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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
...://github.com/christophertbrown/iRep). We classified complete MGE s as viruses if they contained viral structural genes. Genomes lacking viral structural genes were categorized as plasmids or other MGEs (such as transposons or conjugative elements) based on length, the presence of transposases (classified using ISFinder) (Siguier et al...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...Barcelona, Spain Corresponding authors: claudia.carareto@unesp.br, cristina.vieira@univ.lyon1.frAbstractHost shifts in insects are considered a key process with the potential to contribute to reproductive isolation and speciation. Both genomic and transcriptomic variation are attributed to such a process...
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Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
...rearrangements, including chromosomal fission and fusion events. A special type of SVs are transposable elements (TEs), mobile genomic sequences that can autonomously create new copies of themselves. SVs can induce reorganization of the resulting in the disruption, loss, reordering, or duplication of genes...
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Research: Phylogenetic relatedness rather than aquatic habitat fosters horizontal transfer of transposable elements in animals
- Héloïse Muller,
- Rosina Savisaar,
- Jean Peccoud,
- Sylvain Charlat,
- and Clément Gilbert
Genome Res. September 2025 35: 2011-2022; Published in Advance August 8, 2025, doi:10.1101/gr.280432.125
...of transposable elements (HTT) is an important driver of evolution, yet the factors conditioning this phenomenon remain poorly characterized. Here, we screen 247 animal s from four phyla (annelids, arthropods, mollusks, chordates), spanning 19 independent transitions between aquatic and terrestrial lifestyles...
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Resource: Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle
- Alexander S. Leonard,
- Xena M. Mapel,
- and Hubert Pausch
Genome Res. February 2024 34: 300-309; Published in Advance February 14, 2024, doi:10.1101/gr.278267.123
...Pan-genotyped structural variation improves molecular phenotype mapping in cattle Alexander S. Leonard, Xena M. Mapel and Hubert Pausch Animal Genomics, ETH Zurich, 8092 Zurich, Switzerland Corresponding authors: alleonard@ethz.ch, hubert.pausch@usys.ethz.chAbstractExpression and splicing...
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Research: Major impacts of widespread structural variation on sorghum
- Zhihai Zhang,
- Joao Paulo Gomes Viana,
- Bosen Zhang,
- Kimberly K.O. Walden,
- Hans Müller Paul,
- Stephen P. Moose,
- Geoffrey P. Morris,
- Chris Daum,
- Kerrie W. Barry,
- Nadia Shakoor,
- and Matthew E. Hudson
Genome Res. February 2024 34: 286-299; Published in Advance March 13, 2024, doi:10.1101/gr.278396.123
...Corresponding author: mhudson@illinois.eduAbstractGenetic diversity is critical to crop breeding and improvement, and dissection of the genomic variation underlying agronomic traits can both assist breeding and give insight into basic biological mechanisms. Although recent analyses in plants reveal many...
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Research: Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements
- Hosiana Abewe,
- Alexandra Richey,
- Jeffery M. Vahrenkamp,
- Matthew Ginley-Hidinger,
- Craig M. Rush,
- Noel Kitchen,
- Xiaoyang Zhang,
- and Jason Gertz
Genome Res. March 2025 35: 393-403; Published in Advance March 3, 2025, doi:10.1101/gr.279699.124
...genomic structure and gene expression is complex and has been described as context specific by several studies (Chen et al. 2024; Pollex et al. 2024b). Some studies have reported minimal changes in expression when large perturbations in architecture are observed, whereas other studies have found large...
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Commentary: Implications of the first complete human genome assembly Genome Res. April 2022 32: 595-598; Published in Advance March 31, 2022, doi:10.1101/gr.276723.122

...disease susceptibility is linked to structural variation, within noncoding regions of the human . Most DNA in the human still has unknown functions and is referred to as “genomic dark matter.” Recent work has centered on uncovering key roles for this DNA, which is mainly derived from transposable elements...
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Research: Mutagenesis of human genomes by endogenous mobile elements on a population scale
- Nelson T. Chuang,
- Eugene J. Gardner,
- Diane M. Terry,
- Jonathan Crabtree,
- Anup A. Mahurkar,
- Guillermo L. Rivell,
- Charles C. Hong,
- James A. Perry,
- and Scott E. Devine
Genome Res. December 2021 31: 2225-2235; Published in Advance November 12, 2021, doi:10.1101/gr.275323.121
...), and SVA elements (Mills et al. 2007). When these mobile elements are inserted into genes or other functionally important genomic sites, they can cause human diseases (for review, see Hancks and Kazazian 2016; Kazazian and Moran 2017). Kazazian et al. (1988) discovered the earliest examples of disease...
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Method: Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC
- Byron J. Smith,
- Chunyu Zhao,
- Veronika Dubinkina,
- Xiaofan Jin,
- Liron Zahavi,
- Saar Shoer,
- Jacqueline Moltzau-Anderson,
- Eran Segal,
- and Katherine S. Pollard
Genome Res. May 2025 35: 1247-1260; Published in Advance April 10, 2025, doi:10.1101/gr.279543.124
...hypothesize that these might indicate important physiological similarities that distinguish high-engraftment strains from the others. Among 85 genes in these shared clusters, the most common COG category annotation was X (“Mobilome”) reinforcing that phage, plasmids, and other mobile genetic elements...
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