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Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
- Marin Volarić,
- Evelin Despot-Slade,
- Damira Veseljak,
- Brankica Mravinac,
- and Nevenka Meštrović
Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
...Long-read assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events Marin Volarić1,2, Evelin Despot-Slade1,2, Damira Veseljak1, Brankica Mravinac1 and Nevenka Meštrović1 1Ruđer Bošković Institute, 10000 Zagreb, Croatia...
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LETTER: Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions
- Laurie Gordon,
- Shan Yang,
- Mary Tran-Gyamfi,
- Dan Baggott,
- Mari Christensen,
- Aaron Hamilton,
- Richard Crooijmans,
- Martien Groenen,
- Susan Lucas,
- Ivan Ovcharenko,
- and Lisa Stubbs
Genome Res. November 2007 17: 1603-1613; Published in Advance October 5, 2007, doi:10.1101/gr.6775107
...Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions Laurie Gordon 1 , 2 , 5 , Shan Yang 1 , 5 , Mary Tran-Gyamfi 1 , 2 , Dan Baggott 1 , Mari Christensen 1 , 2...
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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
...architecture, with stretches of heterochromatic DNA dominated by long retrotransposon insertions interspersed with compact, gene-rich regions. The absence of an enrichment of SSPs within TE-rich regions suggest a partially different genomic organization compared with the frequent TE...
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LETTER: Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse
- Ann-Marie Mallon,
- Laurens Wilming,
- Joseph Weekes,
- James G.R. Gilbert,
- Jennifer Ashurst,
- Sandrine Peyrefitte,
- Lucy Matthews,
- Matthew Cadman,
- Richard McKeone,
- Chris A. Sellick,
- Ruth Arkell,
- Marc R.M. Botcherby,
- Mark A. Strivens,
- R. Duncan Campbell,
- Simon Gregory,
- Paul Denny,
- John M. Hancock,
- Jane Rogers,
- and Steve D.M. Brown
Genome Res. October 2004 14: 1888-1901; Published in Advance September 13, 2004, doi:10.1101/gr.2478604
...Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13) Svea 36H Mouse Ann-Marie Mallon 1 , 4 , Laurens Wilming 2 , 4 , Joseph Weekes 1 , James G.R. Gilbert 2 , Jennifer Ashurst 2...
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LETTER: Methylation-Spanning Linker Libraries Link Gene-Rich Regions and Identify Epigenetic Boundaries in Zea mays
- Yinan Yuan,
- Phillip J. SanMiguel,
- and Jeffrey L. Bennetzen
Genome Res. September 1, 2002 12: 1345-1349; doi:10.1101/gr.185902
...Methylation-Spanning Linker Libraries Link Gene-Rich Regions and Identify Epigenetic Boundaries in Zea mays Yinan Yuan 1 , Phillip J. SanMiguel 2 , and Jeffrey L. Bennetzen 1 , 3 1Department of Biological Sciences, Purdue University, West...
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Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
...spread into gene-rich regions (Volarić et al. 2024), resembling the euchromatic satDNA dynamics observed in Drosophila melanogaster and its close relatives (Sproul et al. 2020). A growing number of studies report satDNA arrays in euchromatic regions, indicating that euchromatin is not inhospitable...
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Research: Gaps and complex structurally variant loci in phased genome assemblies
- David Porubsky,
- Mitchell R. Vollger,
- William T. Harvey,
- Allison N. Rozanski,
- Peter Ebert,
- Glenn Hickey,
- Patrick Hasenfeld,
- Ashley D. Sanders,
- Catherine Stober,
- Human Pangenome Reference Consortium,
- Jan O. Korbel,
- Benedict Paten,
- Tobias Marschall,
- and Evan E. Eichler
Genome Res. April 2023 33: 496-510; Published in Advance May 10, 2023, doi:10.1101/gr.277334.122
...of African ancestry carry more CNV bases (∼3.5 Mbp) compared with other non-African populations (Supplemental Fig. S23) consistent with previous reports (Sudmant et al. 2015; Chaisson et al. 2019; Byrska-Bishop et al. 2022). The regions are particularly gene-rich, and we identify 420 protein-coding genes...
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METHODS: Parallel Construction of Orthologous Sequence-Ready Clone Contig Maps in Multiple Species
- James W. Thomas,
- Arjun B. Prasad,
- Tyrone J. Summers,
- Shih-Queen Lee-Lin,
- Valerie V.B. Maduro,
- Jacquelyn R. Idol,
- Joseph F. Ryan,
- Pamela J. Thomas,
- Jennifer C. McDowell,
- and Eric D. Green
Genome Res. August 1, 2002 12: 1277-1285; doi:10.1101/gr.283202
.... , Badri H. , Christensen M. , Grosa M. , Ha C. , Hammond S. , Vargas M. , Wehri E. , et al. ( 2001 ) Homology-driven assembly of a sequence-ready mouse BAC contig map spanning regions related to the 46-Mb gene-rich euchromatic segments of human chromosome 19. Genomics 74 : 129 – 141 . ↵ Li R. , Mignot E...
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RESEARCH: Comparative Sequence Analysis of a Gene-Rich Cluster at Human Chromosome 12p13 and its Syntenic Region in Mouse Chromosome 6
- M. Ali Ansari-Lari,
- John C. Oeltjen,
- Scott Schwartz,
- Zheng Zhang,
- Donna M. Muzny,
- Jing Lu,
- James H. Gorrell,
- A. Craig Chinault,
- John W. Belmont,
- Webb Miller,
- and Richard A. Gibbs
Genome Res. January 1, 1998 8: 29-40
...Comparative Sequence Analysis of a Gene-Rich Cluster at Human Chromosome 12p13 and its Syntenic Region in Mouse Chromosome 6 M. Ali Ansari-Lari 1 , John C. Oeltjen 1 , Scott Schwartz 2 , Zheng Zhang 2 , Donna M. Muzny 1 , Jing Lu 1...
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ARTICLES: Long-range map of a 3.5-Mb region in Xp11.23-22 with a sequence-ready map from a 1.1-Mb gene-rich interval.
- D Schindelhauer,
- H Hellebrand,
- L Grimm,
- I Bader,
- T Meitinger,
- M Wehnert,
- M Ross,
- and A Meindl
Genome Res. November 1996 6: 1056-1069; doi:10.1101/gr.6.11.1056
...with the cosmid clones identified by hybridiza- tion with the probe M27[3 (data not shown). DISCUSSION YAC Instability in a Gene-rich Region A genomic map is an important ool especially for the cloning of gene-rich regions. Colinearity between the constructed YAC contigs and the ge- nomic restriction map has...
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