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Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
- Yujie Chen,
- Yiran Hou,
- Qinglin Zeng,
- Irene Wang,
- Meiru Shang,
- Kwangdeok Shin,
- Christopher Hemauer,
- Xiaoyun Xing,
- Junsu Kang,
- Guoyan Zhao,
- and Ting Wang
Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
...and chromatin accessibility map across regenerative stages provides new insights into regeneration regulatory mechanisms and serves as a valuable resource for the community.The zebrafish (Danio rerio) serves as an excellent model organism for studying complex tissue regeneration processes owing to its...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...patterns through early development.ResultsThe genomic landscape of zebrafish TEsUsing RepeatMasker to annotate the Danio rerio reference (GRCz11), we mapped the location of sequences related to a total of 1931 nonredundant TE families cataloged in Dfam and Repbase (Bao et al. 2015; Storer et al. 2021...
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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
.... cristatus and internally/proximally in L. helveticus and P. waltl. The availability of linkage maps of L. vulgaris and T. cristatus (France et al. 2025) allowed us to establish that the MHC region is actually located at the opposite ends of linkage group (LG) 1 in these two species, and a comparison...
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Resource: Epigenomics of embryogenesis in turbot
- Oscar Aramburu,
- Belen G Pardo,
- Ada Jimenez-Gonzalez,
- Andrés Blanco-Hortas,
- Daniel Macqueen,
- Carmen Bouza,
- and Paulino Martinez
Genome Res. November 4, 2025 gr.280355.124; Published in Advance November 4, 2025, doi:10.1101/gr.280355.124
...,148,829 (H3K27ac) and 98,992,315 (H3K27me3) raw reads 237 were produced on average, with a mapping rate of 94.80% and no obvious 238 deviation from the expected fragment size, insert size, and sequence read 239 length distributions (Supplemental table S3B and S3C, Supplemental figure 240 S1B and S1C...
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RESOURCE: The LN54 Radiation Hybrid Map of Zebrafish Expressed Sequences
- Neil Hukriede,
- Dan Fisher,
- Jonathan Epstein,
- Lucille Joly,
- Patricia Tellis,
- Yi Zhou,
- Brad Barbazuk,
- Kristine Cox,
- Laura Fenton-Noriega,
- Candace Hersey,
- Jennifer Miles,
- Xiaoming Sheng,
- Anhua Song,
- Rick Waterman,
- Stephen L. Johnson,
- Igor B. Dawid,
- Mario Chevrette,
- Leonard I. Zon,
- John McPherson,
- and Marc Ekker
Genome Res. December 1, 2001 11: 2127-2132; Published in Advance November 12, 2001, doi:10.1101/gr.210601
...The LN54 Radiation Hybrid Map of Zebrafish Expressed Sequences Neil Hukriede 1 , 7 , Dan Fisher 2 , 7 , Jonathan Epstein 1 , 7 , Lucille Joly 3 , Patricia Tellis 4 , Yi Zhou 5 , Brad Barbazuk 2 , Kristine Cox 2...
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Method: High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9
- Gaurav K. Varshney,
- Wuhong Pei,
- Matthew C. LaFave,
- Jennifer Idol,
- Lisha Xu,
- Viviana Gallardo,
- Blake Carrington,
- Kevin Bishop,
- MaryPat Jones,
- Mingyu Li,
- Ursula Harper,
- Sunny C. Huang,
- Anupam Prakash,
- Wenbiao Chen,
- Raman Sood,
- Johan Ledin,
- and Shawn M. Burgess
Genome Res. July 2015 25: 1030-1042; Published in Advance June 5, 2015, doi:10.1101/gr.186379.114
...with streamlined mutant identification methods utilizing fluorescent PCR and multiplexed, high-throughput sequencing. We report germline transmission data from 162 loci targeting 83 genes in the zebrafish , in which we obtained a 99% success rate for generating mutations and an average germline transmission rate...
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RESOURCE: The zebrafish gene map defines ancestral vertebrate chromosomes
- Ian G. Woods,
- Catherine Wilson,
- Brian Friedlander,
- Patricia Chang,
- Daengnoy K. Reyes,
- Rebecca Nix,
- Peter D. Kelly,
- Felicia Chu,
- John H. Postlethwait,
- and William S. Talbot
Genome Res. September 2005 15: 1307-1314; Published in Advance August 18, 2005, doi:10.1101/gr.4134305
..., degenerative mutations. Genetics 151 : 1531 -1545. ↵ Gates, M.A., Kim, L., Egan, E.S., Cardozo, T., Sirotkin, H.I., Dougan, S.T., Lashkari, D., Abagyan, R., Schier, A.F., and Talbot, W.S. 1999 . A genetic linkage map for zebrafish: Comparative analysis and localization of genes and expressed sequences. Genome...
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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
...are indicated under Ygua: 1, 00013F_0; 2, 000200F_0; 3, 000250F_0; 4, 000181F_0; and 5, 000149F_0.A genetic linkage map based on SNP markers deduced from EST and BAC end sequences (Tripathi et al. 2009b) had served as guide for the assembly of both the previously published female and male s. The most distal sex...
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LETTER: A Comparative Map of the Zebrafish Genome
- Ian G. Woods,
- Peter D. Kelly,
- Felicia Chu,
- Phuong Ngo-Hazelett,
- Yi-Lin Yan,
- Hui Huang,
- John H. Postlethwait,
- and William S. Talbot
Genome Res. December 1, 2000 10: 1903-1914; doi:10.1101/gr.164600
...genes and expressed sequence tags (ESTs) on zebrafish linkage group LG 17 and the positions of their human counterparts on chromosome (Hsa) 14. ( B ) Maps showing 11 genes and ESTs on zebrafish LG 8 and the positions of their human counterparts on the short arm of Hsa 1. In both panels, the entire...
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RESOURCE: A Consensus Linkage Map of the Chicken Genome
- Martien A.M. Groenen,
- Hans H. Cheng,
- Nat Bumstead,
- Bernard F. Benkel,
- W. Elwood Briles,
- Terry Burke,
- Dave W. Burt,
- Lyman B. Crittenden,
- Jerry Dodgson,
- Jossi Hillel,
- Sue Lamont,
- Abel Ponce de Leon,
- Morris Soller,
- Hideaki Takahashi,
- and Alain Vignal
Genome Res. January 1, 2000 10: 137-147; doi:10.1101/gr.10.1.137
...mammals. The map contains 350 markers within expressed sequences, 235 of which represent identified genes or sequences that have significant sequence identity to known genes. This improves the contribution of the chicken linkage map to comparative gene mapping considerably and clearly shows...

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