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Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
...of diverse taxa, including yeast, birds, and dogs (Axelsson et al. 2012; Berglund et al. 2015; Lam and Keeney 2015; Singhal et al. 2015). In insects, the prevalence of recombination hotspots is not well studied. Fine-scale recombination maps in the fruit fly Drosophila melanogaster and honey bee A. mellifera...
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Method: Long-read reconstruction of many diverse haplotypes with devider
- Jim Shaw,
- Christina Boucher,
- Yun William Yu,
- Noelle Noyes,
- and Heng Li
Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
...of a single low-abundance strain characterized viral strain frequencies (Boyle et al. 2022; Markov et al. 2023).We first simulated near full-length reads (30 kb mean length with 500 bp standard deviation) and 95% accuracy at 3000× total coverage; that is, a 1% abundant haplotype would have 30× coverage (Fig...
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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
...Asgard viruses, including Opia virus from this study, reveals a diverse range of genomic lengths (Fig. 5B; Supplemental Table S8). The Opia virus, with its 40,094 bp , falls within the mid-range of Asgard viral sizes, which span from ∼15 kb to >100 kb. This variation in size likely reflects the diverse...
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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
...Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear s Yu-Chi Chen1,2, David L.J. Vendrami3,4,5,6, Maximilian L. Huber2, Luisa E.Y. Handel2, Christopher R. Cooney7, Joseph I. Hoffman3,4,5,6,8 and Toni I. Gossmann1,2,3,5 1Computational Systems Biology, Faculty...
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Research: Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
- Keegan S. Krick,
- Marissa Maroni,
- Erica Korb,
- Kristen W. Lynch,
- and Elizabeth A. Heller
Genome Res. June 2025 35: 1301-1312; Published in Advance April 24, 2025, doi:10.1101/gr.280082.124
...). Conversely, genes with altered splicing at later time points were more associated with neuronal activity (synaptic trafficking/structure), whereas differentially expressed genes showed no functional enrichment. Importantly, neither splicing nor transcript abundance reflected the activation of stress pathways...
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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: Memory-bound k-mer selection for large and evolutionarily diverse reference libraries
- Ali Osman Berk Şapcı and
- Siavash Mirarab
Genome Res. September 2024 34: 1455-1467; Published in Advance August 29, 2024, doi:10.1101/gr.279339.124
...their attempts to find representative species, the number of s sampled per taxon in each taxonomic rank varies three orders of magnitude. The true imbalance in evolutionary history (where some clades are much more diverse, abundant, and species-rich than others) in addition to biases in sampling (where some...
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Method: Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
- Alejandro Paniagua,
- Cristina Agustín-García,
- Francisco J. Pardo-Palacios,
- Thomas Brown,
- Maite De Maria,
- Nancy D. Denslow,
- Camila J. Mazzoni,
- and Ana Conesa
Genome Res. April 2025 35: 1053-1064; Published in Advance December 23, 2024, doi:10.1101/gr.279864.124
...Evaluation of strategies for evidence-driven annotation using long-read RNA-seq Alejandro Paniagua1,2,6, Cristina Agustín-García1,6, Francisco J. Pardo-Palacios1, Thomas Brown3,4, Maite De Maria5, Nancy D. Denslow5, Camila J. Mazzoni3,4 and Ana Conesa1 1Institute for Integrative Systems Biology...
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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
...Rearrangements of viral and human s at human papillomavirus integration events and their allele-specific impacts on cancer regulation Vanessa L. Porter1,2,3, Michelle Ng1,3, Kieran O'Neill1, Signe MacLennan1,2,3, Richard D. Corbett1, Luka Culibrk1,4, Zeid Hamadeh5,6, Marissa Iden7,8, Rachel Schmidt...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...of Ecology, Stockholm University, SE-106 91 Stockholm, Sweden; 3Butterfly Diversity and Evolution Lab, Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain Corresponding author: aleix.palahi@ebc.uu.seAbstractRecombination is a key molecular mechanism that has profound implications on both micro...
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