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Method: A simple method for finding related sequences by adding probabilities of alternative alignments
- Martin C. Frith
Genome Res. August 2024 34: 1165-1173; Published in Advance August 16, 2024, doi:10.1101/gr.279464.124
....In a pioneering study, Bucher and Hofmann (1996) used a log likelihood ratio to compare two hypotheses, that two sequences have a related segment or not: (4) Each hypothesis has probabilities for the lengths of the two sequences. Their two hypotheses are identical in this regard. Thus, the sequence lengths never...
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Research: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
- Thomas D. Lewin,
- Isabel Jiah-Yih Liao,
- Mu-En Chen,
- John D.D. Bishop,
- Peter W.H. Holland,
- and Yi-Jyun Luo
Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
...bryozoan s. We also discover at least five derived chromosomal fusion events shared between bryozoans and brachiopods, supporting the traditional but highly debated Lophophorata hypothesis and suggesting macrosynteny to be a potentially powerful source of phylogenetic information. Finally, we show...
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Research: The genomic consequences and persistence of sociality in spiders
- Jilong Ma,
- Jesper Bechsgaard,
- Anne Aagaard,
- Palle Villesen,
- Trine Bilde,
- and Mikkel Heide Schierup
Genome Res. March 2025 35: 499-511; Published in Advance February 20, 2025, doi:10.1101/gr.279503.124
..., sociality is accompanied by a transition from outcrossing to inbreeding. In concert, these traits reduce effective population size, potentially rendering transitions to sociality “evolutionarily dead-ends.” We addressed this hypothesis in a comparative genomic study in spiders, in which sociality has...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...cut-offs matching the hypothesis of no difference between the two gene groups. (D) Distribution of the percentage of CpG methylation (sampled at UG) across ASE or non-ASE secretome gene bodies (here defined as start to stop codon) including ±2 kbp flanking regions. Solid lines represent mean...
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Research: Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype
- Arne Sahm,
- Konstantin Riege,
- Marco Groth,
- Martin Bens,
- Johann Kraus,
- Martin Fischer,
- Hans Kestler,
- Christoph Englert,
- Ralf Schaible,
- Matthias Platzer,
- and Steve Hoffmann
Genome Res. December 2024 34: 2217-2228; Published in Advance December 4, 2024, doi:10.1101/gr.279025.124
...of freshwater polyps with remarkable regeneration abilities and a potentially unlimited life span under laboratory conditions. By sequencing of single cells and whole animals, we found that the mutation rates in Hydra’s stem cells are even slightly higher than in humans or mice. A potential explanation...
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Resource: An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
- Chong Li,
- Marc Jan Bonder,
- Sabriya Syed,
- Matthew Jensen,
- Human Genome Structural Variation Consortium (HGSVC),
- HGSVC Functional Analysis Working Group,
- Mark B. Gerstein,
- Michael C. Zody,
- Mark J.P. Chaisson,
- Michael E. Talkowski,
- Tobias Marschall,
- Jan O. Korbel,
- Evan E. Eichler,
- Charles Lee,
- and Xinghua Shi
Genome Res. December 2024 34: 2304-2318; Published in Advance December 5, 2024, doi:10.1101/gr.279419.124
...−10, Fisher's exact test), likely due to the known enrichment of TAD boundaries within cCRE regions (Madani Tonekaboni et al. 2019). A similar hypothesis was supported by permutation test results on 10,000 rounds of putatively generated SVs that shared the same distribution of counts and length per chromosome...
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Research: Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization
- Kazuaki Yamaguchi,
- Yoshinobu Uno,
- Mitsutaka Kadota,
- Osamu Nishimura,
- Ryo Nozu,
- Kiyomi Murakumo,
- Rui Matsumoto,
- Keiichi Sato,
- and Shigehiro Kuraku
Genome Res. September 2023 33: 1527-1540; Published in Advance August 17, 2023, doi:10.1101/gr.276840.122
...et al. 2021). However, this hypothesis needs to be examined by incorporating more diverse vertebrate taxa into the comparison, on a solid basis of experimentally validated karyotypic configurations of individual species.View larger version: In this window In a new window Figure 1. Shark species...
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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
...the hypothesis that the independent specialization of ampliconic gene repertoires proposed by Mueller et al. (2013) was influenced by (1) the high rates of gene family birth and death in the mouse lineage, and (2) the limited additional taxon sampling from fragmented draft quality assemblies. Second, we examined...
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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
...in Ne is consistent with recurrent founder effects during the recolonization of Scandinavia after the LGP, and is compatible with the hypothesis of secondary contact and recurrent backcrossing underlying the observed chromosome number cline across Eurasia (Lukhtanov et al. 2018; Talla et al. 2019...
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Method: Variations in antibody repertoires correlate with vaccine responses
- Yana Safonova,
- Sung Bong Shin,
- Luke Kramer,
- James Reecy,
- Corey T. Watson,
- Timothy P.L. Smith,
- and Pavel A. Pevzner
Genome Res. April 2022 32: 791-804; Published in Advance March 31, 2022, doi:10.1101/gr.276027.121
...is a more complex task than in traditional eQTL studies.First, whereas the set of genes in eQTL studies is fixed and shared by all individuals, the antibody repertoire is composed of a virtually unlimited set of proteins, and there are typically few antibodies shared between any two individuals. Thus, given...

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