mapped to the clean contigs using BWA (Li and Durbin 2009). The contigs were assembled into chromosome-level scaffolds using YaHS 1.2a.1 (Zhou et al. 2023...
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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
...). Nanopore reads were used for de novo assembly of the different Y Chromosomes. Assemblies of repetitive regions, including the Y, are challenging, and these regions are often collapsed, highly fragmented, or missing in whole- assemblies (Hoskins et al. 2007; Chang and Larracuente 2019). We thus followed...
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Research: Rearrangement of macronucleus chromosomes correspond to TAD-like structures of micronucleus chromosomes in Tetrahymena thermophila
- Zhengyu Luo,
- Tengfei Hu,
- Hong Jiang,
- Ruoyu Wang,
- Qianlan Xu,
- Simo Zhang,
- Jun Cao,
- and Xiaoyuan Song
Genome Res. March 2020 30: 406-414; Published in Advance March 12, 2020, doi:10.1101/gr.241687.118
...-range gene regulation in T. theromphila. Together, our results showed that the gene-dense, fragmented MAC shows no obvious A/B compartments, TADs, and chromatin loops, but each MAC chromosome is a single isolated unit that is similar to the chromosome territory in mammals.TAD-like structures are present...
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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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