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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
...Anna Grandchamp1, Lucas Kühl1, Marie Lebherz1, Kathrin Brüggemann1, John Parsch2 and Erich Bornberg-Bauer1,3 1Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany; 2Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152...
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Method: Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change
- Apurva Narechania,
- Dean Bobo,
- Kevin Deitz,
- Rob DeSalle,
- Paul J. Planet,
- and Barun Mathema
Genome Res. October 2024 34: 1651-1660; Published in Advance September 25, 2024, doi:10.1101/gr.278594.123
...of information entropy (Shannon 1948). Rather than using these numbers to compute traditional ecological quantities like the diversity of species in an area, we use them to compute the diversity of genomic information. For example, we envision each unique k-mer a species and each a transect sampled from the pan...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36) (Bolger et al. 2014). Trimmed reads were used with KAT v2.4.2 (Mapleson et al. 2017) hist to produce k-mer frequency histogram. Genome size and heterozygosity were estimated with GenomeScope 2.0 (Ranallo-Benavidez et al. 2020). PacBio subreads were...
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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
...microbiome reads, where the true origin of each read is known. We found that k-mer-based tools, Kraken2 and Centrifuge, had the highest species-level recall. This means that they correctly classified the greatest number of reads to the species level, beating BLAST-based pipelines using equivalent databases...
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Research: Extreme heterochiasmy and high rates of sex-reversed recombination result in large yet homomorphic sex chromosomes in the Emei moustache toad
- Siyu Xie,
- Jun Li,
- Wanyan Chen,
- Lydia J.M. Fong,
- Chunhua Huang,
- Yan Feng,
- Qingbo Ai,
- Mian Zhao,
- Judith E. Mank,
- and Hua Wu
Genome Res. June 2025 35: 1325-1336; Published in Advance April 24, 2025, doi:10.1101/gr.280161.124
...Tables S13–S16).To further identify the Y Chromosome, we used k-mer analysis to detect male-specific k-mers, often referred as Y-mers (Torres et al. 2018; Almeida et al. 2021; Kabir et al. 2022), from paired-end short reads of 20 males and 20 females (Supplemental Data Set S1). In an XY system...
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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
...-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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Research: Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
- Itai Sharon,
- Michael J. Morowitz,
- Brian C. Thomas,
- Elizabeth K. Costello,
- David A. Relman,
- and Jillian F. Banfield
Genome Res. January 2013 23: 111-120; Published in Advance August 30, 2012, doi:10.1101/gr.142315.112
...of parameters (coverage-related parameters and k-mer size) for each coverage bin. For each iteration, assembly parameters that fit the coverage bin with the highest coverage remaining are used, and the data assembled using Velvet (Zerbino and Birney 2008) (ABySS [Simpson et al. 2009] was used for the last...
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Research: Dynamic DNA N⁶-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus
- Yongqiang Liu,
- Junhua Niu,
- Fei Ye,
- Therese Solberg,
- Borong Lu,
- Chundi Wang,
- Mariusz Nowacki,
- and Shan Gao
Genome Res. February 2024 34: 256-271; Published in Advance March 12, 2024, doi:10.1101/gr.278796.123
...Yongqiang Liu1,2,7, Junhua Niu1,2,7, Fei Ye1,2,7, Therese Solberg3,4,5, Borong Lu1,2, Chundi Wang1,6, Mariusz Nowacki3 and Shan Gao1,2 1MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; 2...
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Method: Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
- Yuhong Sun,
- Zhanwen Cheng,
- Xiang Li,
- Qing Yang,
- Bixi Zhao,
- Ziqi Wu,
- and Yu Xia
Genome Res. April 2023 33: 612-621; Published in Advance April 11, 2023, doi:10.1101/gr.277266.122
...: 1103–1110. doi:10.1038/s41592-020-00971-x ↵Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27: 722–736. doi:10.1101/gr.215087.116 ↵Kovaka S, Fan Y, Ni B, Timp W, Schatz...
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Resource: The western redcedar genome reveals low genetic diversity in a self-compatible conifer
- Tal J. Shalev,
- Omnia Gamal El-Dien,
- Macaire M.S. Yuen,
- Shu Shengqiang,
- Shaun D. Jackman,
- René L. Warren,
- Lauren Coombe,
- Lise van der Merwe,
- Ada Stewart,
- Lori B. Boston,
- Christopher Plott,
- Jerry Jenkins,
- Guifen He,
- Juying Yan,
- Mi Yan,
- Jie Guo,
- Jesse W. Breinholt,
- Leandro G. Neves,
- Jane Grimwood,
- Loren H. Rieseberg,
- Jeremy Schmutz,
- Inanc Birol,
- Matias Kirst,
- Alvin D. Yanchuk,
- Carol Ritland,
- John H. Russell,
- and Joerg Bohlmann
Genome Res. October 2022 32: 1952-1964; Published in Advance September 15, 2022, doi:10.1101/gr.276358.121
...; Hizume et al. 2001). The WRC assembled at 7.95 Gbp. This discrepancy may be partially explained by filtering of k-mers with very high depth of coverage in GenomeScope to remove organelle-derived reads, which may also remove other heterochromatic sequences such as centromeres and telomeres; however...
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