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Research: Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints
- Manuel Irimia,
- Juan J. Tena,
- Maria S. Alexis,
- Ana Fernandez-Miñan,
- Ignacio Maeso,
- Ozren Bogdanović,
- Elisa de la Calle-Mustienes,
- Scott W. Roy,
- José L. Gómez-Skarmeta,
- and Hunter B. Fraser
Genome Res. December 2012 22: 2356-2367; Published in Advance June 21, 2012, doi:10.1101/gr.139725.112
...features, we provide extensive evidence that many conserved ancient linkages involve (1) the coordinated transcription of neighboring genes, or (2) genomic regulatory blocks (GRBs) in which transcriptional enhancers controlling developmental genes are contained within nearby bystander genes. In addition...
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Methods: Multigenome DNA sequence conservation identifies Hox cis-regulatory elements
- Steven G. Kuntz,
- Erich M. Schwarz,
- John A. DeModena,
- Tristan De Buysscher,
- Diane Trout,
- Hiroaki Shizuya,
- Paul W. Sternberg,
- and Barbara J. Wold
Genome Res. December 2008 18: 1955-1968; Published in Advance November 3, 2008, doi:10.1101/gr.085472.108
...W. Diane Trout Schwarz ErichM Schwarz Steven G Kuntz J DeModena Wold, B Erich Sternberg, PW Kuntz Erich M Kuntz Steven G. De Buysscher, Tristan B Wold DeModena SG Kuntz Erich M Schwarz genome;gr.085472.108 10.1101/gr.085472.108 1088-9051 Multigenome DNA sequence conservation identifies Hox cis-regulatory...
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Research: An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
- Ignacio Maeso,
- Manuel Irimia,
- Juan J. Tena,
- Esther González-Pérez,
- David Tran,
- Vydianathan Ravi,
- Byrappa Venkatesh,
- Sonsoles Campuzano,
- José Luis Gómez-Skarmeta,
- and Jordi Garcia-Fernàndez
Genome Res. April 2012 22: 642-655; Published in Advance January 10, 2012, doi:10.1101/gr.132233.111
...as genomic regulatory blocks (GRBs) (Becker and Lenhard 2007; Kikuta et al. 2007) and create evolutionarily ‘‘solid’’ regions of conserved microsynteny. The presence of conserved GRBs had been previously described only within vertebrates or within insects (Engstrom et al. 2007; Kikuta et al. 2007), but none...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...constitute a principal driver of evolution, shaping its architecture and regulatory networks. In this context, Tuberaceae can become an important model system to study their genomic impact; however, the family lacks high-quality assemblies. Here, we investigate the interplay between TEs and Tuberaceae...
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Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
- Charles Plessy,
- Michael J. Mansfield,
- Aleksandra Bliznina,
- Aki Masunaga,
- Charlotte West,
- Yongkai Tan,
- Andrew W. Liu,
- Jan Grašič,
- María Sara del Río Pisula,
- Gaspar Sánchez-Serna,
- Marc Fabrega-Torrus,
- Alfonso Ferrández-Roldán,
- Vittoria Roncalli,
- Pavla Navratilova,
- Eric M. Thompson,
- Takeshi Onuma,
- Hiroki Nishida,
- Cristian Cañestro,
- and Nicholas M. Luscombe
Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
...(for a recent review, see Wanninger 2024). There are many other examples of highly conserved microsyntenies across metazoans, in many cases related to the functional constraints imposed by cis-regulatory elements on the coordinated transcription of nearby genes. This includes genomic regulatory blocks...
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Letter: Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention
- Andrew L. Hufton,
- Susanne Mathia,
- Helene Braun,
- Udo Georgi,
- Hans Lehrach,
- Martin Vingron,
- Albert J. Poustka,
- and Georgia Panopoulou
Genome Res. November 2009 19: 2036-2051; Published in Advance August 24, 2009, doi:10.1101/gr.093237.109
...and Georgia Panopoulou 1 Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany Abstract Animal genomes possess highly conserved cis -regulatory sequences that are often found near genes that regulate transcription and development. Researchers have proposed...
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Research: Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila
- Marcin von Grotthuss,
- Michael Ashburner,
- and José M. Ranz
Genome Res. August 2010 20: 1084-1096; Published in Advance July 2, 2010, doi:10.1101/gr.103713.109
...(Goode et al. 2005; Kikuta et al. 2007). These regulatory blocks are enriched for highly conserved noncoding elements, which have been shown to affect the expression of neighboring genes (Glazov et al. 2005; Vavouri et al. 2007). The conservation of regulatory landscapes has also been documented...
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Research: Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution
- Gang Li,
- Brian W. Davis,
- Terje Raudsepp,
- Alison J. Pearks Wilkerson,
- Victor C. Mason,
- Malcolm Ferguson-Smith,
- Patricia C. O'Brien,
- Paul D. Waters,
- and William J. Murphy
Genome Res. September 2013 23: 1486-1495; Published in Advance June 20, 2013, doi:10.1101/gr.154286.112
...versus Y chromosome intragenomic conflict in the mouse. PLoS Genet 8: e1002900. Engstrom PG, Ho Sui SJ, Drivenes O, Becker TS, Lenhard B. 2007. Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Res 17: 1898–1908. Graves JAM. 2006. Sex chromosome specialization...
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LETTER: On the origin of new genes in Drosophila
- Qi Zhou,
- Guojie Zhang,
- Yue Zhang,
- Shiyu Xu,
- Ruoping Zhao,
- Zubing Zhan,
- Xin Li,
- Yun Ding,
- Shuang Yang,
- and Wen Wang
Genome Res. September 2008 18: 1446-1455; Published in Advance June 11, 2008, doi:10.1101/gr.076588.108
...Academy Sciences, Beijing 100086, China; 3 Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China ↵ 4 These authors contributed equally to this work. Abstract Several mechanisms have been proposed to account for the origination of new genes. Despite extensive...

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