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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...that are putatively orthologous. These regions display considerable structural variation between different D. melanogaster strains, exhibiting differences in copy number and organization of homologous repeat units between haplotypes. In the histone cluster, although we observe minimal genetic exchange indicative...
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Method: Highly accurate assembly polishing with DeepPolisher
- Mira Mastoras,
- Mobin Asri,
- Lucas Brambrink,
- Prajna Hebbar,
- Alexey Kolesnikov,
- Daniel E. Cook,
- Maria Nattestad,
- Julian Lucas,
- Taylor S. Won,
- Pi-Chuan Chang,
- Andrew Carroll,
- Benedict Paten,
- Kishwar Shafin,
- and and the Human Pangenome Reference Consortium
Genome Res. July 2025 35: 1595-1608; Published in Advance May 19, 2025, doi:10.1101/gr.280149.124
...Mira Mastoras1, Mobin Asri1, Lucas Brambrink2, Prajna Hebbar1, Alexey Kolesnikov2, Daniel E. Cook2, Maria Nattestad2, Julian Lucas1, Taylor S. Won1, Pi-Chuan Chang2, Andrew Carroll2, Benedict Paten1, Kishwar Shafin2, and the Human Pan Reference Consortium3 1UC Santa Cruz Genomics Institute...
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Method: CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes
- Marzia Rossato,
- Luca Marcolungo,
- Luca De Antoni,
- Giulia Lopatriello,
- Elisa Bellucci,
- Gaia Cortinovis,
- Giulia Frascarelli,
- Laura Nanni,
- Elena Bitocchi,
- Valerio Di Vittori,
- Leonardo Vincenzi,
- Filippo Lucchini,
- Kirstin E. Bett,
- Larissa Ramsay,
- David James Konkin,
- Massimo Delledonne,
- and Roberto Papa
Genome Res. May 2023 33: 787-797; Published in Advance May 1, 2023, doi:10.1101/gr.277628.122
....delledonne@univr.it, r.papa@staff.univpm.itAbstractHigh-throughput genotyping enables the large-scale analysis of genetic diversity in population genomics and -wide association studies that combine the genotypic and phenotypic characterization of large collections of accessions. Sequencing-based approaches...
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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France; 4Institut Universitaire de France (IUF), 75231 Paris Cedex 05, France ↵5 These authors contributed equally to this work. Corresponding author: dgresham@nyu.eduAbstractCopy number variants (CNVs), duplications and deletions of genomic...
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Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
- Nora Zidane,
- Carla Rodrigues,
- Valérie Bouchez,
- Martin Rethoret-Pasty,
- Virginie Passet,
- Sylvain Brisse,
- and Chiara Crestani
Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
...diagnostics and public health surveillance owing to their high throughput and low error rates (Fox et al. 2014; Pfeiffer et al. 2018). This has provided scientists worldwide with high-resolution data for bacterial strain subtyping, which is indispensable for accurate and reliable public health surveillance...
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Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
...BX, United Kingdom Corresponding authors: alessio.marcozzi@gmail.com, j.deridder-4@umcutrecht.nlAbstractShallow -wide cell-free DNA sequencing holds great promise for noninvasive cancer monitoring by providing reliable copy number alteration (CNA) and fragmentomic profiles. Single...
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Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
- Yangyang Liu,
- Bingqiang Liu,
- and Juntao Liu
Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
...the cellular life cycle, intricately intertwined with epigenetics, gene expression, and various cellular activities (Lanctôt et al. 2007; Sexton et al. 2007, 2012; Cavalli and Misteli 2013; Dixon et al. 2015). In the past two decades, chromatin conformational capture methods, particularly the high-throughput...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
.... The green box contains four genomic regions that share the most frequent version of the 27-mer unit (5′-ACTCTCTGTGGCTTCCCACTATATTTT-3′), which we call type1. The blue box contains five genomic regions that share many copies of both type1 and another version of the 27-mer, type2 (5...
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Method: Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics
- Alexey Vorobev,
- Marion Dupouy,
- Quentin Carradec,
- Tom O. Delmont,
- Anita Annamalé,
- Patrick Wincker,
- and Eric Pelletier
Genome Res. April 2020 30: 647-659; Published in Advance March 23, 2020, doi:10.1101/gr.253070.119
...(Foster et al. 2011). In order to accurately do so, additional information on their genomic potential is required and can be accessed through the MGT collection.Little is known about the nature of a diatom-tintinnid association detected in MGT-136. One hypothesis suggests a mutualistic symbiosis, where...
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Method: Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
- Romain Derelle,
- Johanna von Wachsmann,
- Tommi Mäklin,
- Joel Hellewell,
- Timothy Russell,
- Ajit Lalvani,
- Leonid Chindelevitch,
- Nicholas J. Croucher,
- Simon R. Harris,
- and John A. Lees
Genome Res. October 2024 34: 1661-1673; Published in Advance October 15, 2024, doi:10.1101/gr.279449.124
...and Melinda Gates Foundation, Westminster, London SW1E 6AJ, United Kingdom ↵7 These authors contributed equally to this work. Corresponding author: jlees@ebi.ac.ukAbstractSequence variation observed in populations of pathogens can be used for important public health and evolutionary genomic analyses...
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