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Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
...in the Pristionchus system.Pristionchus-associated microbiota harbor previously uncharacterized bacterial strainsThe predicted proteomes of all 84 s were taken to reconstruct a bacterial phylogeny (see Methods; Fig. 1). The different lineages were mostly consistent with previous genus assignments based on 16S...
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Research: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
...from 3221 assemblies, we show that the copy number of retroelements correlates with that of ZNFs across at least 750 million years of metazoan evolution. Using computational predictions, we show that ZNFs preferentially bind TEs in diverse animal species. We further investigate the largest ZNF...
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Review: Leveraging the power of long reads for targeted sequencing
- Shruti V. Iyer,
- Sara Goodwin,
- and William Richard McCombie
Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
...Shruti V. Iyer, Sara Goodwin and William Richard McCombie Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA Corresponding author: mccombie@cshl.eduAbstractLong-read sequencing technologies have improved the contiguity and, as a result, the quality of assemblies by generating...
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Resource: A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
- Jack F. Cazet,
- Stefan Siebert,
- Hannah Morris Little,
- Philip Bertemes,
- Abby S. Primack,
- Peter Ladurner,
- Matthias Achrainer,
- Mark T. Fredriksen,
- R. Travis Moreland,
- Sumeeta Singh,
- Suiyuan Zhang,
- Tyra G. Wolfsberg,
- Christine E. Schnitzler,
- Andreas D. Baxevanis,
- Oleg Simakov,
- Bert Hobmayer,
- and Celina E. Juliano
Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
...and improved version of the Hydra single-cell atlas using the AEP-strain as a reference and subsequently uncovered two previously molecularly uncharacterized cell types: somatic gonad ectoderm and mature isorhiza nematocytes. We then combined our CRE annotations with the AEP single-cell atlas to identify novel...
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Research: Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes
- Monica R. Sanchez,
- Celia Payen,
- Frances Cheong,
- Blake T. Hovde,
- Sarah Bissonnette,
- Adam P. Arkin,
- Jeffrey M. Skerker,
- Rachel B. Brem,
- Amy A. Caudy,
- and Maitreya J. Dunham
Genome Res. March 2019 29: 396-406; Published in Advance January 11, 2019, doi:10.1101/gr.232330.117
...of predictive errors, highlighting the importance of implementing experimental methods to directly test gene function in previously uncharacterized s to improve current methods of annotation.The gold standard of gene function characterization relies on observing phenotypes of targeted deletions of predicted...
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Method: The multicomparative 2-n-way genome suite
- Gennady Churakov,
- Fengjun Zhang,
- Norbert Grundmann,
- Wojciech Makalowski,
- Angela Noll,
- Liliya Doronina,
- and Jürgen Schmitz
Genome Res. October 2020 30: 1508-1516; Published in Advance July 29, 2020, doi:10.1101/gr.262261.120
...@uni-muenster.deAbstractTo effectively analyze the increasing amounts of available genomic data, improved comparative analytical tools that are accessible to and applicable by a broad scientific community are essential. We built the “2-n-way” software suite to provide a fundamental and innovative processing framework for revealing...
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Research: The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes
- Drew R. Schield,
- Daren C. Card,
- Nicole R. Hales,
- Blair W. Perry,
- Giulia M. Pasquesi,
- Heath Blackmon,
- Richard H. Adams,
- Andrew B. Corbin,
- Cara F. Smith,
- Balan Ramesh,
- Jeffery P. Demuth,
- Esther Betrán,
- Marc Tollis,
- Jesse M. Meik,
- Stephen P. Mackessy,
- and Todd A. Castoe
Genome Res. April 2019 29: 590-601; Published in Advance March 21, 2019, doi:10.1101/gr.240952.118
...of 559 bp and N50 length of 718 bp.We annotated repeat elements present in the improved assembly using libraries from complete squamate s (Supplemental Methods) constructed using RepeatModeler v.1.0.9 (Smit and Hubley 2015). De novo and homology-based predictions were then performed using RepeatMasker v...
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Research: Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals
- Ulrike Böhme,
- Thomas D. Otto,
- James A. Cotton,
- Sascha Steinbiss,
- Mandy Sanders,
- Samuel O. Oyola,
- Antoine Nicot,
- Sylvain Gandon,
- Kailash P. Patra,
- Colin Herd,
- Ellen Bushell,
- Katarzyna K. Modrzynska,
- Oliver Billker,
- Joseph M. Vinetz,
- Ana Rivero,
- Chris I. Newbold,
- and Matthew Berriman
Genome Res. April 2018 28: 547-560; Published in Advance March 2, 2018, doi:10.1101/gr.218123.116
....View this table: In this window In a new window Table 1. Genome statistics for avian malaria compared with existing Plasmodium reference sThe P. gallinaceum and P. relictum s contain 5273 and 5146 genes (Table 1), respectively (Fig. 1). Those in P. gallinaceum were predicted ab initio and manually curated using P...
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Review: Accurate and complete genomes from metagenomes
- Lin-Xing Chen,
- Karthik Anantharaman,
- Alon Shaiber,
- A. Murat Eren,
- and Jillian F. Banfield
Genome Res. March 2020 30: 315-333; Published in Advance March 18, 2020, doi:10.1101/gr.258640.119
...-read-based analyses. First, they enable the identification of complete open reading frames. Second, assemblies provide larger genomic contexts (e.g., operons). In combination, these considerations improve predictions of metabolic capacities. Further, assembled sequences provide information about gene synteny...
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Resource: Genome-scale phylogenetic function annotation of large and diverse protein families
- Barbara E. Engelhardt,
- Michael I. Jordan,
- John R. Srouji,
- and Steven E. Brenner
Genome Res. November 2011 21: 1969-1980; Published in Advance July 22, 2011, doi:10.1101/gr.104687.109
...an approximation method to SIFTER 2.0 and show a 500-fold improvement in speed with minimal impact on prediction results in the functionally diverse sulfotransferase protein family. On the Nudix protein family, previously inaccessible to the SIFTER framework because of the 66 possible molecular functions, SIFTER...
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