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Research: Differences in activity and stability drive transposable element variation in tropical and temperate maize
- Shujun Ou,
- Armin Scheben,
- Tyler Collins,
- Yinjie Qiu,
- Arun S. Seetharam,
- Claire C. Menard,
- Nancy Manchanda,
- Jonathan I. Gent,
- Michael C. Schatz,
- Sarah N. Anderson,
- Matthew B. Hufford,
- and Candice N. Hirsch
Genome Res. August 2024 34: 1140-1153; Published in Advance September 9, 2024, doi:10.1101/gr.278131.123
...(Yang et al. 2013; Huang et al. 2018) alter gene expression, leading to earlier and day-length insensitive flowering in temperate maize. Expression differences can also result from insertions into intron sequences, such as a Mutator-like TE in an intron of DSX2 (Fang et al. 2020) that increases...
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Method: Three-dimensional missense tolerance ratio analysis
- Riley E. Perszyk,
- Anders S. Kristensen,
- Polina Lyuboslavsky,
- and Stephen F. Traynelis
Genome Res. August 2021 31: 1447-1461; Published in Advance July 22, 2021, doi:10.1101/gr.275528.121
...caveat is that all point mutants in the validation were assayed in NMDARs, where both copies of the subunit in the tetrameric receptor contains the mutation. In contrast, tolerance selection occurs in individuals that most often are heterozygous carriers of the mutation; therefore, the majority...
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Research: Hidden variation in polyploid wheat drives local adaptation
- Laura-Jayne Gardiner,
- Ryan Joynson,
- Jimmy Omony,
- Rachel Rusholme-Pilcher,
- Lisa Olohan,
- Daniel Lang,
- Caihong Bai,
- Malcolm Hawkesford,
- David Salt,
- Manuel Spannagl,
- Klaus F.X. Mayer,
- John Kenny,
- Michael Bevan,
- Neil Hall,
- and Anthony Hall
Genome Res. September 2018 28: 1319-1332; Published in Advance August 9, 2018, doi:10.1101/gr.233551.117
...representing global genetic diversity. We identify independent variation in methylation, genotype, and transposon copy number. We show that these, so far unexploited, sources of variation have had a significant impact on the wheat and that ancestral methylation states become preferentially “hard coded...
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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
...recombination rate is expected to lead to reduced genetic variation via background selection (loss of neutral variants linked to deleterious mutations during purifying selection) (Charlesworth 1994; Comeron 2017) and selective sweeps/hitch-hiking (haplotypes around advantageous mutations increase in frequency...
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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
...Željka Pezer1,2, Bettina Harr1, Meike Teschke1, Hiba Babiker1 and Diethard Tautz1 1Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany Corresponding author: zpezer@irb.hr ↵2 Present address: Ruder Bošković Institute, 10000 Zagreb, Croatia AbstractCopy number variation represents...
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Research: Somatic structural variation targets neurodevelopmental genes and identifies SHANK2 as a tumor suppressor in neuroblastoma
- Gonzalo Lopez,
- Karina L. Conkrite,
- Miriam Doepner,
- Komal S. Rathi,
- Apexa Modi,
- Zalman Vaksman,
- Lance M. Farra,
- Eric Hyson,
- Moataz Noureddine,
- Jun S. Wei,
- Malcolm A. Smith,
- Shahab Asgharzadeh,
- Robert C. Seeger,
- Javed Khan,
- Jaime Guidry Auvil,
- Daniela S. Gerhard,
- John M. Maris,
- and Sharon J. Diskin
Genome Res. September 2020 30: 1228-1242; Published in Advance August 13, 2020, doi:10.1101/gr.252106.119
...chromosomal alterations as the main candidate driver mutations in many tumors. Structural variations (insertions, deletions, duplications and translocations, and inversions) can also function as potent cancer drivers, as shown with the discovery of rearrangements near the TERT gene driving aberrant telomerase...
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Research: Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana
- Maximilian O. Press,
- Rajiv C. McCoy,
- Ashley N. Hall,
- Joshua M. Akey,
- and Christine Queitsch
Genome Res. August 2018 28: 1169-1178; Published in Advance July 3, 2018, doi:10.1101/gr.231753.117
...contribute to phenotypic variation. Intronic STR mutations can disrupt splicing, altering gene function (Li et al. 2004) and contributing to human disease (for review, see Ranum and Day 2002). In humans, unascertained diversity of splice forms contributes substantially to disease (Cummings et al. 2017...
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Research: Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor
- Ruth A. Swanson-Wagner,
- Steven R. Eichten,
- Sunita Kumari,
- Peter Tiffin,
- Joshua C. Stein,
- Doreen Ware,
- and Nathan M. Springer
Genome Res. December 2010 20: 1689-1699; Published in Advance October 29, 2010, doi:10.1101/gr.109165.110
...whether structural variation was observed and the type of variation and the y-axis indicates the number of genotypes that contain the structural variant. Copy number variation in diverse maize genotypes Genome Research 1691 www..org that these structural variants are tolerated in the homozygous state and...
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Research: Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania
- Matthew B. Rogers,
- James D. Hilley,
- Nicholas J. Dickens,
- Jon Wilkes,
- Paul A. Bates,
- Daniel P. Depledge,
- David Harris,
- Yerim Her,
- Pawel Herzyk,
- Hideo Imamura,
- Thomas D. Otto,
- Mandy Sanders,
- Kathy Seeger,
- Jean-Claude Dujardin,
- Matthew Berriman,
- Deborah F. Smith,
- Christiane Hertz-Fowler,
- and Jeremy C. Mottram
Genome Res. December 2011 21: 2129-2142; Published in Advance October 28, 2011, doi:10.1101/gr.122945.111
...and variation in chromosome number. Increased gene copy number due to chromosome amplification may contribute to alterations in gene expression in response to environmental conditions in the host, providing a genetic basis for disease tropism. [Supplemental material is available for this article...
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Resource: Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum
- Alistair Miles,
- Zamin Iqbal,
- Paul Vauterin,
- Richard Pearson,
- Susana Campino,
- Michel Theron,
- Kelda Gould,
- Daniel Mead,
- Eleanor Drury,
- John O'Brien,
- Valentin Ruano Rubio,
- Bronwyn MacInnis,
- Jonathan Mwangi,
- Upeka Samarakoon,
- Lisa Ranford-Cartwright,
- Michael Ferdig,
- Karen Hayton,
- Xin-zhuan Su,
- Thomas Wellems,
- Julian Rayner,
- Gil McVean,
- and Dominic Kwiatkowski
Genome Res. September 2016 26: 1288-1299; Published in Advance August 16, 2016, doi:10.1101/gr.203711.115
...of conversion tracts. We observe several instances of meiotic recombination within copy number variants associated with drug resistance, demonstrating a mechanism whereby fitness costs associated with resistance mutations could be compensated and greater phenotypic plasticity could be acquired. Footnotes...
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