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RESOURCE: Sequence-based estimation of minisatellite and microsatellite repeat variability
- Matthieu Legendre,
- Nathalie Pochet,
- Theodore Pak,
- and Kevin J. Verstrepen
Genome Res. December 2007 17: 1787-1796; Published in Advance October 31, 2007, doi:10.1101/gr.6554007
...: 4 , doi: 10.1186/1471-2105-5-4 . ↵ Denoeud, F. , Vergnaud, G. , Benson, G. ( 2003 ) Predicting human minisatellite polymorphism . Genome Res. 13 : 856 – 867 . ↵ Ellegren, H. ( 2004 ) Microsatellites: Simple sequences with complex evolution . Nat. Rev. Genet. 5 : 435 – 445 . ↵ Fidalgo, M. , Barrales...
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Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
- Meilin Zhang,
- Heng Du,
- Yu Zhang,
- Yue Zhuo,
- Zhen Liu,
- Yahui Xue,
- Lei Zhou,
- Sixuan Zhou,
- Wanying Li,
- and Jian-Feng Liu
Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
..., China ↵3 These authors contributed equally to this work. Corresponding author: liujf@cau.edu.cnAbstractAs the scale of deep whole- sequencing (WGS) data has grown exponentially, hundreds of millions of single nucleotide polymorphisms (SNPs) have been identified in livestock. Utilizing these massive SNP...
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LETTER: CeRep25B Forms Chromosome-Specific Minisatellite Arrays in Caenorhabditis elegans
- Dave Pilgrim
Genome Res. November 1, 1998 8: 1192-1201; doi:10.1101/gr.8.11.1192
...if the polymorphism (eP97) is due to a change in the CeRep25B microsatellite array. The eP97 polymorphism was detected following digestion with Cla I, which produced a 4.5-kb band in the canonical wild-type stain (N2), and a 4.95-kb band in RC301. Analysis of the unc-45 genomic sequence predicts fragment sizes...
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Method: Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter
- Niccoló Tesi,
- Alex Salazar,
- Yaran Zhang,
- Sven van der Lee,
- Marc Hulsman,
- Lydian Knoop,
- Sanduni Wijesekera,
- Jana Krizova,
- Anne-Fleur Schneider,
- Maartje Pennings,
- Kristel Sleegers,
- Erik-Jan Kamsteeg,
- Marcel Reinders,
- and Henne Holstege
Genome Res. November 2024 34: 1942-1953; Published in Advance October 15, 2024, doi:10.1101/gr.279351.124
..., facilitating not only expansions and contractions of the repeating motif sequence, but also allelic diversity within the sequence (Pearson et al. 2005; Lynch et al. 2008). Several definitions of TRs have been introduced based on the motif length and size variability, including microsatellites, minisatellites...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...suggesting (Hillier et al. 2005; Li et al. 2015; Tyson et al. 2018).C. elegans’ original reference (Table 1) was generated from the standard wild-type strain, N2 (Brenner 1974). Unfortunately, N2 was probably genetically polymorphic even when it was first frozen in 1969 (Sterken et al. 2015); it continued...
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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
...female, whereas eusocial Blattodea workers are of both sexes. Hymenoptera colonies are headed by one or a small number of queens, whereas Blattodea colonies contain both a king and a queen.The hypotheses proposed to explain the high recombination rates observed in eusocial Hymenoptera predict...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...and the presence/absence polymorphisms between the nuclear s; however, they lacked the resolution to identify individual haplotypes (Cuomo et al. 2017; Schwessinger et al. 2018, 2020; Vasquez-Gross et al. 2020). The latest fully haplotype-phased and nuclear-assigned T2T s have provided the first insights...
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Research: Natural variation in C. elegans short tandem repeats
- Gaotian Zhang,
- Ye Wang,
- and Erik C. Andersen
Genome Res. October 2022 32: 1852-1861; Published in Advance October 4, 2022, doi:10.1101/gr.277067.122
...been identified among wild Caenorhabditis elegans strains, the natural diversity in STRs remains unknown. Here, we characterized the distribution of 31,991 STRs with motif lengths of 1–6 bp in the reference of C. elegans. Of these STRs, 27,667 harbored polymorphisms across 540 wild strains and only...
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METHODS: Evaluation of Single Nucleotide Polymorphism Typing with Invader on PCR Amplicons and Its Automation
- Charles A. Mein,
- Bryan J. Barratt,
- Michael G. Dunn,
- Thorsten Siegmund,
- Annabel N. Smith,
- Laura Esposito,
- Sarah Nutland,
- Helen E. Stevens,
- Amanda J. Wilson,
- Michael S. Phillips,
- Nancy Jarvis,
- Scott Law,
- Monika de Arruda,
- and John A. Todd
Genome Res. March 1, 2000 10: 330-343; doi:10.1101/gr.10.3.330
...Evaluation of Single Nucleotide Polymorphism Typing with Invader on PCR Amplicons and Its Automation Charles A. Mein 1 , Bryan J. Barratt 1 , Michael G. Dunn 1 , Thorsten Siegmund 1 , Annabel N. Smith 1 , Laura Esposito 1...
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LETTER: Simple Sequence Repeats in Escherichia coli: Abundance, Distribution, Composition, and Polymorphism
- Riva Gur-Arie,
- Cyril J. Cohen,
- Yuval Eitan,
- Leora Shelef,
- Eric M. Hallerman,
- and Yechezkel Kashi
Genome Res. January 1, 2000 10: 62-71; doi:10.1101/gr.10.1.62
...Simple Sequence Repeats in Escherichia coli : Abundance, Distribution, Composition, and Polymorphism Riva Gur-Arie 3 , Cyril J. Cohen 3 , Yuval Eitan , Leora Shelef 1 , Eric M. Hallerman 2 , and Yechezkel Kashi 4...

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