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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
...et al. 1999). Differences in the scale and extent of synteny conservation have led to the concepts of micro- and macrosynteny. Microsynteny (also known as “collinearity” in genomics) refers to the conservation of gene content and order within sets of tightly linked orthologous genes. Generally...
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Method: Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain
- Jenna Kalleberg,
- Jacob Rissman,
- and Robert D. Schnabel
Genome Res. August 2025 35: 1859-1874; Published in Advance June 2, 2025, doi:10.1101/gr.279542.124
...the bovine genomic community run parallel to those for humans, including the 1000 Bull Genomes (1kBulls), Bovine Pan, and Ruminant Telomere-to-Telomere (RT2T) consortia (The 1000 Genomes Project Consortium 2010; Hayes and Daetwyler 2019; Jarvis et al. 2022; Kaminow et al. 2022; Nurk et al. 2022; Zhou et al...
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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
...dystrophy cohort. (A) Precision-recall curves (PRC) of benchmark using held-out N2 pairs; We ran multitissue Watershed-SV using both 10 kb (solid) and 100 kb (dashed) distance limit as well as WGS-only model and CADD-SV with the same setup. (B) Top positive genomic annotation effect sizes (β) for seven...
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Review: k-mer approaches for biodiversity genomics
- Katharine M. Jenike,
- Lucía Campos-Domínguez,
- Marilou Boddé,
- José Cerca,
- Christina N. Hodson,
- Michael C. Schatz,
- and Kamil S. Jaron
Genome Res. February 2025 35: 219-230; Published in Advance January 31, 2025, doi:10.1101/gr.279452.124
..., complete telomere-to-telomere (T2T) assemblies are being produced for an ever-increasing array of species (Nurk et al. 2022; Chen et al. 2023; Zhang et al. 2023), and large global efforts to capture the genomic diversity of life are well underway (Lewin et al. 2022). However, as of this writing, the vast...
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Method: Genetic complexity of killer-cell immunoglobulin-like receptor genes in human pangenome assemblies
- Tsung-Kai Hung,
- Wan-Chi Liu,
- Sheng-Kai Lai,
- Hui-Wen Chuang,
- Yi-Che Lee,
- Hong-Ye Lin,
- Chia-Lang Hsu,
- Chien-Yu Chen,
- Ya-Chien Yang,
- Jacob Shujui Hsu,
- and Pei-Lung Chen
Genome Res. August 2024 34: 1211-1223; Published in Advance September 9, 2024, doi:10.1101/gr.278358.123
...employed. Therein lies the potential scope for refinement to further enhance output quality. The Telomere-to-Telomere (T2T) consortium sequenced the complete haploid human , T2T-CHM13, encompassing each autosome and X Chromosome (Nurk et al. 2022). Later, the Human Pan Reference Consortium (HPRC) released...
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Research: Deciphering D4Z4 CpG methylation gradients in fascioscapulohumeral muscular dystrophy using nanopore sequencing
- Russell J. Butterfield,
- Diane M. Dunn,
- Brett Duval,
- Sarah Moldt,
- and Robert B. Weiss
Genome Res. September 2023 33: 1439-1454; Published in Advance October 5, 2023, doi:10.1101/gr.277871.123
...a BAC clone, but an attempt to sequence the array from genomic DNA as part of a whole analysis resulted in only a small number of full-length reads from the D4Z4 array limiting utility of this technique (Mitsuhashi et al. 2017). Nanopore Cas9-targeted sequencing (nCATS) is a recently developed tool...
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Method: Highly accurate assembly polishing with DeepPolisher
- Mira Mastoras,
- Mobin Asri,
- Lucas Brambrink,
- Prajna Hebbar,
- Alexey Kolesnikov,
- Daniel E. Cook,
- Maria Nattestad,
- Julian Lucas,
- Taylor S. Won,
- Pi-Chuan Chang,
- Andrew Carroll,
- Benedict Paten,
- Kishwar Shafin,
- and and the Human Pangenome Reference Consortium
Genome Res. July 2025 35: 1595-1608; Published in Advance May 19, 2025, doi:10.1101/gr.280149.124
...on short reads. Recently, new approaches have begun to emerge for correcting the state-of-the-art telomere-to-telomere (T2T) assemblies generated with a combination of PacBio high fidelity (HiFi) and ONT long reads. To polish the first fully complete human (CHM13), the T2T consortium leveraged Deep...
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Method: Long-read reconstruction of many diverse haplotypes with devider
- Jim Shaw,
- Christina Boucher,
- Yun William Yu,
- Noelle Noyes,
- and Heng Li
Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
...for a CfxA2 beta-lactamase gene. We find clear recombination blocks for these AMR gene haplotypes, showcasing devider's ability to unveil evolutionary signals for heterogeneous mixtures.The presence of highly similar genomic sequences within a single organism or a group of organisms is common in biological...
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Research: Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants
- Jing Xia,
- Aarthi Venkat,
- Rachel E. Bainbridge,
- Michael L. Reese,
- Karine G. Le Roch,
- Ferhat Ay,
- and Jon P. Boyle
Genome Res. May 2021 31: 834-851; Published in Advance April 27, 2021, doi:10.1101/gr.262816.120
...and genomic resources. However, as for many other eukaryotes, the T. gondii contains hundreds of sequence gaps owing to repetitive and/or unclonable sequences that disrupt the assembly process. Here, we use the Oxford Nanopore Minion platform to generate near-complete de novo assemblies for multiple strains...
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