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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
...Bio) and Oxford Nanopore Technologies (ONT), has markedly enhanced both the efficiency and accuracy of genomic studies (Sedlazeck et al. 2018). These technological advances have also propelled pan analyses. Initially developed for bacterial studies (Sherman and Salzberg 2020), the pan approach has now gained...
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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
..., using Oxford Nanopore Technologies' MinION long-read sequencing. We characterize the S. bayanus and compare it with its parent species, Saccharomyces uvarum and Saccharomyces eubayanus, and other S. bayanus s to better understand evolution after a relatively recent hybridization event. We observe...
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Resource: Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes
- Wenjuan Yu,
- Haohui Luo,
- Jinbao Yang,
- Shengchen Zhang,
- Heling Jiang,
- Xianjia Zhao,
- Xingqi Hui,
- Da Sun,
- Liang Li,
- Xiu-qing Wei,
- Stefano Lonardi,
- and Weihua Pan
Genome Res. February 2024 34: 326-340; Published in Advance March 1, 2024, doi:10.1101/gr.278232.123
...long reads that can span most repetitive regions in eukaryotic s and thus have simplified the de novo assembly problem. A notable example of SMS is Pacific Biosciences (PacBio) HiFi technology that can provide reads >10 kbp with very high accuracy (<0.01% sequencing error). Oxford Nanopore Technologies...
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Method: Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
- Yuhong Sun,
- Zhanwen Cheng,
- Xiang Li,
- Qing Yang,
- Bixi Zhao,
- Ziqi Wu,
- and Yu Xia
Genome Res. April 2023 33: 612-621; Published in Advance April 11, 2023, doi:10.1101/gr.277266.122
...compositions.Unlike the endeavors made before sequencing, Nanopore sequencing (Oxford Nanopore Technology, ONT) users can program their system to reverse the voltage polarity of the sequencing pore to eject reads identified as not of interest, which provides a potential solution to enrich rare species...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...%) and Gopherus (44%) whose assemblies were generated using longer read sequencing (Pacific Biosciences [PacBio] or Oxford Nanopore Technologies [ONT], respectively). Transposable elements (TEs) such as long terminal repeats (LTRs), long interspersed nuclear elements (LINEs), short interspersed nuclear elements...
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Review: Leveraging the power of long reads for targeted sequencing
- Shruti V. Iyer,
- Sara Goodwin,
- and William Richard McCombie
Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
...al. 2022; Hoyt et al. 2022). This review will discuss targeted long-read strategies employed on the two main long-read platforms: Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio). It will focus on methods such as long-range PCR, hybridization, Cas9-mediated approaches, and on...
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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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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...of the relationships between individual exons. The LRS technology space is currently dominated by Pacific Biosciences (PacBio; https://www.pacb.com/products-and-services/applications/rna-sequencing/ [accessed April 25, 2024]) and Oxford Nanopore Technologies (ONT) (Box 1). PacBio utilizes single-molecule real...
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Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
...as a template (Eid et al. 2009). This was followed by the release of the Oxford Nanopore Technologies (ONT) platform, which measures changes in current induced by the movement of a nucleic acid molecule through a nanopore. Since then, both technologies’ capabilities have found numerous applications spanning...
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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
...in the Supplemental Material, Supplemental Table S1, for each sample. Two Oxford Nanopore Technologies (ONT) long-read native DNA sequencing libraries were prepared for each species according to the manufacturer's protocol 1D genomic DNA by ligation (SQK-LSK109). Eucalyptus marginata was an exception, which had one...
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