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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
...for the speciation and adaptations such as mimicry (Joron et al. 2011; Hill et al. 2019; de Vos et al. 2020), mostly owing to reciprocal translocation and repeated events of fusion and fission among a highly dynamic number of chromosomes between species.To better understand the phenomenon of scrambling, we study...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
.... By aligning the sequencing data of L. oculatus and A. spatula to Chromosome 3 of A. spatula, we found that, at the fusion region, the sequencing depth of a 2-kb fragment in L. oculatus was zero, whereas A. spatula showed a relatively high sequencing depth in the fusion region. Further genomic feature analysis...
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Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
- Qian Qin,
- Victoria Popic,
- Kirsty Wienand,
- Houlin Yu,
- Emily White,
- Akanksha Khorgade,
- Asa Shin,
- Christophe Georgescu,
- Catarina D. Campbell,
- Arthur Dondi,
- Niko Beerenwinkel,
- Francisca Vazquez,
- Aziz M. Al'Khafaji,
- and Brian J. Haas
Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
...exceptions. By combining short and long reads in CTAT-LR-Fusion, we are able to further maximize the detection of fusion splicing isoforms and fusion-expressing tumor cells.Genomic rearrangements involving chromosomal translocations or deletions can yield fusion genes, in some cases activating oncogenes...
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Mini-Review: The paradox of R-loops: guardians of the genome or drivers of disease?
- Shachinthaka D. Dissanayaka Mudiyanselage,
- Phillip Wulfridge,
- and Kavitha Sarma
Genome Res. September 2025 35: 1919-1928; Published in Advance August 6, 2025, doi:10.1101/gr.278992.124
...-ChIP, RHΔ is expressed in vivo with an epitope tag, and genomic sequences bound by RHΔ are recovered via chromatin immunoprecipitation. (F) MapR uses a purified RHΔ–MNase fusion protein to bind and cleave chromatin fragments containing R-loops, which are then purified and sequenced.To provide an orthogonal...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...fusions or fissions. Also, the comparison of T. panzhihuanense with the long-read-based high-quality Morchella sextelata M. Kuo assembly revealed relatively high levels of mesosynteny conservation between the two species (Fig. 5B; Supplemental Fig. S14B). Indeed, 61% of the T. panzhihuanense and 70...
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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
...in the three-dimensional (3D) chromatin structure in turtles compared to other amniotes beyond the fusion/fission events detected in the linear s. Namely, whole- comparisons revealed distinct trends of chromosome rearrangements in turtles: (1) a low rate of reshuffling in Apalone (Trionychidae) whose karyotype...
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Resource: Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
- José Carlos Montañés,
- Marta Huertas,
- Simone G. Moro,
- William R. Blevins,
- Mercè Carmona,
- José Ayté,
- Elena Hidalgo,
- and M. Mar Albà
Genome Res. June 2022 32: 1215-1227; Published in Advance May 26, 2022, doi:10.1101/gr.276516.121
...José Carlos Montañés1, Marta Huertas1, Simone G. Moro1, William R. Blevins1,4, Mercè Carmona2, José Ayté2, Elena Hidalgo2 and M. Mar Albà1,3 1Evolutionary Genomics Group, Research Program on Biomedical Informatics, Hospital del Mar Medical Research Institute (IMIM) and Universitat Pompeu Fabra (UPF...
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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...: chirag@iisc.ac.inAbstractAffordable genotyping methods are essential in genomics. Commonly used genotyping methods primarily support single-nucleotide variants and short indels but neglect structural variants. Additionally, accuracy of read alignments to a reference is unreliable in highly polymorphic...
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Research: ISWI1 complex proteins facilitate developmental genome editing in Paramecium
- Aditi Singh,
- Lilia Häußermann,
- Christiane Emmerich,
- Emily Nischwitz,
- Brandon K.B. Seah,
- Falk Butter,
- Mariusz Nowacki,
- and Estienne C. Swart
Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
...or His N-terminal fusion proteins or untagged proteins were used for the pulldown. Pulldown specificity was validated using glutathione agarose (GST) or nickel-IMAC agarose (Ni2 + NTA) beads. Unspecific binding or cross-reactivity of tagged proteins in the IP fraction of the pulldowns was not observed...
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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
...of macrochromosome ends (e.g., with higher GC content) is thought to be a remnant of the fusion of one or more microchromosome(s) to a macrochromosome (Waters et al. 2021). This hypothesis is not supported by our observation that even species possessing no explicit microchromosomes (e.g., western clawed frog) have...
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