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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...with detecting alterations in tandem repeats (TRs), and more generally, with variations found within repetitive sequences (e.g., segmental duplications, satellite sequences, transposable elements), leaving a large fraction of the inaccessible. Short-reads also have limited power to phase variants within the same...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...derivative of the N2 strain. We use improved long-read sequencing and manual assembly of 43 recalcitrant genomic regions to overcome deficiencies of prior N2 and VC2010 assemblies and to assemble tandem repeat loci, including a 772 kb sequence for the 45S rRNA genes. Although many differences from earlier...
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Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
- Mikhail O. Maksimov,
- Cynthia Wu,
- David G. Ashbrook,
- Flavia Villani,
- Vincenza Colonna,
- Nima Mousavi,
- Nichole Ma,
- Lu Lu,
- Jonathan K. Pritchard,
- Alon Goren,
- Robert W. Williams,
- Abraham A. Palmer,
- and Melissa Gymrek
Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
...A novel quantitative trait locus implicates Msh3 in the propensity for -wide short tandem repeat expansions in mice Mikhail O. Maksimov1,2,12, Cynthia Wu3,12, David G. Ashbrook4, Flavia Villani4, Vincenza Colonna4,5, Nima Mousavi6, Nichole Ma1, Lu Lu4, Jonathan K. Pritchard7,8, Alon Goren1...
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Research: Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response
- Ariadna Picart-Picolo,
- Stefan Grob,
- Nathalie Picault,
- Michal Franek,
- Christel Llauro,
- Thierry Halter,
- Tom R. Maier,
- Edouard Jobet,
- Julie Descombin,
- Panpan Zhang,
- Vijayapalani Paramasivan,
- Thomas J. Baum,
- Lionel Navarro,
- Martina Dvořáčková,
- Marie Mirouze,
- and Frédéric Pontvianne
Genome Res. November 2020 30: 1583-1592; Published in Advance October 8, 2020, doi:10.1101/gr.261586.120
...thaliana, a significant loss of ribosomal RNA (rRNA) genes with a past history of a mutation for the chromatin assembly factor 1 (CAF1) complex causes rapid changes in the structure. Using long-read sequencing and microscopic approaches, we have identified up to 15 independent large tandem duplications...
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Research: Evolution of genome structure in the Drosophila simulans species complex
- Mahul Chakraborty,
- Ching-Ho Chang,
- Danielle E. Khost,
- Jeffrey Vedanayagam,
- Jeffrey R. Adrion,
- Yi Liao,
- Kristi L. Montooth,
- Colin D. Meiklejohn,
- Amanda M. Larracuente,
- and J.J. Emerson
Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
...and Drosophila melanogaster s (Britten and Kohne 1968; International Human Genome Sequencing Consortium 2001; Treangen and Salzberg 2012; Hoskins et al. 2015). These sequences include repeated tandem arrays of noncoding sequences like satellite DNAs, self-replicating selfish elements like transposable elements...
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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
...ends of the LR assembly capture short (<25 kb) parts of the tandem repeat arrays predicted by the OM data. These contig ends consisted entirely of complex arrangements of the crowSat1 satellite subunit as tandems and palindromes. Thus, it seems possible that LR technologies and assembly algorithms...
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Research: Discovery and genotyping of structural variation from long-read haploid genome sequence data
- John Huddleston,
- Mark J.P. Chaisson,
- Karyn Meltz Steinberg,
- Wes Warren,
- Kendra Hoekzema,
- David Gordon,
- Tina A. Graves-Lindsay,
- Katherine M. Munson,
- Zev N. Kronenberg,
- Laura Vives,
- Paul Peluso,
- Matthew Boitano,
- Chen-Shin Chin,
- Jonas Korlach,
- Richard K. Wilson,
- and Evan E. Eichler
Genome Res. May 2017 27: 677-685; Published in Advance November 28, 2016, doi:10.1101/gr.214007.116
...) consisted of tandem repeats or complex arrays of different repeat classes (Supplemental Table S2). It is interesting to note that this single diploid identifies 44% as many SVs as reported for 2504 diploid s in Phase 3 of the 1000 Genomes Project (Sudmant et al. 2015b) and that 89% of all SVs we detected...
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Research: Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution
- Chang Liu,
- Congmao Wang,
- George Wang,
- Claude Becker,
- Maricris Zaidem,
- and Detlef Weigel
Genome Res. August 2016 26: 1057-1068; Published in Advance May 25, 2016, doi:10.1101/gr.204032.116
...promoters, including convergent, divergent, and tandem promoter pairs. (B) Correlation between H3K27me3 and gene expression. In the four control sets, upon shifting the coordinates of H3K27me3 peaks, genesmarkedwith H3K27me3 are no longer associated with reduced expression. (C) Fraction of promoters...
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Resource: Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set
- Joana Damas,
- Rebecca O'Connor,
- Marta Farré,
- Vasileios Panagiotis E. Lenis,
- Henry J. Martell,
- Anjali Mandawala,
- Katie Fowler,
- Sunitha Joseph,
- Martin T. Swain,
- Darren K. Griffin,
- and Denis M. Larkin
Genome Res. May 2017 27: 875-884; Published in Advance November 30, 2016, doi:10.1101/gr.213660.116
...Combined length (Mb) 888.67 687.59 Damas et al. 880 Genome Research www..org (Morgulis et al. 2006) with the -sdust option and Tandem Repeats Finder (Benson 1999). Chicken gene (version of 27/04/2014) and repetitive sequence (version of 11/06/2012) annotations were downloaded from the UCSC Genome Browser...
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Research: Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection
- Simon R. Harris,
- Carl Robinson,
- Karen F. Steward,
- Katy S. Webb,
- Romain Paillot,
- Julian Parkhill,
- Matthew T.G. Holden,
- and Andrew S. Waller
Genome Res. September 2015 25: 1360-1371; Published in Advance July 9, 2015, doi:10.1101/gr.189803.115
...a wild-type has locus (Supplemental Fig. 11). A specific PCR that spanned the IS3 element that borders the has locus was used to confirm that the amplification of the has locus in strain 851 occurs in tandem. Comparison of the multiple isolates recovered from persistently infected horses showed that even...
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