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Resource: Whole-genome sequencing of diverse 351 cultured prokaryotes including as-yet-unsequenced type strains
- Shingo Kato,
- Sachiko Masuda,
- Arisa Shibata,
- Takashi Itoh,
- Mitsuo Sakamoto,
- Ken Shirasu,
- and Moriya Ohkuma
Genome Res. April 2026 36: 875-884; Published in Advance April 7, 2026, doi:10.1101/gr.281026.125
...Whole- sequencing of diverse 351 cultured prokaryotes including as-yet-unsequenced type strains Shingo Kato1, Sachiko Masuda2, Arisa Shibata2, Takashi Itoh1, Mitsuo Sakamoto1, Ken Shirasu2 and Moriya Ohkuma1 1Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki...
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Research: Evidence for selfing in a vertebrate from whole-genome sequencing
- Astrid Böhne,
- Zeynep Oğuzhan,
- Ioannis Chrysostomakis,
- Simon Vitt,
- Denis Meuthen,
- Sebastian Martin,
- Sandra Kukowka,
- and Timo Thünken
Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
...-mer-spectra analysis revealed a similar size across all four sequenced individuals (mean size across k-mer sizes 20, 30, and 40: 800–817 Mb) and pointed toward lower estimates of -wide heterozygosity in both offspring (mean heterozygosity across k-mer sizes 20, 30, and 40; wildI: 0.097%, parent: 0.119%, offspring1: 0...
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Method: Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples
- Shuangxi Ji,
- Tong Zhu,
- Ankit Sethia,
- and Wenyi Wang
Genome Res. April 2024 34: 633-641; Published in Advance April 8, 2024, doi:10.1101/gr.278456.123
..., but not by the intersection calls, as false negatives; any calls reported by the intersection calls, but not by the consensus, as false positives. We calculated precision, recall, and F1 score to evaluate the accuracy of a call set against a truth set. Definitions of VAF bins, sequencing depth bins, clonality, and variant...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...with annotations of accessible chromatin regions identified using ATAC-seq data from the liver and brain. Analysis of the overlap between TEs and accessible chromatin revealed a large depletion of TEs in accessible chromatin. Although TEs represent ∼52% of the sequence, TE insertions only represent <20...
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Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
...offers guidance to design cost-effective experimental strategies that do not compromise on discovering novel biology.Over the last five years, long-read sequencing (LRS) technologies have transformed the landscape of genetic variant discovery in two fundamental ways. First, they have increased...
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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
...metrics for constraint are available in the dog: constrained CDS, human ortholog LOEUF (loss of function observed over expected upper fraction), and variant phyloP score. Constrained CDS and variant phyloP score both represent evolutionary conservation of canine genomic sequence derived from the Zoonomia...
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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...at the Institute of Agriculture Biology and Biotechnology (IABB; CNR) (Morello et al. 2024). We performed 88× coverage short-read Illumina sequencing to account for potential genetic differences owing to independent clonal propagation over thousands of generations between this accession and that of the Rutgers...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...by DNA sequencing (ChIP-seq) of an ever growing number of TFs in different cell types, species, and conditions are revealing repeat-associated binding sites (RABS) whereby reproducible TF-DNA interactions fall within subtypes of major repeat families (Bourque et al. 2008). Coincident with their discovery...
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Method: Identifying crossovers and shared genetic material in whole genome sequencing data from families
- Kelley Paskov,
- Brianna Chrisman,
- Nathaniel Stockham,
- Peter Yigitcan Washington,
- Kaitlyn Dunlap,
- Jae-Yoon Jung,
- and Dennis P. Wall
Genome Res. October 2023 33: 1747-1756; Published in Advance October 25, 2023, doi:10.1101/gr.277172.122
...be used to identify crossovers from family sequencing data.As whole- sequencing (WGS) becomes ubiquitous, large family-based cohorts are now available, which have the potential to reveal more about how genetic material is transmitted within families and about how shared genetic material contributes...
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Research: An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
- Elise Parey,
- Alexandra Louis,
- Jérôme Montfort,
- Yann Guiguen,
- Hugues Roest Crollius,
- and Camille Berthelot
Genome Res. September 2022 32: 1685-1697; Published in Advance August 12, 2022, doi:10.1101/gr.276953.122
...several duplicated chromosomes, contradicting current paradigms that asymmetrical evolution is specific to allopolyploids. Altogether, our results offer novel insights into evolutionary dynamics following ancient polyploidizations in vertebrates.Since the first teleost fish sequence was published in 2002...

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