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Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
- Clotilde Garrido,
- Cintia Gómez-Muñoz,
- Etienne Kornobis,
- Nicolas Agier,
- Oana Ilioaia,
- Gilles Fischer,
- and Zhou Xu
Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
...response and inappropriate repair. In the budding yeast Saccharomyces cerevisiae, these include Rap1 and its cofactors Rif1/Rif2, which are bound to double-stranded DNA (dsDNA) in numbers roughly proportional to TL (Marcand et al. 1997; Levy and Blackburn 2004). In addition, owing to the incomplete...
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Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
...parts using the Qiagen blood and tissue kit following the standard protocol, including treatment with 4 µL RNase and 25 µL Proteinase K. The DNA extraction product was cleaned and concentrated with ZymoResearch genomic DNA Clean & Concentrator kit. For most samples, the RNase treatment was repeated...
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Research: Highly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversity
- Cory A. Weller,
- Ilya Andreev,
- Michael J. Chambers,
- Morgan Park,
- NISC Comparative Sequencing Program,
- Joshua S. Bloom,
- and Meru J. Sadhu
Genome Res. May 2023 33: 729-740; Published in Advance May 1, 2023, doi:10.1101/gr.277515.122
..., Gettle N, Gilchrist C, Zhang Z, Stelkens R. 2021. Genomic evidence of an ancient East Asian divergence event in wild Saccharomyces cerevisiae. Genome Biol Evol 13: evab001. doi:10.1093/gbe/evab001 ↵Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27: 573...
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Research: Reactivation of transposable elements following hybridization in fission yeast
- Sergio Tusso,
- Fang Suo,
- Yue Liang,
- Li-Lin Du,
- and Jochen B.W. Wolf
Genome Res. February 2022 32: 324-336; Published in Advance December 14, 2021, doi:10.1101/gr.276056.121
...families. These results are consistent with full-length elements being mostly of young age and solo LTRs being of much older origin.In the S. pombe reference strain, ∼70% of Tf2 mobilization events involve homologous recombination between newly synthesized cDNA and a pre-existing copy of Tf2; the remaining...
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Method: Double insertion of transposable elements provides a substrate for the evolution of satellite DNA
- Michael P. McGurk and
- Daniel A. Barbash
Genome Res. May 2018 28: 714-725; Published in Advance March 27, 2018, doi:10.1101/gr.231472.117
...elements are separated by identical 33-nt duplications of rDNA sequence, consistent with the tandem originating when two R1 elements inserted in the same rDNA unit and then subsequently expanded by unequal exchange (Fig. 1C; Roiha et al. 1981). Tandem dimers of DNA transposons have been found in bacterial...
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Research: The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible
- Yue Hao,
- Makenzie E. Mabry,
- Patrick P. Edger,
- Michael Freeling,
- Chunfang Zheng,
- Lingling Jin,
- Robert VanBuren,
- Marivi Colle,
- Hong An,
- R. Shawn Abrahams,
- Jacob D. Washburn,
- Xinshuai Qi,
- Kerrie Barry,
- Christopher Daum,
- Shengqiang Shu,
- Jeremy Schmutz,
- David Sankoff,
- Michael S. Barker,
- Eric Lyons,
- J. Chris Pires,
- and Gavin C. Conant
Genome Res. May 2021 31: 799-810; Published in Advance April 16, 2021, doi:10.1101/gr.270033.120
...48 Gb were used as input for Canu. The following parameters were modified for assembly: minReadLength = 1000, GenomeSize = 500 Mb, corOutCoverage = 200 “batOptions=-dg 3 -db 3 – dr 1 -ca 500 -cp 50”. All other parameters were left as default. The assembly graph was visualized using Bandage (Wick et...
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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
...acetic acid production and were included in the superior pool (Fig. 2F). The same number of segregants producing negligible acetic acid as parent S288c was included in the inferior pool (Fig. 2E).Equal quantities of cell biomass from the segregants in each pool were combined and subjected to genomic DNA...
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Research: Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions
- Yuning Zhang,
- Tiffany D. Ho,
- Nicolas E. Buchler,
- and Raluca Gordân
Genome Res. July 2021 31: 1216-1229; Published in Advance May 11, 2021, doi:10.1101/gr.275145.120
...) and thyroid hormone receptor (THR) proteins directly compete for binding to response elements involved in regulating lipid metabolism, cell growth, and differentiation (Miyamoto et al. 1997). In fungi, a well-known example of competitive TF-DNA binding is that of Saccharomyces cerevisiae basic helix...
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Research: DNA mismatch repair preferentially protects genes from mutation
- Eric J. Belfield,
- Zhong Jie Ding,
- Fiona J.C. Jamieson,
- Anne M. Visscher,
- Shao Jian Zheng,
- Aziz Mithani,
- and Nicholas P. Harberd
Genome Res. January 2018 28: 66-74; Published in Advance December 12, 2017, doi:10.1101/gr.219303.116
...): (CDS) coding DNA sequence; (UTRs) untranslated regions; (TE) transposable element; (Other) noncoding RNAs and pseudogenes. Orange bars show relative distribution (%) of SNVs in WT MA lines between different genomic annotation categories; data from Ossowski et al. (2010) and Jiang et al. (2014) were...
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Research: Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication
- Vinay Tripuraneni,
- Gonen Memisoglu,
- Heather K. MacAlpine,
- Trung Q. Tran,
- Wei Zhu,
- Alexander J. Hartemink,
- James E. Haber,
- and David M. MacAlpine
Genome Res. May 2021 31: 775-788; Published in Advance April 2, 2021, doi:10.1101/gr.271155.120
...end-resectioning are closely coupled events, we also profiled total DNA coverage to estimate the extent of end-resectioning in each sample (Supplemental Fig. 3). Similar to the MNase chromatin accessibility data, we observed a decrease in genomic DNA coverage for wild-type cells (∼1.9-fold), which...

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