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Research: Transposon accumulation at xenobiotic gene family loci in aphids
- Tobias Baril,
- Adam Pym,
- Chris Bass,
- and Alex Hayward
Genome Res. October 2023 33: 1718-1733; Published in Advance October 18, 2023, doi:10.1101/gr.277820.123
...extracted, and those present in fewer than three s were removed. The amino acid sequences for each gene from all species were extracted and saved in individual FASTA files. For each gene, sequences were aligned using MAFFT (version 7.453; ‐‐auto) (Katoh and Standley 2013). The subsequent alignments were...
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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
...inert status confirmed by the lack of a start codon and/or interruption by stop codons or frameshift mutations.Note that the mere presence of a homologous noncoding sequence in an outgroup is not sufficient to establish a de novo origin of the ORFan because it is possible that the outgroup sequence...
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Method: Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes
- Hongke Peng,
- Jafar S. Jabbari,
- Luyi Tian,
- Changqing Wang,
- Yupei You,
- Chong Chyn Chua,
- Natasha S. Anstee,
- Noorul Amin,
- Andrew H. Wei,
- Nadia M. Davidson,
- Andrew W. Roberts,
- David C.S. Huang,
- Matthew E. Ritchie,
- and Rachel Thijssen
Genome Res. April 2025 35: 942-955; Published in Advance January 10, 2025, doi:10.1101/gr.279322.124
...and nonclonal mechanisms of selection and adaptation in response to therapeutic pressure is of importance. Moreover, the influence of isoform usage on cell states further underscores the need for comprehensive methodologies. In response to these challenges, alternative methods have emerged to link...
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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...RNA-Val (Supplemental Table S7).Transposon mutagenesis defines mutational tolerance in CNV strainsWe sought to investigate the genetic impact of CNVs using high-throughput genetics. Previous studies using transposon mutagenesis in bacteria and yeast have shown that transposon insertion density reflects tolerance...
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Research: Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain
- James L. Shepherdson,
- David M. Granas,
- Jie Li,
- Zara Shariff,
- Stephen P. Plassmeyer,
- Alex S. Holehouse,
- Michael A. White,
- and Barak A. Cohen
Genome Res. October 2024 34: 1540-1552; Published in Advance September 25, 2024, doi:10.1101/gr.279415.124
...degenerative retinopathies, but most are variants of uncertain significance. We performed a deep mutational scan (DMS) of nearly all possible single amino acid substitutions in CRX using a cell-based transcriptional reporter assay, curating a high-confidence list of nearly 2000 variants with altered...
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Research: Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage
- Emily Lowry,
- Yiqing Wang,
- Tal Dagan,
- and Amir Mitchell
Genome Res. August 2024 34: 1154-1164; Published in Advance August 16, 2024, doi:10.1101/gr.279517.124
...is the same in bacteria using mutation accumulation experiments with repeated exposure to colibactin producers. Ampicillin-resistant DNA damage reporter cells were cocultured for 24 h with genetically engineered colibactin producers and spotted on selective agar. A single reporter colony was then grown...
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Resource: A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality
- Jane Hawkey,
- Ben Vezina,
- Jonathan M. Monk,
- Louise M. Judd,
- Taylor Harshegyi,
- Sebastián López-Fernández,
- Carla Rodrigues,
- Sylvain Brisse,
- Kathryn E. Holt,
- and Kelly L. Wyres
Genome Res. May 2022 32: 1004-1014; Published in Advance March 11, 2022, doi:10.1101/gr.276289.121
...for all substrates in all strains. The latter were associated with 194 distinct reactions (1–32 reactions each, median = 1, Supplemental Table 7), encompassing eight subsystem categories: cell membrane metabolism (n = 76 reactions), lipid metabolism (n = 42), amino acid metabolism (n = 33), transport...
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Research: The chromatin landscape of the histone-possessing Bacteriovorax bacteria
- Georgi K. Marinov,
- Benjamin Doughty,
- Anshul Kundaje,
- and William J. Greenleaf
Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124
...to eukaryotes and most archaea, with eukaryotic nucleosomal histones deriving from their archaeal ancestors. In contrast, bacteria lack histones as a rule. However, histone proteins have recently been identified in a few bacterial clades, most notably the phylum Bdellovibrionota, and these histones have been...
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Research: Inference of selective forces on house mouse genomes during secondary contact in East Asia
- Kazumichi Fujiwara,
- Shunpei Kubo,
- Toshinori Endo,
- Toyoyuki Takada,
- Toshihiko Shiroishi,
- Hitoshi Suzuki,
- and Naoki Osada
Genome Res. March 2024 34: 366-375; Published in Advance March 20, 2024, doi:10.1101/gr.278828.123
...the selective pressures driving this distinct pattern of Y Chromosome haplotypes in southern China, we conducted Wright–Fisher model simulations. The model assumes that a small fraction of the subspecies musculus individuals with longer haplotypes of the SD locus on the sex chromosomes (corresponding to Sly...
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Method: A full-proteome, interaction-specific characterization of mutational hotspots across human cancers
- Siwei Chen,
- Yuan Liu,
- Yingying Zhang,
- Shayne D. Wierbowski,
- Steven M. Lipkin,
- Xiaomu Wei,
- and Haiyuan Yu
Genome Res. January 2022 32: 135-149; Published in Advance December 28, 2021, doi:10.1101/gr.275437.121
.... 2010; Kircher et al. 2014). However, not all mutations can be simply interpreted as causing a gross loss of protein. Many cancer mutations exert their oncogenic effects through altering specific aspects of protein activity and give cancer cells a selective advantage. One promising route to decipher...

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