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Research: Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently
- Sophia David,
- Christophe Rusniok,
- Massimo Mentasti,
- Laura Gomez-Valero,
- Simon R. Harris,
- Pierre Lechat,
- John Lees,
- Christophe Ginevra,
- Philippe Glaser,
- Laurence Ma,
- Christiane Bouchier,
- Anthony Underwood,
- Sophie Jarraud,
- Timothy G. Harrison,
- Julian Parkhill,
- and Carmen Buchrieser
Genome Res. November 2016 26: 1555-1564; Published in Advance September 23, 2016, doi:10.1101/gr.209536.116
...a worldwide distributed epidemic Legionella pneumophila clone that emerged within a highly diverse species. Genome Res 18: 431–441. Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P, Cheng L, Pessia A, Aanensen DM,Mather AE, Page AJ, et al. 2014. Dense genomic sampling identifies highways...
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Research: Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization
- Cyril Matthey-Doret,
- Morgan J. Colp,
- Pedro Escoll,
- Agnès Thierry,
- Pierrick Moreau,
- Bruce Curtis,
- Tobias Sahr,
- Matt Sarrasin,
- Michael W. Gray,
- B. Franz Lang,
- John M. Archibald,
- Carmen Buchrieser,
- and Romain Koszul
Genome Res. September 2022 32: 1698-1710; Published in Advance September 15, 2022, doi:10.1101/gr.276375.121
...Chromosome-scale assemblies of Acanthamoeba castellanii s provide insights into Legionella pneumophila infection–related chromatin reorganization Cyril Matthey-Doret1,2,6, Morgan J. Colp3,6, Pedro Escoll4, Agnès Thierry1, Pierrick Moreau1, Bruce Curtis3, Tobias Sahr4, Matt Sarrasin5, Michael W...
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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
...community with more than 10 strains and an HIV-1 coinfection data set. We use devider to investigate the within-host diversity of a long-read bovine gut meta enriched for AMR genes, discovering 13 distinct haplotypes for a tet(Q) tetracycline-resistance gene with >18,000× coverage and six haplotypes...
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Research: Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of bla_KPC
- Angela Gomez-Simmonds,
- Medini K. Annavajhala,
- Dwayne Seeram,
- Todd W. Hokunson,
- Heekuk Park,
- and Anne-Catrin Uhlemann
Genome Res. November 2024 34: 1895-1907; Published in Advance October 4, 2024, doi:10.1101/gr.279355.124
...) patients (39%) or non-ICU inpatients (43%) although a subset were obtained in the emergency department (10%) or outpatient setting (8%). blaKPC was identified in 460/605 (76%) isolates (39% blaKPC-2; 58% blaKPC-3; 2% blaKPC-4; 0.5% blaKPC-56) demonstrating substantial species and clonal diversity (Fig. 1A...
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Method: Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
- Rachel M. Petersen,
- Christopher M. Vockley,
- and Amanda J. Lea
Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
...multiplexed mSTARR-seq, an extension of mSTARR-seq that can incorporate genetically diverse input and is thus capable of experimentally testing for interactions between DNAm and genotype in high throughput.In this study, we apply multiplexed mSTARR-seq to identify allelic differences in regulatory function...
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Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
- Reuben M. Buckley,
- Nüket Bilgen,
- Alexander C. Harris,
- Peter Savolainen,
- Cafer Tepeli,
- Metin Erdoğan,
- Aitor Serres Armero,
- Dayna L. Dreger,
- Frank G. van Steenbeek,
- Marjo K. Hytönen,
- Heidi G. Parker,
- Jessica Hale,
- Hannes Lohi,
- Bengi Çınar Kul,
- Adam R. Boyko,
- and Elaine A. Ostrander
Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
...prioritized according to functional impact, we can identify trait associations for variants often overlooked by traditional -wide association studies (GWASs).The rigid population structure and extreme phenotypic diversity across breeds is an essential component of our analysis. By definition, dog breeds...
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Resource: A harmonized public resource of deeply sequenced diverse human genomes
- Zan Koenig,
- Mary T. Yohannes,
- Lethukuthula L. Nkambule,
- Xuefang Zhao,
- Julia K. Goodrich,
- Heesu Ally Kim,
- Michael W. Wilson,
- Grace Tiao,
- Stephanie P. Hao,
- Nareh Sahakian,
- Katherine R. Chao,
- Mark A. Walker,
- Yunfei Lyu,
- gnomAD Project Consortium,
- Heidi L. Rehm,
- Benjamin M. Neale,
- Michael E. Talkowski,
- Mark J. Daly,
- Harrison Brand,
- Konrad J. Karczewski,
- Elizabeth G. Atkinson,
- and Alicia R. Martin
Genome Res. May 2024 34: 796-809; Published in Advance May 15, 2024, doi:10.1101/gr.278378.123
...A harmonized public resource of deeply sequenced diverse human s Zan Koenig1,2,13, Mary T. Yohannes1,2,13, Lethukuthula L. Nkambule1,2, Xuefang Zhao3,4,5, Julia K. Goodrich2,3, Heesu Ally Kim1, Michael W. Wilson3, Grace Tiao3, Stephanie P. Hao3,4,5, Nareh Sahakian6, Katherine R. Chao3, Mark A...
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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
...-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems...
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Research: Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders
- Alberto Gómez-Carballa,
- Xabier Bello,
- Jacobo Pardo-Seco,
- Federico Martinón-Torres,
- and Antonio Salas
Genome Res. October 2020 30: 1434-1448; Published in Advance September 2, 2020, doi:10.1101/gr.266221.120
...and also diversity values, showing substantially heterogeneous patterns worldwide (Supplemental Table S3).Phylogeographic information allows reconstructing dynamics of (sub)haplogroups worldwide (Fig. 4). The two main clades (A and B) and most of their main first step–derived subclades (e.g., A1, A3, B1, B...
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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
...inhibited by RecBCD are identified, growth of a newly isolated phage, named LLS, is enhanced by RecBCD. LLS's sequence reveals it is related to bacteriophage λ but encodes no recombination-promoting (Rec) proteins or associated RecBCD inhibitor. However, it contains an unexpectedly high number of Chi sites...
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