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Research: Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei
- Gregor Jessberger,
- Csilla Várnai,
- Roman R. Stocsits,
- Wen Tang,
- Georg Stary,
- and Jan-Michael Peters
Genome Res. December 2023 33: 2094-2107; Published in Advance December 21, 2023, doi:10.1101/gr.277865.123
.... These processes are fundamental for inheritance but incompletely understood. We analyzed these processes in the frog Xenopus laevis, whose sperm can be assembled into functional pronuclei in egg extracts in vitro. In such extracts, cohesin extrudes DNA into loops, but in vivo cohesin only assembles topologically...
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Resource: Automated identification of conserved synteny after whole-genome duplication
- Julian M. Catchen,
- John S. Conery,
- and John H. Postlethwait
Genome Res. August 2009 19: 1497-1505; Published in Advance May 22, 2009, doi:10.1101/gr.090480.108
...lineages, like salmonids, catastomids, goldfish, Xenopus laevis, and even a rodent (Uyeno and Smith 1972; Allendorf and Thorgaard 1984; Schmid and Steinlein 1991; Risinger and Larhammar 1993; Larhammar and Risinger 1994; Gallardo et al. 1999; David et al. 2003; Mungpakdee et al. 2008a,b). Given...
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LETTER: Extrachromosomal Circular DNA of Tandemly Repeated Genomic Sequences in Drosophila
- Sarit Cohen,
- Keren Yacobi,
- and Daniel Segal
Genome Res. June 2003 13: 1133-1145; doi:10.1101/gr.907603
...contains circular multimers of tandemly repeated genes such as histones, rDNA, Stellate , and the Suppressor of Stellate . Multimers of centromeric heterochromatin sequences are included in eccDNA as well. Our findings are consistent with the hypothesis that intramolecular homologous recombination...
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LETTER: Identification of a conserved family of Meis1-related homeobox genes.
- S Steelman,
- J J Moskow,
- K Muzynski,
- C North,
- T Druck,
- J C Montgomery,
- K Huebner,
- I O Daar,
- and A M Buchberg
Genome Res. February 1997 7: 142-156; doi:10.1101/gr.7.2.142
...function, we cloned and characterized Mrgs from the mouse and human s. We report the sequence of Mrg1 and MRG2 as well as their chromosomal locations in murine and human s. Both Mrgs share a high degree of sequence identity with the protein coding region of Meis1. We have also cloned the Xenopus laevis...
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ARTICLE: A Genetic Linkage Map for Zebrafish: Comparative Analysis and Localization of Genes and Expressed Sequences
- Michael A. Gates,
- Lisa Kim,
- Elizabeth S. Egan,
- Timothy Cardozo,
- Howard I. Sirotkin,
- Scott T. Dougan,
- Deval Lashkari,
- Ruben Abagyan,
- Alexander F. Schier,
- and William S. Talbot
Genome Res. April 1, 1999 9: 334-347; doi:10.1101/gr.9.4.334
...USA; 2Stanford DNA Sequencing and Technology Center, Palo Alto, California 94305 USA Abstract Genetic screens in zebrafish ( Danio rerio ) have isolated mutations in hundreds of genes with essential functions. To facilitate the identification of candidate genes for these mutations, we have...
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Review: k-mer approaches for biodiversity genomics
- Katharine M. Jenike,
- Lucía Campos-Domínguez,
- Marilou Boddé,
- José Cerca,
- Christina N. Hodson,
- Michael C. Schatz,
- and Kamil S. Jaron
Genome Res. February 2025 35: 219-230; Published in Advance January 31, 2025, doi:10.1101/gr.279452.124
...libraries using k-mer spectraOne of the most common direct applications of k-mers in genomics is for characterization of a sequencing data set using the distribution of k-mer coverages; this is commonly referred to as k-mer spectrum or k-mer histogram. A typical k-mer spectrum of a moderately heterozygous...
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LETTER: The evolutionary dynamics of α-satellite
- M. Katharine Rudd,
- Gregory A. Wray,
- and Huntington F. Willard
Genome Res. January 2006 16: 88-96; Published in Advance December 12, 2005, doi:10.1101/gr.3810906
...a suitable resource to begin to address questions of centromere biology and evolution. We have previously characterized the types of α-satellite in the assembly ( Rudd and Willard 2004 ), including their physical relationship to extensive pericentromeric sequence duplications that are, in most cases, distal...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...(e.g., Xenopus laevis) than with teleost fish (e.g., Danio rerio), despite sharing a more recent common ancestry with teleosts (Supplemental Fig. S1K). Nonreference whole- alignment using Progressive Cactus (Armstrong et al. 2020) revealed up to 83.35% sequence identity between A. spatula...
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ARTICLE: The Complete Human Olfactory Subgenome
- Gustavo Glusman,
- Itai Yanai,
- Irit Rubin,
- and Doron Lancet
Genome Res. May 1, 2001 11: 685-702; doi:10.1101/gr.171001
... Repertoire We have performed a comprehensive data mining effort for OR genes in several data sources that together constitute the first draft of the human ( International Human Genome Sequencing Consortium 2001 ). This led to the identification of a total of 906 human potential coding regions of OR genes...
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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
...development. Based on comprehensive sequencing data, our main aim was to determine the status and potential mechanisms of maintaining homomorphic sex chromosome in L. boringii.ResultsGenome assembly and sex chromosome identificationWe used a combination of long-read Pacific Biosciences (PacBio), short...

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