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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...Oxford Nanopore Technologies, Oxford OX4 4DQ, United Kingdom ↵4 These authors contributed equally to this work. Corresponding authors: adam.phillippy@nih.gov, sergey.koren@nih.govAbstractThe Telomere-to-Telomere Consortium recently finished the first truly complete sequence of a human . To resolve...
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Method: Telomere-to-telomere assembly by preserving contained reads
- Sudhanva Shyam Kamath,
- Mehak Bindra,
- Debnath Pal,
- and Chirag Jain
Genome Res. November 2024 34: 1908-1918; Published in Advance October 15, 2024, doi:10.1101/gr.279311.124
...Sudhanva Shyam Kamath, Mehak Bindra, Debnath Pal and Chirag Jain Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, India Corresponding author: chirag@iisc.ac.inAbstractAutomated telomere-to-telomere (T2T) de novo assembly of diploid and polyploid s...
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Mini-Review: Toward telomere-to-telomere cat genomes for precision medicine and conservation biology
- William J. Murphy and
- Andrew J. Harris
Genome Res. May 2024 34: 655-664; Published in Advance June 7, 2024, doi:10.1101/gr.278546.123
...Toward telomere-to-telomere cat s for precision medicine and conservation biology William J. Murphy1,2,3 and Andrew J. Harris1,3 1Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA; 2Department of Biology, Texas A&M University, College...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...the counts and types of gene families shared across different numbers of s. (D) Proportion and counts of genes belonging to each gene family group (as shown in panel B) for each strain of C. nigoni and C. briggsae. (E) Box plot comparing the mean values of nucleotide sequence diversity (π nucleotide) of C...
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Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
...shown to lead to recombination hotspots. The first, which is best understood in humans and the mouse, is governed by the PRDM9 protein. A zinc-finger domain recognizes a specific DNA sequence motif and then performs a histone modification in the vicinity, which marks the sequence for a DNA double...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...transcription factor binding (Hamdi et al. 2016). Future massively parallel reporter assays or CRISPR-Cas9 disruptions of quasi-prime sequences with CRISPR-Cas9 will be interesting to systematically examine the cis-regulatory effects and mechanisms at human quasi-primes loci. These results further validate our...
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Research: Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth
- Clarence Zheng,
- Sherwood R. Casjens,
- Alan R. Davidson,
- Susan K. Amundsen,
- and Gerald R. Smith
Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
...proteins have been recognized by sequence homology as robust members of the bacterial SSB family (Casjens et al. 2004, 2005), and they have similar AlphaFold 3-predicted structures (Fig. 4A; Abramson et al. 2024). We call this protein sequence type “SSB-1” (Supplemental Table S2). The Rec modules of phage...
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Method: Identifying crossovers and shared genetic material in whole genome sequencing data from families
- Kelley Paskov,
- Brianna Chrisman,
- Nathaniel Stockham,
- Peter Yigitcan Washington,
- Kaitlyn Dunlap,
- Jae-Yoon Jung,
- and Dennis P. Wall
Genome Res. October 2023 33: 1747-1756; Published in Advance October 25, 2023, doi:10.1101/gr.277172.122
...was then passed into PhasingFamilies. We used these families to validate crossovers and IBD among families.We also applied PhasingFamilies to the NA12878 platinum , along with her spouse and 11 children to validate crossover calls. Crossover locations for the 11 children have been called using two sequencing...
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Resource: Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform
- Liubomir Chorbadjiev,
- Murat Cokol,
- Zohar Weinstein,
- Kevin Shi,
- Christopher Fleisch,
- Nikolay Dimitrov,
- Svetlin Mladenov,
- Ivo Todorov,
- Iordan Ivanov,
- Simon Xu,
- Steven Ford,
- Yoon-ha Lee,
- Boris Yamrom,
- Steven Marks,
- Adriana Munoz,
- Alex Lash,
- Natalia Volfovsky,
- and Ivan Iossifov
Genome Res. October 2025 35: 2352-2362; Published in Advance September 16, 2025, doi:10.1101/gr.280356.124
...-SFARI.The substantial reduction in sequencing costs has made generating whole-exome or whole- sequences for large family collections feasible. This development allows for the direct observation and analysis of genetic variants across the entire frequency spectrum, spanning from common to rare and de novo mutations...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
..., nested repeat architectures and make EquiRep particularly well-suited for characterizing satellite repeats in complete telomere-to-telomere (T2T) assemblies.We are optimistic that the computational efficiency of EquiRep can be largely improved. Currently, the self-local alignment step presents...
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