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Research: Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements
- Luisa Berná,
- Pablo Marquez,
- Andrés Cabrera,
- Gonzalo Greif,
- María E. Francia,
- and Carlos Robello
Genome Res. May 2021 31: 823-833; Published in Advance April 27, 2021, doi:10.1101/gr.262832.120
.... However, the study of its biology has been unheeded by the established paradigm that it is virtually identical to its close relative, the widely studied human pathogen Toxoplasma gondii. By revisiting the sequence, assembly, and annotation using third-generation sequencing technologies, here we show...
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Research: Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization
- Kazuaki Yamaguchi,
- Yoshinobu Uno,
- Mitsutaka Kadota,
- Osamu Nishimura,
- Ryo Nozu,
- Kiyomi Murakumo,
- Rui Matsumoto,
- Keiichi Sato,
- and Shigehiro Kuraku
Genome Res. September 2023 33: 1527-1540; Published in Advance August 17, 2023, doi:10.1101/gr.276840.122
...Elasmobranch sequencing reveals evolutionary trends of vertebrate karyotype organization Kazuaki Yamaguchi1,6, Yoshinobu Uno1,7, Mitsutaka Kadota1, Osamu Nishimura1, Ryo Nozu2,8, Kiyomi Murakumo3, Rui Matsumoto3, Keiichi Sato2,3 and Shigehiro Kuraku1,4,5 1Laboratory for Phyloinformatics, RIKEN...
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Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
- Reuben M. Buckley,
- Nüket Bilgen,
- Alexander C. Harris,
- Peter Savolainen,
- Cafer Tepeli,
- Metin Erdoğan,
- Aitor Serres Armero,
- Dayna L. Dreger,
- Frank G. van Steenbeek,
- Marjo K. Hytönen,
- Heidi G. Parker,
- Jessica Hale,
- Hannes Lohi,
- Bengi Çınar Kul,
- Adam R. Boyko,
- and Elaine A. Ostrander
Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
...with lost opportunities for identifying genetic variants that play fundamental roles in mammalian biology. Nevertheless, the recent Dog10K release of whole- sequence (WGS) data from over 2000 dogs (Ostrander et al. 2019; Meadows et al. 2023), inclusive of 321 breeds and populations, means the time is ripe...
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Research: Optical genome mapping identifies rare structural variants in neural tube defects
- Nikhil S. Sahajpal,
- Jane Dean,
- Benjamin Hilton,
- Timothy Fee,
- Cindy Skinner,
- Alex Hastie,
- Barbara R. DuPont,
- Alka Chaubey,
- Michael J. Friez,
- and Roger E. Stevenson
Genome Res. April 2025 35: 798-809; Published in Advance March 19, 2025, doi:10.1101/gr.279318.124
...or accompanied by anomalies of other systems. The genetic basis of NTDs remains poorly understood using karyotyping, chromosomal microarray, and short-read sequencing, with only a limited number of pathogenic variants identified. Collectively, these technologies may fail to detect rare structural variants (SVs...
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Research: Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
- Judith Arres,
- Santosh Elavalli,
- Shalini Behl,
- Daniel Matias Sanchez,
- Ayesha Al Ali,
- Abdelrahman Ahmed Yehia Abdelaziz Saad,
- Azza Attia,
- Cyla Minas,
- Sharika Pariyachery,
- Shariq Ahmed,
- Fatmah Aldhuhoori,
- Nitu Thulasidharan,
- Gurunath Katagi,
- Omar Soliman,
- Shilp Purohit,
- Vinay Kusuma,
- Raony Cardenas,
- Thyago Cardoso,
- Luis F. Paulin,
- Philippe Sanio,
- Joseph Mafofo,
- Haiguo Wu,
- Val Zvereff,
- Albarah El-Khani,
- Fahed Al Marzooqi,
- Tiago R. Magalhães,
- Fritz J. Sedlazeck,
- and Javier Quilez
Genome Res. March 2026 36: 460-471; Published in Advance February 11, 2026, doi:10.1101/gr.280134.124
...should therefore be absent in the parents (GM27631 and GM27632). By analyzing the trio samples from each sequencing platform, we confirmed, as expected, a single copy of the pathogenic variant in the proband and its absence in both parents.We also evaluated three indels causing CF (556delA, del508...
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Method: De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data
- Arthur Dondi,
- Nico Borgsmüller,
- Pedro F. Ferreira,
- Brian J. Haas,
- Francis Jacob,
- Viola Heinzelmann-Schwarz,
- Tumor Profiler Consortium,
- and Niko Beerenwinkel
Genome Res. April 2025 35: 900-913; Published in Advance March 19, 2025, doi:10.1101/gr.279281.124
...identified by comparing variants from tumor biopsies with those from matched normal biopsies derived from respective healthy tissue. However, as matched normals are rarely available, methods to detect somatic variants de novo were developed for bulk sequencing, mainly relying on germline variant allele...
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Research: Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing
- Jesper Eisfeldt,
- Edward J. Higginbotham,
- Felix Lenner,
- Jennifer Howe,
- Bridget A. Fernandez,
- Anna Lindstrand,
- Stephen W. Scherer,
- and Lars Feuk
Genome Res. November 2024 34: 1763-1773; Published in Advance October 29, 2024, doi:10.1101/gr.279263.124
...Resolving complex duplication variants in autism spectrum disorder using long-read sequencing Jesper Eisfeldt1,2, Edward J. Higginbotham3,4, Felix Lenner5, Jennifer Howe3,4, Bridget A. Fernandez6,7, Anna Lindstrand1,2, Stephen W. Scherer3,4,8 and Lars Feuk5 1Department of Molecular Medicine...
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Research: A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia
- Sivaranjani Namasivayam,
- Rodrigo P. Baptista,
- Wenyuan Xiao,
- Erica M. Hall,
- Joseph S. Doggett,
- Karin Troell,
- and Jessica C. Kissinger
Genome Res. May 2021 31: 852-865; Published in Advance April 27, 2021, doi:10.1101/gr.266403.120
...that are present in equal ratios in the mitochondrion (Hikosaka et al. 2011). The coccidian Eimeria, the species closest to Toxoplasma gondii with a published mtDNA sequence and structure, is detected as a linear concatemer of a repeating 6.2-kb sequence similar to that of Plasmodium, albeit with the genes...
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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...and human sequences.In sample T2, HBV integrated into the centromere of Chr 8, with eight major HBV integration sites identified in an ∼34 Mb region of the 8q23–24 . Copy number analysis revealed oscillation in the 8q23–24 region and deletion in the telomere region. Notably, HBV integration...
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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
...assemblies showed indications of collapsed or erroneous sequences (Table 2). We verified true errors by checking for distinct patterns of single-nucleotide variants (SNVs) in the read alignments, or by identifying clear boundaries with soft-clipped reads surrounding the region. If assembly errors were...

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