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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
...to the underrepresentation of repetitive elements.View larger version: In this window In a new window Figure 2. Genome conservation and chromosomal rearrangements. (A) Genespace plot depicting chromosomal syntenies (of sequences >1 Mb) and rearrangements (of >5 genes) between turtles and chicken. Chromosomes are scaled...
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Research: Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
- David Thybert,
- Maša Roller,
- Fábio C.P. Navarro,
- Ian Fiddes,
- Ian Streeter,
- Christine Feig,
- David Martin-Galvez,
- Mikhail Kolmogorov,
- Václav Janoušek,
- Wasiu Akanni,
- Bronwen Aken,
- Sarah Aldridge,
- Varshith Chakrapani,
- William Chow,
- Laura Clarke,
- Carla Cummins,
- Anthony Doran,
- Matthew Dunn,
- Leo Goodstadt,
- Kerstin Howe,
- Matthew Howell,
- Ambre-Aurore Josselin,
- Robert C. Karn,
- Christina M. Laukaitis,
- Lilue Jingtao,
- Fergal Martin,
- Matthieu Muffato,
- Stefanie Nachtweide,
- Michael A. Quail,
- Cristina Sisu,
- Mario Stanke,
- Klara Stefflova,
- Cock Van Oosterhout,
- Frederic Veyrunes,
- Ben Ward,
- Fengtang Yang,
- Golbahar Yazdanifar,
- Amonida Zadissa,
- David J. Adams,
- Alvis Brazma,
- Mark Gerstein,
- Benedict Paten,
- Son Pham,
- Thomas M. Keane,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. April 2018 28: 448-459; Published in Advance March 21, 2018, doi:10.1101/gr.234096.117
...and their relative priority have been based on a combination of factors including their value as model organisms (Mouse Genome Sequencing Consortium 2002; Rat Genome Sequencing Project Consortium 2004; Lindblad-Toh et al. 2005) or agriculture species (The Bovine Genome Sequencing and Analysis Consortium 2009...
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Resource: Breakpoint graphs and ancestral genome reconstructions
- Max A. Alekseyev and
- Pavel A. Pevzner
Genome Res. May 2009 19: 943-957; Published in Advance February 13, 2009, doi:10.1101/gr.082784.108
..., macaque, mouse, rat, dog, and opossum. MGRA relies on the notion of the multiple breakpoint graphs to overcome some limitations of the existing approaches to ancestral genome reconstructions. MGRA also generates the rearrangement-based characters guiding the phylogenetic tree reconstruction when...
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Resource: Genome-scale phylogenetic function annotation of large and diverse protein families
- Barbara E. Engelhardt,
- Michael I. Jordan,
- John R. Srouji,
- and Steven E. Brenner
Genome Res. November 2011 21: 1969-1980; Published in Advance July 22, 2011, doi:10.1101/gr.104687.109
...of the 30 experimental annotations (all but the annotations for rat sequences), and we could not exclude self-annotations. Evaluating SIFTER using leave-one-out cross-validation with exact computation yields 70.0% accuracy. For comparison, BLASTGO achieves 83.3% accuracy, PFP achieves 76.7%, FFPred achieves...
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Research: Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome
- Erik Axelsson,
- Matthew T. Webster,
- Abhirami Ratnakumar,
- The LUPA Consortium,
- Chris P. Ponting,
- and Kerstin Lindblad-Toh
Genome Res. January 2012 22: 51-63; Published in Advance October 17, 2011, doi:10.1101/gr.124123.111
...Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome Erik Axelsson 1 , 4 , Matthew T. Webster 1 , Abhirami Ratnakumar 1 , The LUPA Consortium , Chris P. Ponting 2 and Kerstin Lindblad-Toh 1...
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RESOURCE: The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution
- Matthew M. Hill,
- Karl W. Broman,
- Elia Stupka,
- William C. Smith,
- Di Jiang,
- and Arend Sidow
Genome Res. August 2008 18: 1369-1379; Published in Advance June 2, 2008, doi:10.1101/gr.078576.108
...et al. 2004 ; Zhao et al. 2004 ; Woods et al. 2005 ; Kasahara et al. 2007 ). Interchromosomal rearrangements are common even between mouse and rat, two species whose neutral evolutionary distance is less than one-tenth of that between the two Cionas ( Gibbs et al. 2004 ). To estimate the extent...
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LETTER: Biased clustered substitutions in the human genome: The footprints of male-driven biased gene conversion
- Timothy R. Dreszer,
- Gregory D. Wall,
- David Haussler,
- and Katherine S. Pollard
Genome Res. October 2007 17: 1420-1430; Published in Advance September 4, 2007, doi:10.1101/gr.6395807
.... Since recombination is mutagenic, a mutation bias would be consistent with the association we find between bias and current large-scale recombination rates. In order to evaluate the possibility of a local, directed mutation bias, an analysis of the site-frequency spectrum in a large resequencing study...
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Research: Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions
- Željka Pezer,
- Bettina Harr,
- Meike Teschke,
- Hiba Babiker,
- and Diethard Tautz
Genome Res. August 2015 25: 1114-1124; Published in Advance July 6, 2015, doi:10.1101/gr.187187.114
...smaller in length, amplitude, and frequency, suggesting stronger selective constraints against structural variation in genes whose disruption might lead to disease.Amplifications versus deletionsStructural variations include both amplifications and deletions of genomic regions, which are processes...
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Chicken Special/Letters: Evolution and functional classification of vertebrate gene deserts
- Ivan Ovcharenko,
- Gabriela G. Loots,
- Marcelo A. Nobrega,
- Ross C. Hardison,
- Webb Miller,
- and Lisa Stubbs
Genome Res. January 2005 15: 137-145; Published in Advance December 8, 2004, doi:10.1101/gr.3015505
...We utilized the phylogenetic hidden Markov model (phastCons) conservation profile (Siepel and Haussler 2004a , b ) of the human calculated from the human/chimp/mouse/rat/chicken multiz alignments as available from the UCSC Genome Browser database ( Karolchik et al. 2003 ). PhastCons conservation...
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Resource: Exploration of fine-scale recombination rate variation in the domestic horse
- Samantha K. Beeson,
- James R. Mickelson,
- and Molly E. McCue
Genome Res. October 2019 29: 1744-1752; Published in Advance August 21, 2019, doi:10.1101/gr.243311.118
...in the class II region of the major histocompatibility complex. Nat Genet 29: 217–222. doi:10.1038/ng1001-217 ↵Jensen-Seaman MI, Furey TS, Payseur BA, Lu Y, Roskin KM, Chen C, Thomas MA, Haussler D, Jacob HJ. 2004. Comparative recombination rates in the rat, mouse, and human s. Genome Res 14: 528–538. doi:10...

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