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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
..., Section 3.Comparative genomics of the histone clusterFigure 3A shows a schematic view of the histone locus across four different assemblies: iso-1 (FlyBase), iso-1 (HiFi), A4, and A3. The iso-1 FlyBase assembly contains a gap represented by empty space and is scaled to match our assembly's 113 copies...
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Mini-Review: The paradox of R-loops: guardians of the genome or drivers of disease?
- Shachinthaka D. Dissanayaka Mudiyanselage,
- Phillip Wulfridge,
- and Kavitha Sarma
Genome Res. September 2025 35: 1919-1928; Published in Advance August 6, 2025, doi:10.1101/gr.278992.124
...without RF collapse, and a reconstituted yeast replication system demonstrated that RFs can bypass naked R-loops (Kumar et al. 2021). Consistent with these findings, in bacterial systems, RNA polymerase bound to R-loops temporally stalls RFs more effectively than R-loops alone (Brüning and Marians 2020...
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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
...to high homogenization within a single cluster (Ganley and Kobayashi 2011; Hori et al. 2021; Garcia et al. 2024). The complex IGS region, similarly to what is observed in humans and budding yeast (Ganley and Kobayashi 2011; Hori et al. 2021), is composed of tandemly arranged repeats and can undergo...
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Research: A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia
- Sivaranjani Namasivayam,
- Rodrigo P. Baptista,
- Wenyuan Xiao,
- Erica M. Hall,
- Joseph S. Doggett,
- Karin Troell,
- and Jessica C. Kissinger
Genome Res. May 2021 31: 852-865; Published in Advance April 27, 2021, doi:10.1101/gr.266403.120
.... However, the sequence information contained in these contigs as well as individual unassembled T. gondii genomic and EST reads (Sanger chemistry) that matched mtDNA from related species, served as a template for PCR primer design that carefully avoided NUMTs (Supplemental Table S1). Mitochondria...
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Method: Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays
- Shaleen Shrestha,
- Jared Allan Sewell,
- Clarissa Stephanie Santoso,
- Elena Forchielli,
- Sebastian Carrasco Pro,
- Melissa Martinez,
- and Juan Ignacio Fuxman Bass
Genome Res. September 2019 29: 1533-1544; doi:10.1101/gr.248823.119
...IP-seq to address many central human functional genomics problems such as determining whether disease-associated single nucleotide variants (SNVs) and short insertions/deletions (indels) in noncoding regions alter TF binding, as well as identifying TFs that bind to specific DNA motifs and repetitive genomic DNA...
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Research: Unique genetic basis of the distinct antibiotic potency of high acetic acid production in the probiotic yeast Saccharomyces cerevisiae var. boulardii
- Benjamin Offei,
- Paul Vandecruys,
- Stijn De Graeve,
- María R. Foulquié-Moreno,
- and Johan M. Thevelein
Genome Res. September 2019 29: 1478-1494; Published in Advance August 29, 2019, doi:10.1101/gr.243147.118
...unusually high levels of acetic acid, which is strongly inhibitory to bacterial growth in agar-well diffusion assays and could be vital for its unique application as a probiotic among yeasts. Using pooled-segregant whole- sequence analysis with S. boulardii and S. cerevisiae parent strains, we succeeded...
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Research: Numerical and spatial patterning of yeast meiotic DNA breaks by Tel1
- Neeman Mohibullah and
- Scott Keeney
Genome Res. February 2017 27: 278-288; Published in Advance December 6, 2016, doi:10.1101/gr.213587.116
...-labeling of electrophoretically separated genomic DNA are often unable to distinguish lone DSBs from the clustered DSBs that form in the absence of Tel1, leading to underestimated DSB levels (Garcia et al. 2015).To circumvent limitations of gel-based quantification of broken chromosomes, we assayed Spo11-oligo levels instead...
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Research: Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control
- Todd P. Michael,
- Evan Ernst,
- Nolan Hartwick,
- Philomena Chu,
- Douglas Bryant,
- Sarah Gilbert,
- Stefan Ortleb,
- Erin L. Baggs,
- K. Sowjanya Sree,
- Klaus J. Appenroth,
- Joerg Fuchs,
- Florian Jupe,
- Justin P. Sandoval,
- Ksenia V. Krasileva,
- Ljudmylla Borisjuk,
- Todd C. Mockler,
- Joseph R. Ecker,
- Robert A. Martienssen,
- and Eric Lam
Genome Res. February 2021 31: 225-238; Published in Advance December 23, 2020, doi:10.1101/gr.266429.120
...of the pathways associated with multicellular and developmental processes are not under TOD control in W. australiana, where genes that cycle the conditions tested predominantly have carbon processing and chloroplast-related functions. The Wolffia and TOD expression data set thus provide insight...
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Research: Mechanisms of precise genome editing using oligonucleotide donors
- Yinan Kan,
- Brian Ruis,
- Taylor Takasugi,
- and Eric A. Hendrickson
Genome Res. July 2017 27: 1099-1111; Published in Advance March 29, 2017, doi:10.1101/gr.214775.116
...and establishes guidelines for PGE in human cells. [Supplemental material is available for this article.] Genome editing is the intentional alteration of the genetic information in living cells or organisms. Since Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated 9 (CRISPR/Cas9) (Jinek...
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Research: Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments
- Barbara Dunn,
- Chandra Richter,
- Daniel J. Kvitek,
- Tom Pugh,
- and Gavin Sherlock
Genome Res. May 2012 22: 908-924; Published in Advance February 27, 2012, doi:10.1101/gr.130310.111
...genomic similarity to bread yeasts by both microsatellite repeat and multilocus sequence analysis (Fay and Benavides 2005a; Ayoub et al. 2006; Legras et al. 2007). The remaining nine commercial wine strains do not appear in any distinct clusters.Of the remaining non-wine strains, the two ale strains...

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