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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
...to previously published gar and bowfin s (Supplemental Fig. S1J). These analyses establish that the new A. spatula and L. osseus s are the most complete holostean assemblies currently available.Gars have a stable chromosomal architectureDespite diverging more than 100 million years ago (Grande 2010; Brownstein...
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Method: HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
- Sergey Nurk,
- Brian P. Walenz,
- Arang Rhie,
- Mitchell R. Vollger,
- Glennis A. Logsdon,
- Robert Grothe,
- Karen H. Miga,
- Evan E. Eichler,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. September 2020 30: 1291-1305; Published in Advance August 14, 2020, doi:10.1101/gr.263566.120
...a vertebrate project may benefit from longer reads to span midsized identical repeats. We also identified an apparent bias in the current HiFi chemistry at low-complexity A/G (T/C) repeats, leading to coverage drops and assembly fragmentation. This issue warrants further investigation and may limit...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...generating crucial control data sets: the 1000 Genomes Project ONT Sequencing Consortium is producing LRS data from 1kGP samples to aid in filtering and prioritizing SNVs and SVs (Gustafson et al. 2024), while the All of Us (AoU) initiative has begun a long-read arm to sequence blood samples from Americans...
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Method: Detection and analysis of ancient segmental duplications in mammalian genomes
- Lianrong Pu,
- Yu Lin,
- and Pavel A. Pevzner
Genome Res. June 2018 28: 901-909; Published in Advance May 7, 2018, doi:10.1101/gr.228718.117
...and impact within the current human project assembly. Genome Res 11: 1005–1017. ↵Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE. 2002. Recent segmental duplications in the human . Science 297: 1003–1007. ↵Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
.... Additionally, although we expected an increase in TF occupancy at the PHO8 promoter because it was upregulated, this increased occupancy extended well into the shared promoter of CWC21–KRE2 (Supplemental Fig. S9). This suggests that the regulation of CWC21–KRE2 may be impacted by the transcriptional mechanisms...
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Research: H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity
- Kei Fukuda,
- Chikako Shimura,
- and Yoichi Shinkai
Genome Res. October 2025 35: 2199-2210; Published in Advance August 5, 2025, doi:10.1101/gr.280732.125
...statementThe authors declare no competing interests.AcknowledgmentsY.S. was supported by a RIKEN internal research fund (Pioneering project “Genome building from TADs”) and by the Japan Society for the Promotion of Science (JSPS) (Grant-in-Aid for Transformative Research Areas [A], 25H01302; Grant...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
..., and evolution of such arrays.The rapid development of long-read sequencing technologies (Marx 2023) and informatics approaches (Chin et al. 2013, 2016; Berlin et al. 2015; Koren et al. 2017) led to a proliferation of assemblies that approached the quality of consortium-led reference sequencing projects...
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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
...constitute a principal driver of evolution, shaping its architecture and regulatory networks. In this context, Tuberaceae can become an important model system to study their genomic impact; however, the family lacks high-quality assemblies. Here, we investigate the interplay between TEs and Tuberaceae...
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Research: Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
- Peter O. Mulhair,
- Liam Crowley,
- Douglas H. Boyes,
- Amber Harper,
- Owen T. Lewis,
- Darwin Tree of Life Consortium,
- and Peter W.H. Holland
Genome Res. January 2023 33: 32-44; Published in Advance December 8, 2022, doi:10.1101/gr.277118.122
...A in Z. pyrina) and others having multiple copies of several of the four Shx genes (Supplemental Fig. S5). It is currently unclear whether these large gene arrays are adaptive, having been driven by selection, or whether they are neutral and a consequence of a genomic region prone to duplication...
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Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
- Amy R. Vandiver,
- Allen Herbst,
- Paul Stothard,
- and Jonathan Wanagat
Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
...-up, in accordance with the manufacturer's instructions; 150 bp paired-end sequencing was performed on Illumina NextSeq 500 through the UCLA Technology Center for Genomics and Bioinformatics.Data accessThe fibroblast sequencing data generated in this study have been submitted to the NCBI BioProject database (https...

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