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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cisregulatory modules acting during vertebrate organogenesis Daniela M. Riley,1,7 Randa Elsayed,1,7 Mark D. Walsh,2,7 Simaran Johal,2 Ying Lin,3,4 Harry Walton,1 Till Bretschneider,5 Sascha Ott,1...
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Research: The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores
- Yulong Liu,
- Gang Zhai,
- Jingzhi Su,
- Yulong Gong,
- Bingyuan Yang,
- Qisheng Lu,
- Longwei Xi,
- Yutong Zheng,
- Jingyue Cao,
- Haokun Liu,
- Junyan Jin,
- Zhimin Zhang,
- Yunxia Yang,
- Xiaoming Zhu,
- Zhongwei Wang,
- Gaorui Gong,
- Jie Mei,
- Zhan Yin,
- Rodolphe E. Gozlan,
- Shouqi Xie,
- and Dong Han
Genome Res. July 2024 34: 981-996; Published in Advance August 9, 2024, doi:10.1101/gr.278476.123
...annotated genes (Supplemental Fig. S4; Supplemental Table S9). The of L. longirostris had a syntenic relationship with the of Ictalurus punctatus and Pelteobagrus fulvidraco (Supplemental Fig. S5). We found that all chromosomes in P. fulvidraco have strong genomic collinearity with L. longirostris...
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Research: Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
- Satyam P. Srivastav,
- Cédric Feschotte,
- and Andrew G. Clark
Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123
...RNA abundance, is considered active in all strains except A2. Comparison of such syntenic piCs between strains in their native assemblies provides validation of the variable activity of piCs across strains presented earlier from annotation pipelines (Fig. 1B). In addition, we also note that although genomic...
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Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
...-copy ortholog (BUSCO) completeness of 97.65% and an N50 of 33,053,486, representing a substantial improvement over previous genomic resources for the species (Charlesworth et al. 2021b). We recovered 23 chromosomes, numbered based on the syntenic comparison with the P. reticulata female assembly (Fig. 1B...
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Resource: Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser
- Xiaoyu Zhuo,
- Silas Hsu,
- Deepak Purushotham,
- Prashant Kumar Kuntala,
- Jessica K. Harrison,
- Alan Y. Du,
- Samuel Chen,
- Daofeng Li,
- and Ting Wang
Genome Res. May 2023 33: 824-835; Published in Advance May 8, 2023, doi:10.1101/gr.277550.122
...methylC tracks (Yue et al. 2014; Zhou et al. 2014; Yang et al. 2020). By displaying the Hoxc gene cluster from both the mouse and zebrafish reference s and their syntenic relationship, we can appreciate that only a small fraction of their genomic sequences can be aligned with each other after hundreds...
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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
...Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; 6McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA; 7Department of Life Sciences, Texas A&M University, Corpus Christi, Texas 78412, USA; 8Developmental Biochemistry, Biozentrum...
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Research: An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
- Elise Parey,
- Alexandra Louis,
- Jérôme Montfort,
- Yann Guiguen,
- Hugues Roest Crollius,
- and Camille Berthelot
Genome Res. September 2022 32: 1685-1697; Published in Advance August 12, 2022, doi:10.1101/gr.276953.122
...to a different ancestral chromosome in our comparative map are not overrepresented in synteny-inconsistent trees (7% vs. 14% for all zebrafish genes), suggesting that their orthology relationships and chromosomal reassignations are overall well-supported by their sequences and syntenic gene neighborhoods...
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Research: Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
- Aitor Serres-Armero,
- Brian W. Davis,
- Inna S. Povolotskaya,
- Carlos Morcillo-Suarez,
- Jocelyn Plassais,
- David Juan,
- Elaine A. Ostrander,
- and Tomas Marques-Bonet
Genome Res. May 2021 31: 762-774; Published in Advance April 16, 2021, doi:10.1101/gr.266049.120
..., Spain; 2Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA; 3Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA; 4...
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Resource: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons
- Qicheng Ma,
- Satyam P. Srivastav,
- Stephanie Gamez,
- Gargi Dayama,
- Fabiana Feitosa-Suntheimer,
- Edward I. Patterson,
- Rebecca M. Johnson,
- Erik M. Matson,
- Alexander S. Gold,
- Douglas E. Brackney,
- John H. Connor,
- Tonya M. Colpitts,
- Grant L. Hughes,
- Jason L. Rasgon,
- Tony Nolan,
- Omar S. Akbari,
- and Nelson C. Lau
Genome Res. March 2021 31: 512-528; Published in Advance January 8, 2021, doi:10.1101/gr.265157.120
...University Genome Science Institute and the National Emerging Infectious Disease Laboratory, Boston, Massachusetts 02118, USA ↵8 These authors contributed equally to this work. Corresponding author: nclau@bu.eduAbstractAlthough mosquitoes are major transmission vectors for pathogenic arboviruses, viral...
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Research: A massively parallel 3′ UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization
- Adam J. Litterman,
- Robin Kageyama,
- Olivier Le Tonqueze,
- Wenxue Zhao,
- John D. Gagnon,
- Hani Goodarzi,
- David J. Erle,
- and K. Mark Ansel
Genome Res. June 2019 29: 896-906; Published in Advance May 31, 2019, doi:10.1101/gr.242552.118
..., nucleotide content, and functional activity. GC-rich, structured RNA motifs have been previously identified as contributing to rapid turnover of mRNAs in a human cell line (Goodarzi et al. 2012). Additionally, a recent in vivo massively parallel reporter assay in zebrafish embryos identified GC-rich elements...

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