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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...to investigate potential associations between the local recombination rate and different genomic features. Such information can be used to deduce the effects of recombination on base composition and/or regulatory mechanisms modulating the recombination landscape. A potential driver of an association between...
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Research: Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization
- Kazuaki Yamaguchi,
- Yoshinobu Uno,
- Mitsutaka Kadota,
- Osamu Nishimura,
- Ryo Nozu,
- Kiyomi Murakumo,
- Rui Matsumoto,
- Keiichi Sato,
- and Shigehiro Kuraku
Genome Res. September 2023 33: 1527-1540; Published in Advance August 17, 2023, doi:10.1101/gr.276840.122
...a gnathostome-wide comparison of the syntenic location of one-to-one orthologs, including the zebra shark (Fig. 3B; Supplemental Fig. 3). A considerable proportion of the one-to-one orthologs are shared between eMAC and large chromosomes of chicken and spotted gar (Fig. 3B). The majority of the genomic regions...
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Research: Convergent recombination cessation between mating-type genes and centromeres in selfing anther-smut fungi
- Fantin Carpentier,
- Ricardo C. Rodríguez de la Vega,
- Sara Branco,
- Alodie Snirc,
- Marco A. Coelho,
- Michael E. Hood,
- and Tatiana Giraud
Genome Res. June 2019 29: 944-953; Published in Advance May 1, 2019, doi:10.1101/gr.242578.118
...that the events of recombination cessation occurred independently in the two sister species. Our study shows that natural selection can repeatedly lead to similar genomic patterns and phenotypes, and that different evolutionary paths can lead to distinct yet equally beneficial responses to selection. Our study...
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Research: Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers
- Reto Burri,
- Alexander Nater,
- Takeshi Kawakami,
- Carina F. Mugal,
- Pall I. Olason,
- Linnea Smeds,
- Alexander Suh,
- Ludovic Dutoit,
- Stanislav Bureš,
- Laszlo Z. Garamszegi,
- Silje Hogner,
- Juan Moreno,
- Anna Qvarnström,
- Milan Ružić,
- Stein-Are Sæther,
- Glenn-Peter Sætre,
- Janos Török,
- and Hans Ellegren
Genome Res. November 2015 25: 1656-1665; Published in Advance September 9, 2015, doi:10.1101/gr.196485.115
...be explained by variation in recombination rate and the density of targets for selection. We thus conclude that the heterogeneous landscape of differentiation in Ficedula flycatchers evolves mainly as the result of background selection and selective sweeps in genomic regions of low recombination. Our results...
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Research: Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution
- Martin Völker,
- Niclas Backström,
- Benjamin M. Skinner,
- Elizabeth J. Langley,
- Sydney K. Bunzey,
- Hans Ellegren,
- and Darren K. Griffin
Genome Res. April 2010 20: 503-511; Published in Advance March 31, 2010, doi:10.1101/gr.103663.109
...polymorphic and pathogenic variants. Am J Hum Genet 84: 339–350. Backstro¨m N, Forstmeier W, Schielzeth H, Mellenius H, Nam K, Bolund E, Webster MT, Schneider M, Kempenaers B, Ellegren H. 2010. The recombinational landscape of the zebra finch Taeniopygia guttata . Genome Res (this issue). doi: 10.1101/gr...
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Research: Extensive recombination rate variation in the house mouse species complex inferred from genetic linkage maps
- Beth L. Dumont,
- Michael A. White,
- Brian Steffy,
- Tim Wiltshire,
- and Bret A. Payseur
Genome Res. January 2011 21: 114-125; Published in Advance October 26, 2010, doi:10.1101/gr.111252.110
.... 2004) and between chicken and zebra finch (Backstro¨m et al. 2010), indicating that the distant shared ancestry of a genomic region is a poor predictor of contemporary recombination rates. In contrast, the comparison of genetic linkage maps among Nasonia species (Beukeboom et al. 2010) suggests...
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Research: Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
- Matthias H. Weissensteiner,
- Andy W.C. Pang,
- Ignas Bunikis,
- Ida Höijer,
- Olga Vinnere-Petterson,
- Alexander Suh,
- and Jochen B.W. Wolf
Genome Res. May 2017 27: 697-708; Published in Advance March 30, 2017, doi:10.1101/gr.215095.116
...shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we...
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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
..., if shifts in GC content and genomic repeat landscapes are related in colubroid snakes (see also Pasquesi et al. 2018).Sex chromosome evolutionSnake sex chromosomes have evolved multiple times, apparently from different autosomal chromosomes (Gamble et al. 2017), and colubroid Z/W Chromosomes are homologous...
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Research: Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans
- James A. Cahill,
- Joel Armstrong,
- Alden Deran,
- Carolyn J. Khoury,
- Benedict Paten,
- David Haussler,
- and Erich D. Jarvis
Genome Res. November 2021 31: 2035-2049; Published in Advance October 19, 2021, doi:10.1101/gr.275989.121
..., Santa Cruz, California 95064, USA; 3UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95064, USA; 4Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA Corresponding authors: jcahill@rockefeller.edu, ejarvis@rockefeller.eduAbstractVocal learning, the ability...
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