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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
.... melanogaster that address such challenging regions of the D. melanogaster , including the histone and Stellate clusters. To develop a scalable approach for studying genetic variation within tandem arrays, we applied widely used software to easily collectable highly accurate long-read data (Wenger et al. 2019...
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Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
- Tanner D. Jensen,
- Bohan Ni,
- Chloe M. Reuter,
- John E. Gorzynski,
- Sarah Fazal,
- Devon Bonner,
- Rachel A. Ungar,
- Pagé C. Goddard,
- Archana Raja,
- Euan A. Ashley,
- Jonathan A. Bernstein,
- Stephan Zuchner,
- Undiagnosed Diseases Network,
- Michael D. Greicius,
- Stephen B. Montgomery,
- Michael C. Schatz,
- Matthew T. Wheeler,
- and Alexis Battle
Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
...-specific features are separately aggregated for each SV, then collapsed to each gene by regions.To capture longer range SV-gene interactions in the 100 kb Watershed-SV model, we included ABC (Nasser et al. 2021) enhancer-gene links among the annotations. We categorized annotations into three categories based on SV...
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Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...-based assemblies (Brawand et al. 2014), limiting its ability to detect more complex genomic variation.There is currently limited insight into SVs in cichlids via a -wide approach, especially within individual radiations like Lake Malawi, which harbors an estimated more than 800 species predominantly from...
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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
..., B73, affords the opportunity to assess structural variation and complexitywithin this species (Schnable et al. 2009). Detailed analyses of specific loci as well as genomic approaches have identified numerous duplications within the maize , many of which are located in colinear regions (Schnable et...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...and effectiveness in identifying variants across both genic and intergenic regions, ensuring their utility in diverse genomic analyses; different papers have discussed this in more depth (Sherman and Salzberg 2020; Abondio et al. 2023, 2024; Liao et al. 2023; Rocha et al. 2024).DiscussionLong-read sequencing...
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Research: Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii
- Eugenio López-Cortegano,
- Rory J. Craig,
- Jobran Chebib,
- Eniolaye J. Balogun,
- and Peter D. Keightley
Genome Res. January 2023 33: 45-60; Published in Advance December 12, 2022, doi:10.1101/gr.276957.122
...) insertions and excisions, and chromosomal rearrangements, such as inversions and translocations. Such large structural changes are expected to have larger fitness effects than SNMs and indels, and the structural variation that arises from SMs has been implicated in many evolutionary phenomena. For example...
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Research: Chromosome-specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing
- Samantha L. Sholes,
- Kayarash Karimian,
- Ariel Gershman,
- Thomas J. Kelly,
- Winston Timp,
- and Carol W. Greider
Genome Res. April 2022 32: 616-628; Published in Advance October 26, 2021, doi:10.1101/gr.275868.121
..., usually abbreviated, G1-3T. The subtelomeric region in yeast contains specific families of repeated DNA.Deletion of any component of telomerase in yeast leads to progressive telomere shortening, termed ever-shorter telomere (EST) phenotype (Lundblad and Szostak 1989; Lendvay et al. 1996). Previous work...
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Research: Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes
- Ovidiu Popa,
- Einat Hazkani-Covo,
- Giddy Landan,
- William Martin,
- and Tal Dagan
Genome Res. April 2011 21: 599-609; Published in Advance January 26, 2011, doi:10.1101/gr.115592.110
...and recipients per . Directed networks are still quite rare in the literature because they demand specific information about the polarized nature of connections (edges) between entities (vertices), for example, whoto-whom telephone calls (Palla et al. 2007), internet browsing 4Corresponding author. E-mail tal...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...to pericentromeric regions. To corroborate this idea, we compared the density of the satellite repeat BRSATI, a marker of pericentromeric DNA (Phillips and Reed 2000; Howe et al. 2013) to that of LTR and LINE. We found that both LTR and LINE densities were positively correlated with BRSATI density (Spearman's ρ = 0...
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Research: Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast
- Daniel A. Skelly,
- Gennifer E. Merrihew,
- Michael Riffle,
- Caitlin F. Connelly,
- Emily O. Kerr,
- Marnie Johansson,
- Daniel Jaschob,
- Beth Graczyk,
- Nicholas J. Shulman,
- Jon Wakefield,
- Sara J. Cooper,
- Stanley Fields,
- William S. Noble,
- Eric G.D. Muller,
- Trisha N. Davis,
- Maitreya J. Dunham,
- Michael J. MacCoss,
- and Joshua M. Akey
Genome Res. September 2013 23: 1496-1504; Published in Advance May 29, 2013, doi:10.1101/gr.155762.113
...al. 2009; The 1000 Genomes Project Consortium 2010; Gan et al. 2011; Keane et al. 2011; Tennessen et al. 2012). However, interpreting the functional and phenotypic consequences of genetic variation remains challenging and is exacerbated by the paucity of data on the quantitative characteristics...
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