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Research: Topologically associating domains and their role in the evolution of genome structure and function in Drosophila
- Yi Liao,
- Xinwen Zhang,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. March 2021 31: 397-410; Published in Advance February 9, 2021, doi:10.1101/gr.266130.120
...of the influence of TADs on evolution remains preliminary. To study the molecular evolution of TADs in Drosophila species, we constructed a new reference-grade assembly and accompanying high-resolution TAD map for D. pseudoobscura. Comparison of D. pseudoobscura and D. melanogaster, which are separated by ∼49...
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Resource: The genome of the vervet (Chlorocebus aethiops sabaeus)
- Wesley C. Warren,
- Anna J. Jasinska,
- Raquel García-Pérez,
- Hannes Svardal,
- Chad Tomlinson,
- Mariano Rocchi,
- Nicoletta Archidiacono,
- Oronzo Capozzi,
- Patrick Minx,
- Michael J. Montague,
- Kim Kyung,
- LaDeana W. Hillier,
- Milinn Kremitzki,
- Tina Graves,
- Colby Chiang,
- Jennifer Hughes,
- Nam Tran,
- Yu Huang,
- Vasily Ramensky,
- Oi-wa Choi,
- Yoon J. Jung,
- Christopher A. Schmitt,
- Nikoleta Juretic,
- Jessica Wasserscheid,
- Trudy R. Turner,
- Roger W. Wiseman,
- Jennifer J. Tuscher,
- Julie A. Karl,
- Jörn E. Schmitz,
- Roland Zahn,
- David H. O'Connor,
- Eugene Redmond,
- Alex Nisbett,
- Béatrice Jacquelin,
- Michaela C. Müller-Trutwin,
- Jason M. Brenchley,
- Michel Dione,
- Martin Antonio,
- Gary P. Schroth,
- Jay R. Kaplan,
- Matthew J. Jorgensen,
- Gregg W.C. Thomas,
- Matthew W. Hahn,
- Brian J. Raney,
- Bronwen Aken,
- Rishi Nag,
- Juergen Schmitz,
- Gennady Churakov,
- Angela Noll,
- Roscoe Stanyon,
- David Webb,
- Francoise Thibaud-Nissen,
- Magnus Nordborg,
- Tomas Marques-Bonet,
- Ken Dewar,
- George M. Weinstock,
- Richard K. Wilson,
- and Nelson B. Freimer
Genome Res. December 2015 25: 1921-1933; Published in Advance September 16, 2015, doi:10.1101/gr.192922.115
...://creativecommons.org/licenses/ by-nc/4.0/. Resource 25:1921–1933 Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/15; www..org Genome Research 1921 www..org C. a. sabaeuspopulation.Through comparative analyseswithhumanandrhesusmacaque,wecharacterize at high resolution the unique chromosomal fission events...
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Research: Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
- Aaron R. Quinlan,
- Royden A. Clark,
- Svetlana Sokolova,
- Mitchell L. Leibowitz,
- Yujun Zhang,
- Matthew E. Hurles,
- Joshua C. Mell,
- and Ira M. Hall
Genome Res. May 2010 20: 623-635; Published in Advance March 22, 2010, doi:10.1101/gr.102970.109
...one breakpoint of each type at a given complex locus) at complex loci. (del) Deletion; (dup) duplication; (ins) insertion; (inv) inversion. Mapping and assembly of structural variation Genome Research 629 www..org breakpoint, as can occur due to inserted DNA or small-scale rearrangements. When...
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RESOURCE: Initial sequence and comparative analysis of the cat genome
- Joan U. Pontius,
- James C. Mullikin,
- Douglas R. Smith,
- Agencourt Sequencing Team,
- Kerstin Lindblad-Toh,
- Sante Gnerre,
- Michele Clamp,
- Jean Chang,
- Robert Stephens,
- Beena Neelam,
- Natalia Volfovsky,
- Alejandro A. Schäffer,
- Richa Agarwala,
- Kristina Narfström,
- William J. Murphy,
- Urs Giger,
- Alfred L. Roca,
- Agostinho Antunes,
- Marilyn Menotti-Raymond,
- Naoya Yuhki,
- Jill Pecon-Slattery,
- Warren E. Johnson,
- Guillaume Bourque,
- Glenn Tesler,
- NISC Comparative Sequencing Program,
- and Stephen J. O’Brien
Genome Res. November 2007 17: 1675-1689; doi:10.1101/gr.6380007
...Institute, National Institutes of Health, Bethesda, Maryland 20892, USA Abstract The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome assemblies of six mammals...
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REVIEW: Defensins and the dynamic genome: What we can learn from structural variation at human chromosome band 8p23.1
- Edward J. Hollox,
- John C.K. Barber,
- Anthony J. Brookes,
- and John A.L. Armour
Genome Res. November 2008 18: 1686-1697; doi:10.1101/gr.080945.108
...technologies may shed light on the small-scale variation at this locus, although novel approaches are needed to define the large-scale variation at a sequence-level resolution. Sequence-based approaches and paired-end mapping cannot easily capture the large inversion between REPD and REPP. However, physical...
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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...for all samples. Subsequently, SMs were called from read alignments using Sniffles (Smolka et al. 2024), from assembly mappings using dipcall (Li et al. 2018), and from a multisample pan built with minigraph (Li et al. 2020). Leveraging the low error rate of our assemblies (genomic quality values QV > 45...
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