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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...of Staurotypus and Apalone, respectively. We used the Trachemys (Simison et al. 2020) for comparison, as it is an annotated chromosome-level assembly that has been partially mapped physically and some chromosome assignments corrected accordingly (Lee et al. 2020), along with Gopherus evgoodei (Rhie et al. 2021...
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Research: The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes
- Drew R. Schield,
- Daren C. Card,
- Nicole R. Hales,
- Blair W. Perry,
- Giulia M. Pasquesi,
- Heath Blackmon,
- Richard H. Adams,
- Andrew B. Corbin,
- Cara F. Smith,
- Balan Ramesh,
- Jeffery P. Demuth,
- Esther Betrán,
- Marc Tollis,
- Jesse M. Meik,
- Stephen P. Mackessy,
- and Todd A. Castoe
Genome Res. April 2019 29: 590-601; Published in Advance March 21, 2019, doi:10.1101/gr.240952.118
...trace patterns of chromosome-level synteny and composition across amniotes, specifically exploring synteny between reptile and avian s and testing hypotheses about the evolution of GC-isochore structure in reptiles. We further characterize -wide chromatin contacts using Hi-C data to demonstrate...
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LETTER: Determinants of CpG Islands: Expression in Early Embryo and Isochore Structure
- Loïc Ponger,
- Laurent Duret,
- and Dominique Mouchiroud
Genome Res. November 1, 2001 11: 1854-1860; Published in Advance October 15, 2001, doi:10.1101/gr.174501
...) and a demethylase enzyme ( Lin et al. 2000 ). Other studies have shown that the distribution of CGIs varies widely with G + C content along chromosomes; in G + C-rich isochores (H3), the density of CGIs is 15 times higher than in G + C-poor isochores (L1 + L2) ( Aissani and Bernardi 1991 ; Jabbari and Bernardi 1998...
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Dog Special/Letters: Hotspots of mutation and breakage in dog and human chromosomes
- Caleb Webber and
- Chris P. Ponting
Genome Res. December 2005 15: 1787-1797; doi:10.1101/gr.3896805
..., and was derived from phylogenetic analyses (L. Goodstadt and C.P. Ponting, in prep.). Data set D2 facilitated chromosomal mapping of quantities between dog and human s. Fourfold degenerate sites (so-called 4D sites) at the third position of codons encoding eight amino acid types were identified as previously...
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LETTER: An analysis of the gene complement of a marsupial, Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes
- Leo Goodstadt,
- Andreas Heger,
- Caleb Webber,
- and Chris P. Ponting
Genome Res. July 2007 17: 969-981; Published in Advance May 10, 2007, doi:10.1101/gr.6093907
...of the Homo X chromosome that is syntenic to the Monodelphis X chromosome, and the more recently derived regions on the short arm of HSAX that are syntenic to MDO4 and MOD7. The circled regions have been placed on MDO4 and MDO7 in the current Monodelphis assembly 3, but FISH analyses map these regions...
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LETTER: Genomic Structure and Evolution of the Ancestral Chromosome Fusion Site in 2q13–2q14.1 and Paralogous Regions on Other Human Chromosomes
- Yuxin Fan,
- Elena Linardopoulou,
- Cynthia Friedman,
- Eleanor Williams,
- and Barbara J. Trask
Genome Res. November 1, 2002 12: 1651-1662; doi:10.1101/gr.337602
...clones on chimpanzee chromosomes (Fig. 2 ). Chimpanzee chromosomes 12 and 13 are homologous to human 2p and 2q, respectively ( Yunis and Prakash 1982 ; Wienberg et al. 1994 ). RP11–480C16, from one end of the 2qFus contig, hybridizes to chimpanzee 12, indicating that it maps to the centromere...
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ARTICLE: The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern
- Francisco M. De La Vega,
- Hadar Isaac,
- Andrew Collins,
- Charles R. Scafe,
- Bjarni V. Halldórsson,
- Xiaoping Su,
- Ross A. Lippert,
- Yu Wang,
- Marion Laig-Webster,
- Ryan T. Koehler,
- Janet S. Ziegle,
- Lewis T. Wogan,
- Junko F. Stevens,
- Kyle M. Leinen,
- Sheri J. Olson,
- Karl J. Guegler,
- Xiaoqing You,
- Lily H. Xu,
- Heinz G. Hemken,
- Francis Kalush,
- Mitsuo Itakura,
- Yi Zheng,
- Guy de Thé,
- Stephen J. O'Brien,
- Andrew G. Clark,
- Sorin Istrail,
- Michael W. Hunkapiller,
- Eugene G. Spier,
- and Dennis A. Gilbert
Genome Res. April 2005 15: 454-462; Published in Advance March 21, 2005, doi:10.1101/gr.3241705
...The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern Francisco M. De La Vega 1 , 12 , Hadar Isaac 1 , Andrew Collins 2 , Charles R. Scafe 1...
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LETTER: Comparative Analysis of the α-Like Globin Clusters in Mouse, Rat, and Human Chromosomes Indicates a Mechanism Underlying Breaks in Conserved Synteny
- Cristina Tufarelli,
- Ross Hardison,
- Webb Miller,
- Jim Hughes,
- Kevin Clark,
- Nicki Ventress,
- Anna Maria Frischauf,
- and Douglas R. Higgs
Genome Res. April 2004 14: 623-630; doi:10.1101/gr.2143604
...of the U1 snRNP complex, which surprisingly maps to Chromosome 17 in the mouse, and is therefore separated from the functional α-globin gene cluster located on Chromosome 11 ( Fig. 1 ; Tufarelli et al. 2001 ). The region of human Chromosome 16p13.3 beyond LUC7L up to the mouse ortholog of the PKD1 gene (∼2...
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RESEARCH: A Physical Map of Human Chromosome 7: An Integrated YAC Contig Map with Average STS Spacing of 79 kb
- Gerard G. Bouffard,
- Jacquelyn R. Idol,
- Valerie V. Braden,
- Leslie M. Iyer,
- Aimee F. Cunningham,
- Lauren A. Weintraub,
- Jeffrey W. Touchman,
- Rose M. Mohr-Tidwell,
- Dale C. Peluso,
- Robert S. Fulton,
- Melinda S. Ueltzen,
- Jean Weissenbach,
- Charles L. Magness,
- and Eric D. Green
Genome Res. July 1, 1997 7: 673-692; doi:10.1101/gr.7.7.673
...A Physical Map of Human Chromosome 7: An Integrated YAC Contig Map with Average STS Spacing of 79 kb Gerard G. Bouffard 1 , Jacquelyn R. Idol 1 , Valerie V. Braden 1 , Leslie M. Iyer 1 , Aimee F. Cunningham 1 , Lauren A. Weintraub 1...
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LETTER: Construction of a High-Resolution 2.5-Mb Transcript Map of the Human 6p21.2–6p21.3 Region Immediately Centromeric of the Major Histocompatibility Complex
- Nicos Tripodis,
- Sophie Palmer,
- Sam Phillips,
- Sarah Milne,
- Stephan Beck,
- and Jiannis Ragoussis
Genome Res. April 1, 2000 10: 454-472; doi:10.1101/gr.10.4.454
.../KIAA0229 ) have been identified, as well as cDNAs and cDNA contigs. The detailed map of the gene content of this chromosomal segment provides a number of candidate genes, which may be involved in several biological processes that have been associated with this region, such as spermatogenesis...

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