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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
....The LLS has unexpectedly abundant Chi sitesThe s of the well-studied lambdoid phages λ, 21, 434, Sf6, and P22 contain no Chi recombination hotspot sites, and in our lambdoid phage panel (Supplemental Table S3), the s of 172 of 314 Enterobacteriales phages have only one or no Chi site. Thus...
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Method: Secure phasing of private genomes in a trusted execution environment with TX-Phase
- Natnatee Dokmai,
- Kaiyuan Zhu,
- S. Cenk Sahinalp,
- and Hyunghoon Cho
Genome Res. December 2025 35: 2626-2636; Published in Advance November 12, 2025, doi:10.1101/gr.280558.125
...poses a significant challenge in maintaining practical performance under privacy constraints. Here, we introduce TX-Phase, a secure haplotype phasing method based on the framework of trusted execution environments (TEEs). TX-Phase allows users’ private genomic data to be phased while ensuring data...
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Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
...on this comparison, we also draw conclusions about the genomic architecture, evolutionary dynamics, and the main molecular mechanisms that most significantly differentiated their satellitomes.ResultsIdentification of T. freemani satDNAsThe first step was to characterize the T. freemani satellitome. For assembly...
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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...the formation of unfit MHC-I–APG recombinants. This theory, based on research in chicken and rat, assumes a single dominantly expressed MHC-I gene that coevolves with APGs (Kaufman 1999, 2015). Such a state has been suggested as ancestral for jawed vertebrates, with a “lucky” accident of a genomic rearrangement...
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Research: Multiple paralogs and recombination mechanisms contribute to the high incidence of 22q11.2 deletion syndrome
- Lisanne Vervoort,
- Nicolas Dierckxsens,
- Marta Sousa Santos,
- Senne Meynants,
- Erika Souche,
- Ruben Cools,
- Tracy Heung,
- Koen Devriendt,
- Hilde Peeters,
- Donna M. McDonald-McGinn,
- Ann Swillen,
- Jeroen Breckpot,
- Beverly S. Emanuel,
- Hilde Van Esch,
- Anne S. Bassett,
- and Joris R. Vermeesch
Genome Res. April 2025 35: 786-797; Published in Advance November 13, 2024, doi:10.1101/gr.279331.124
...-)long-read sequencing and/or rearrangement-specific long-range PCR. A combination of these methods was applied on 25 families (patient and parent-of-origin, Supplemental Table S1) to identify the 22q11 breakpoint regions in the proband, the genomic elements involved, and gain insights on the recombination mechanisms...
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Research: Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation
- Vanessa L. Porter,
- Michelle Ng,
- Kieran O'Neill,
- Signe MacLennan,
- Richard D. Corbett,
- Luka Culibrk,
- Zeid Hamadeh,
- Marissa Iden,
- Rachel Schmidt,
- Shirng-Wern Tsaih,
- Carolyn Nakisige,
- Martin Origa,
- Jackson Orem,
- Glenn Chang,
- Jeremy Fan,
- Ka Ming Nip,
- Vahid Akbari,
- Simon K. Chan,
- James Hopkins,
- Richard A. Moore,
- Eric Chuah,
- Karen L. Mungall,
- Andrew J. Mungall,
- Inanc Birol,
- Steven J.M. Jones,
- Janet S. Rader,
- and Marco A. Marra
Genome Res. April 2025 35: 653-670; Published in Advance December 5, 2024, doi:10.1101/gr.279041.124
...,8 and Marco A. Marra1,2,3 1Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada; 2Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; 3Michael Smith Laboratories, University of British Columbia, Vancouver...
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Research: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado,
- Ling-Dong Shi,
- Kathryn E. Appler,
- Alexander Crits-Christoph,
- Valerie De Anda,
- Benjamin A. Adler,
- Michael L. Cui,
- Lynn Ly,
- Pedro Leão,
- Richard J. Roberts,
- Rohan Sachdeva,
- Brett J. Baker,
- David F. Savage,
- and Jillian F. Banfield
Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
...Sachdeva1, Brett J. Baker3,4, David F. Savage1,7,8 and Jillian F. Banfield1,4,9,10 1Innovative Genomics Institute, University of California, Berkeley, California 94720, USA; 2Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA; 3Department of Marine Science...
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Method: Localizing unmapped sequences with families to validate the Telomere-to-Telomere assembly and identify new hotspots for genetic diversity
- Brianna Chrisman,
- Chloe He,
- Jae-Yoon Jung,
- Nate Stockham,
- Kelley Paskov,
- Peter Washington,
- Juli Petereit,
- and Dennis P. Wall
Genome Res. October 2023 33: 1734-1746; Published in Advance October 25, 2023, doi:10.1101/gr.277175.122
...divergence from their aligned region in T2T-CHM13, highlighting new hotspots for genetic diversity.The human reference has been one of the major successes of modern genomics and has been heavily relied on to study how genetic variation contributes to disease (Lander et al. 2001; International Human Genome...
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Method: Fast inference of genetic recombination rates in biobank scale data
- Ardalan Naseri,
- William Yue,
- Shaojie Zhang,
- and Degui Zhi
Genome Res. July 2023 33: 1015-1022; Published in Advance June 22, 2023, doi:10.1101/gr.277676.123
...in the reversed prefix order, the condition g[dk[j]] > g[k] − L triggers the enumeration of possible recombination events. The array count stores the total count of recombination events (minor allele counts) for each window. The array pos contains the genomic (physical) position of the sites.View larger version...
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Research: Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes
- Yu-Chi Chen,
- David L.J. Vendrami,
- Maximilian L. Huber,
- Luisa E.Y. Handel,
- Christopher R. Cooney,
- Joseph I. Hoffman,
- and Toni I. Gossmann
Genome Res. June 2025 35: 1313-1324; Published in Advance March 31, 2025, doi:10.1101/gr.279428.124
...coding-like NUMTs within nuclear regions, particularly in areas of low recombination (Gossmann et al. 2014). This selective pressure could further suppress the rate of mutation accumulation in NUMTs.MethodsData collection and selectionGenome assemblies for all mammalian species (available before November...

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