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Method: Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors
- Nitan Shalon,
- David A. Relman,
- and Eitan Yaffe
Genome Res. May 2022 32: 986-1003; Published in Advance April 12, 2022, doi:10.1101/gr.275894.121
...and Cohan 2011; Polz et al. 2013) and facilitates the spread of virulence factors and antimicrobial-resistance determinants within and between microbial species (Maiques et al. 2006; von Wintersdorff et al. 2016; Deng et al. 2019). Extrachromosomal circular mobile genetic elements (ecMGEs), such as plasmids...
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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
...–resolved population metagenomic data sets to track 18 MGEs for which structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via...
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Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
...-mers assigned via lowest common ancestor (LCA) strategies, as in tools such as Kraken2, these nodes are embedded in a broader topological context through their connections to neighboring nodes. This structural context confers two major advantages: (1) It enables abundance estimation via linear optimization...
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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...precisely genotype these long expansions (Mousavi et al. 2019). In contrast, modern long-read sequencing (LRS) technologies, like Oxford Nanopore Technologies (ONT) nanopore sequencing with newer chemistry or Pacific Biosciences (PacBio) high-fidelity circular consensus sequencing (HiFi), can give accurate...
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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
...carried plasmids, and no circular elements of size <500 kbp were detected in Bordetella ONT assemblies (Supplemental Fig. S5). In CdSC, two isolates (FRC1356 and FRC1385) contained one plasmid each, which was generally assembled and circularized correctly (Supplemental Fig. S4). In isolate FRC1385, two...
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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
..., highlighting the inheritance from the common ancestor and maintenance of the insertion over time. Taken together, our results rejected the hypothesis of spread Helitron copies with OR fragments, which could explain the high frequency of these elements upstream of and downstream from ORs. However...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
..., Shanghai 200433, China; 4School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China; 5Department of Precision Medicine, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai 200433, China; 6Experiment Center...
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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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Method: Real-time analysis and visualization of nanopore metagenomic samples with MARTi
- Ned Peel,
- Samuel Martin,
- Darren Heavens,
- Douglas W. Yu,
- Matthew D. Clark,
- and Richard M. Leggett
Genome Res. November 2025 35: 2488-2500; Published in Advance October 27, 2025, doi:10.1101/gr.280550.125
...in metagenomic data analysis.MethodsLowest Common Ancestor algorithmWhen classifying reads using BLAST (nucleotide or protein) or DIAMOND (a BLAST-like protein alignment tool), MARTi implements a Lowest Common Ancestor algorithm (see below) to assign reads to taxa based on the alignment results. This algorithm...
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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
...that is tandemly duplicated in white-headed animals, nor were any predicted regulatory elements disrupted by the duplication.Pan-based genotyping in a diversity panel of short-read-sequenced cattle supports that a complex SVs underlies depigmentation in white-headed cattleTo further validate an association between...

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