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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
...et al. 2019), Spiny Softshell Turtle (Apalone spinifera [ASP], this study), and Northern Giant Musk Turtle (Staurotypus triporcatus [STR], this study]. (B) Heat maps representing interchromosomal mean interactions per chromosome for human, African Elephant, Tasmanian Devil, Platypus, chicken, Emu...
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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...for heterogametic samples, missing genes were also counted for the autosomal sequences as identified by MashMap3 alignment to the existing reference s (CHM13 for human [Nurk et al. 2022], GCA_024206055.1 [Huang et al. 2023] for chicken, and GCF_016772045.2 [Davenport et al. 2022] for sheep).View this table...
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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
...contributed equally to this work. Corresponding authors: scott.ferguson.papers@gmail.com, ashley.jones@anu.edu.auAbstractGenomes have a highly organized architecture (nonrandom organization of functional and nonfunctional genetic elements within chromosomes) that is essential for many biological functions...
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Resource: A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes
- Jing Liu,
- Zongji Wang,
- Jing Li,
- Luohao Xu,
- Jiaqi Liu,
- Shaohong Feng,
- Chunxue Guo,
- Shengchan Chen,
- Zhanjun Ren,
- Jinpeng Rao,
- Kai Wei,
- Yuezhou Chen,
- Erich D. Jarvis,
- Guojie Zhang,
- and Qi Zhou
Genome Res. March 2021 31: 497-511; Published in Advance January 6, 2021, doi:10.1101/gr.271569.120
...a near chromosome-level of ostrich (Zhang et al. 2015) with Illumina reads and optical-mapping, and found that its Z Chromosome (Chr Z) harbors many fewer inversions than chicken and zebra finch, when all three species were compared to the autosomal counterparts of lizard and snake (Zhou et al. 2014...
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Resource: A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate
- Martien A.M. Groenen,
- Per Wahlberg,
- Mario Foglio,
- Hans H. Cheng,
- Hendrik-Jan Megens,
- Richard P.M.A. Crooijmans,
- Francois Besnier,
- Mark Lathrop,
- William M. Muir,
- Gane Ka-Shu Wong,
- Ivo Gut,
- and Leif Andersson
Genome Res. March 2009 19: 510-519; Published in Advance December 16, 2008, doi:10.1101/gr.086538.108
..., L.B. , Dodgson, J. , Hillel, J. , et al. ( 2000 ) A consensus linkage map of the chicken . Genome Res. 10 : 137 – 147 . ↵ Haldane, J.B.S. ( 1922 ) Sex-ratio and unisexual sterility in hybrid animals . J. Genet. 12 : 101 – 109 . ↵ Hillier...
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RESOURCE: A BAC-Based Physical Map of the Chicken Genome
- Chengwei Ren,
- Mi-Kyung Lee,
- Bo Yan,
- Kejiao Ding,
- Bettye Cox,
- Michael N. Romanov,
- Jennifer A. Price,
- Jerry B. Dodgson,
- and Hong-Bin Zhang
Genome Res. December 2003 13: 2754-2758; doi:10.1101/gr.1499303
.... Genet. 2 : 573 -583. ↵ Groenen, M.A.M., Cheng, H.H., Bumstead, N., Benkel, B.F., Briles, W.E., Burke, T., Burt, D.W., Crittenden, L.B., Dodgson, J.B., Hillel, J., et al. 2000 . A consensus linkage map of the chicken . Genome Res. 10 : 137 -147. ↵ The International Human Genome Mapping Consortium. 2001...
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Resource: A chromosome-scale assembly of the axolotl genome
- Jeramiah J. Smith,
- Nataliya Timoshevskaya,
- Vladimir A. Timoshevskiy,
- Melissa C. Keinath,
- Drew Hardy,
- and S. Randal Voss
Genome Res. February 2019 29: 317-324; Published in Advance January 24, 2019, doi:10.1101/gr.241901.118
...). Paedomorphosis reflects the loss of metamorphic changes in a derived species relative to its ancestor. These studies have found that expression of paedomorphosis can largely be attributed to a single genomic region, known as the met QTL. In the last year, sparse meiotic mapping information was also used...
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Research: Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling
- Edward S. Rice,
- Satomi Kohno,
- John St. John,
- Son Pham,
- Jonathan Howard,
- Liana F. Lareau,
- Brendan L. O'Connell,
- Glenn Hickey,
- Joel Armstrong,
- Alden Deran,
- Ian Fiddes,
- Roy N. Platt II,
- Cathy Gresham,
- Fiona McCarthy,
- Colin Kern,
- David Haan,
- Tan Phan,
- Carl Schmidt,
- Jeremy R. Sanford,
- David A. Ray,
- Benedict Paten,
- Louis J. Guillette, Jr.,
- and Richard E. Green
Genome Res. May 2017 27: 686-696; Published in Advance January 30, 2017, doi:10.1101/gr.213595.116
...scale. We computed synteny between the alligator and chicken (Galgal4) s using SyMAP v4.2 (Soderlund et al. 2011). We used both AllMis2 and AllMis1 for comparison and found that the increased contiguity of AllMis2 vastly improved our ability to compute synteny between the chicken and alligator s, more...
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Research: Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome
- Jessica Stapley,
- Tim R. Birkhead,
- Terry Burke,
- and Jon Slate
Genome Res. April 2010 20: 496-502; Published in Advance March 31, 2010, doi:10.1101/gr.102095.109
...large (macro) chromosomes. Linkage mapping studies have shown that microchromosomes have a higher recombination rate than their larger counterparts (International Chicken Genome Sequencing Consortium 2004; Stapley et al. 2008). Increased recombination rate is expected to reduce the amount of background...
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Research: Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation
- Marina Veil,
- Lev Y. Yampolsky,
- Björn Grüning,
- and Daria Onichtchouk
Genome Res. March 2019 29: 383-395; Published in Advance January 23, 2019, doi:10.1101/gr.240572.118
...”) and TF binding at the absence of motifs (“nonconsensus binding”). The heat maps of TF occupancy for the seven groups are shown in Figure 1A, summary profiles in Supplemental Figure S1, and the genomic regions in the Supplemental Table S1. We performed de novo motif search to estimate the relative...

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