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RESOURCE: Chromosome-Specific Single-Locus FISH Probes Allow Anchorage of an 1800-Marker Integrated Radiation-Hybrid/Linkage Map of the Domestic Dog Genome to All Chromosomes
- Matthew Breen,
- Sophie Jouquand,
- Corinne Renier,
- Cathryn S. Mellersh,
- Christophe Hitte,
- Nigel G. Holmes,
- Angélique Chéron,
- Nicola Suter,
- Françoise Vignaux,
- Anna E. Bristow,
- Catherine Priat,
- E. McCann,
- Catherine André,
- Sam Boundy,
- Paul Gitsham,
- Rachael Thomas,
- Wendy L. Bridge,
- Helen F. Spriggs,
- Ed J. Ryder,
- Alistair Curson,
- Jeff Sampson,
- Elaine A. Ostrander,
- Matthew M. Binns,
- and Francis Galibert
Genome Res. October 1, 2001 11: 1784-1795; doi:10.1101/gr.189401
...); or they were mapped at the Animal Health Trust but are currently unpublished ( PDEα on CFA 4, DLAA9 on CFA 12, ROM1 on CFA 18, RHO on CFA 20, RB1 on CFA 22, and RTB on CFA 27). Data from all 103 chromosome-specific markers were typed in duplicate. Radiation Hybrid Mapping The 900 new markers added here...
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LETTER: Transcriptional Response of Lymphoblastoid Cells to Ionizing Radiation
- Kuang-Yu Jen and
- Vivian G. Cheung
Genome Res. September 2003 13: 2092-2100; Published in Advance January 1, 2003, doi:10.1101/gr.1240103
...Transcriptional Response of Lymphoblastoid Cells to Ionizing Radiation Kuang-Yu Jen and Vivian G. Cheung 1 Departments of Pediatrics and Genetics, University of Pennsylvania, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA...
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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
...among metazoans, whereas high recombination rates have not been found among nonsocial species from this insect order. It is unknown whether elevated recombination rates are a ubiquitous feature of all social insects. In many metazoan taxa, recombination is mainly restricted to hotspots a few kilobases...
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Research: Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence
- Scott Ferguson,
- Ashley Jones,
- Kevin Murray,
- Rose Andrew,
- Benjamin Schwessinger,
- and Justin Borevitz
Genome Res. April 2024 34: 606-619; Published in Advance April 8, 2024, doi:10.1101/gr.277999.123
....) and is critical for many biological functions, in particular reproduction and gene expression. However, the conservation and divergence of architecture or structure among a group of radiating plant species that share a common karyotype have not been well described.For effective recombination during meiosis...
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Research: The genomic basis of evolutionary differentiation among honey bees
- Bertrand Fouks,
- Philipp Brand,
- Hung N. Nguyen,
- Jacob Herman,
- Francisco Camara,
- Daniel Ence,
- Darren E. Hagen,
- Katharina J. Hoff,
- Stefanie Nachweide,
- Lars Romoth,
- Kimberly K.O. Walden,
- Roderic Guigo,
- Mario Stanke,
- Giuseppe Narzisi,
- Mark Yandell,
- Hugh M. Robertson,
- Nikolaus Koeniger,
- Panuwan Chantawannakul,
- Michael C. Schatz,
- Kim C. Worley,
- Gene E. Robinson,
- Christine G. Elsik,
- and Olav Rueppell
Genome Res. July 2021 31: 1203-1215; Published in Advance May 4, 2021, doi:10.1101/gr.272310.120
...-coding regions and evolutionary turnover of genes, similar to a genomic study of the radiation of closely related bumble bees (Sun et al. 2021). These two sources of evolutionary change may be important in bee social evolution in addition to regulatory diversification (Kapheim et al. 2015). Practically, rapid...
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Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
- Marta Farré,
- Jaebum Kim,
- Anastasia A. Proskuryakova,
- Yang Zhang,
- Anastasia I. Kulemzina,
- Qiye Li,
- Yang Zhou,
- Yingqi Xiong,
- Jennifer L. Johnson,
- Polina L. Perelman,
- Warren E. Johnson,
- Wesley C. Warren,
- Anna V. Kukekova,
- Guojie Zhang,
- Stephen J. O'Brien,
- Oliver A. Ryder,
- Alexander S. Graphodatsky,
- Jian Ma,
- Harris A. Lewin,
- and Denis M. Larkin
Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118
...for natural selection during animal evolution and adaptation is still an outstanding question in evolutionary biology (White 1968). Whole- comparisons among mammals and birds point to regions in s where the order of orthologous sequences can be maintained for tens of millions of years of evolution (homologous...
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Research: Widespread cis-regulatory convergence between the extinct Tasmanian tiger and gray wolf
- Charles Y. Feigin,
- Axel H. Newton,
- and Andrew J. Pask
Genome Res. October 2019 29: 1648-1658; Published in Advance September 18, 2019, doi:10.1101/gr.244251.118
...as a powerful approach to study patterns of selection on CREs. It has been used to identify positive selection on forelimb-specific enhancers in bats (Booker et al. 2016) and across numerous traits in recent radiations of anole lizards (Tollis et al. 2018). This approach has also proven valuable for studying...
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Research: Noncoding origins of anthropoid traits and a new null model of transposon functionalization
- Ricardo C.H. del Rosario,
- Nirmala Arul Rayan,
- and Shyam Prabhakar
Genome Res. September 2014 24: 1469-1484; Published in Advance July 20, 2014, doi:10.1101/gr.168963.113
...syntenic regions. At a strict P-value threshold of 1 3 10#1;3, we discovered 268,000 ACs covering 4.2% of the syntenic (FDR<0.1%) (see Methods; Supplemental Note 1). In order to prioritize unambiguous examples of gain of function, we discarded from this set any element that showed even weak evidence...
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Research: Pluripotent stem cells escape from senescence-associated DNA methylation changes
- Carmen M. Koch,
- Kristina Reck,
- Kaifeng Shao,
- Qiong Lin,
- Sylvia Joussen,
- Patrick Ziegler,
- Gudrun Walenda,
- Wolf Drescher,
- Bertram Opalka,
- Tobias May,
- Tim Brümmendorf,
- Martin Zenke,
- Tomo Šarić,
- and Wolfgang Wagner
Genome Res. February 2013 23: 248-259; Published in Advance October 18, 2012, doi:10.1101/gr.141945.112
..., particularly SA-hypomethylation preferentially occurred in regions with repressive H3K9me3 and H3K27me3 histone marks and in PRC2 targets—this may contribute to the very low expression of the corresponding genes. Gamma-irradiation does not affect DNAm Ionizing radiation (IR) of MSC induced very similar...
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Research: DNA methylation contributes to natural human variation
- Holger Heyn,
- Sebastian Moran,
- Irene Hernando-Herraez,
- Sergi Sayols,
- Antonio Gomez,
- Juan Sandoval,
- Dave Monk,
- Kenichiro Hata,
- Tomas Marques-Bonet,
- Liewei Wang,
- and Manel Esteller
Genome Res. September 2013 23: 1363-1372; Published in Advance August 1, 2013, doi:10.1101/gr.154187.112
...et al. 2010). The DNA methylation profile was assessed for 288 B-cell lymphoblastoid cell lines (LCL) representing 96 Caucasian-American (CA), 96 AfricanAmerican (AF), and 96 Han Chinese-American (AS) individuals. After sample randomization, DNA samples were hybridized on the Infinium DNA methylation...
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