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Research: Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement
- Peter A. Audano and
- Christine R. Beck
Genome Res. January 2024 34: 7-19; Published in Advance January 4, 2024, doi:10.1101/gr.278203.123
....Pan SV breakpoints disagree with linear reference alignmentsPan graphs are constructed from multiple haplotypes and can be used to negate differences in alignments. The PanGenome Graph Builder (PGGB) (Garrison et al. 2023) constructs graphs from multiple haplotypes simultaneously, and the Minigraph...
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Method: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
- Siavash Raeisi Dehkordi,
- Zhaoyang Jia,
- Joey Estabrook,
- Jen Hauenstein,
- Neil Miller,
- Naz Güleray-Lafci,
- Jürgen Neesen,
- Alex Hastie,
- Alka Chaubey,
- Andy Wing Chun Pang,
- Paul Dremsek,
- and Vineet Bafna
Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
...in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.References ↵Alekseyev MA, Pevzner PA. 2009. Breakpoint graphs and ancestral reconstructions. Genome Res 19: 943–957. doi:10.1101/gr...
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Method: CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing
- Kaiyuan Zhu,
- Matthew G. Jones,
- Jens Luebeck,
- Xinxin Bu,
- Hyerim Yi,
- King L. Hung,
- Ivy Tsz-Lo Wong,
- Shu Zhang,
- Paul S. Mischel,
- Howard Y. Chang,
- and Vineet Bafna
Genome Res. September 2024 34: 1344-1354; Published in Advance July 9, 2024, doi:10.1101/gr.279131.124
...graph Gt and reconstructed breakpoint graph Gr. Cycle interval overlap measures the Jaccard index, weighted by the number of nucleotides, of the genomic intervals defined by Wt and Wr. Cyclic longest common subsequence (LCS) measures the length of the longest common subsequence contained in Wt and Wr...
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Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
- Charles Plessy,
- Michael J. Mansfield,
- Aleksandra Bliznina,
- Aki Masunaga,
- Charlotte West,
- Yongkai Tan,
- Andrew W. Liu,
- Jan Grašič,
- María Sara del Río Pisula,
- Gaspar Sánchez-Serna,
- Marc Fabrega-Torrus,
- Alfonso Ferrández-Roldán,
- Vittoria Roncalli,
- Pavla Navratilova,
- Eric M. Thompson,
- Takeshi Onuma,
- Hiroki Nishida,
- Cristian Cañestro,
- and Nicholas M. Luscombe
Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
...of a gene in one lineage had little predictive power for the position or orientation of that gene in other lineages.Genome scrambling moves short functional regionsWe next identified “breakpoint regions” to search for the molecular breakpoints responsible for scrambling synteny blocks. First, we identified...
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Resource: Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
- Cory Gardner,
- Junhao Chen,
- Christina Hadfield,
- Zhaolian Lu,
- David Debruin,
- Yu Zhan,
- Maureen J. Donlin,
- Tae-Hyuk Ahn,
- and Zhenguo Lin
Genome Res. November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124
...(Supplemental Fig. S7). In addition, the Pearson correlation coefficient for the percentages of genomic content is 0.99 (Supplemental Table S4), supporting the robustness of our inference of the origin of genomic regions.We identified a total of 55 major recombination breakpoints in the 16 pairs of CBS380...
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Research: Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence
- Scott Ferguson,
- Ashley Jones,
- Kevin Murray,
- Rose Andrew,
- Benjamin Schwessinger,
- and Justin Borevitz
Genome Res. April 2024 34: 606-619; Published in Advance April 8, 2024, doi:10.1101/gr.277999.123
...of rearrangements shared by all taxa within that clade are labeled; for example, E. victrix and E. coolabah share 6029 rearrangements.As all alignments and subsequent annotations are relative to the two species involved, directly comparing the breakpoints of annotations to find common rearrangements is not possible...
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Research: Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus
- Nikolaos Vakirlis,
- Véronique Sarilar,
- Guénola Drillon,
- Aubin Fleiss,
- Nicolas Agier,
- Jean-Philippe Meyniel,
- Lou Blanpain,
- Alessandra Carbone,
- Hugo Devillers,
- Kenny Dubois,
- Alexandre Gillet-Markowska,
- Stéphane Graziani,
- Nguyen Huu-Vang,
- Marion Poirel,
- Cyrielle Reisser,
- Jonathan Schott,
- Joseph Schacherer,
- Ingrid Lafontaine,
- Bertrand Llorente,
- Cécile Neuvéglise,
- and Gilles Fischer
Genome Res. July 2016 26: 918-932; Published in Advance May 31, 2016, doi:10.1101/gr.204420.116
...branch (Fig. 2). Remarkably, we found three gene relics, i.e., highly degenerated remnants of genes (Lafontaine et al. 2004), within intergenic sequences corresponding to rearrangement breakpoints. Such relics Reconstruction of history in Lachancea Genome Research 925 www..org E F Figure 5. (A...
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Method: Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples
- Sergey Aganezov and
- Benjamin J. Raphael
Genome Res. September 2020 30: 1274-1290; Published in Advance September 4, 2020, doi:10.1101/gr.256701.119
...number for each adjacency. The karyotype graph describes an alignment between the cancer and healthy (analogous to the breakpoint graph in rearrangement studies) (Alekseyev and Pevzner 2009; Avdeyev et al. 2016). The karyotype graph also represents the information about the cancer sequence that can...
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Methods: Reconstructing contiguous regions of an ancestral genome
- Jian Ma,
- Louxin Zhang,
- Bernard B. Suh,
- Brian J. Raney,
- Richard C. Burhans,
- W. James Kent,
- Mathieu Blanchette,
- David Haussler,
- and Webb Miller
Genome Res. December 2006 16: 1557-1565; Published in Advance September 18, 2006, doi:10.1101/gr.5383506
...this table: In this window In a new window Table 3. Genomic content of breakpoint regions Theoretical analysis We wanted to assess what proportion of the ancestral adjacencies inferred by our method might be correct. We started with a theoretical analysis, which necessitated some rather severe assumptions...
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Research: Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution
- Florent Murat,
- Jian-Hong Xu,
- Eric Tannier,
- Michael Abrouk,
- Nicolas Guilhot,
- Caroline Pont,
- Joachim Messing,
- and Jérôme Salse
Genome Res. November 2010 20: 1545-1557; Published in Advance September 28, 2010, doi:10.1101/gr.109744.110
...drive these chromosome-shuffling events. The recent availability of large amounts of whole sequences from diverse taxa yielded large-scale, wide comparisons in mammals and provided clear identification of synteny breakpoints or junction sequences, which gave rise to a new evolutionary perspective...

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