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Research: An efficient RNA-seq-based segregation analysis identifies the sex chromosomes of Cannabis sativa
- Djivan Prentout,
- Olga Razumova,
- Bénédicte Rhoné,
- Hélène Badouin,
- Hélène Henri,
- Cong Feng,
- Jos Käfer,
- Gennady Karlov,
- and Gabriel A.B. Marais
Genome Res. February 2020 30: 164-172; Published in Advance February 7, 2020, doi:10.1101/gr.251207.119
.... 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357–359. doi:10.1038/nmeth.1923 ↵Laverty KU, Stout JM, Sullivan MJ, Shah H, Gill N, Holbrook L, Deikus G, Sebra R, Hughes TR, Page JE, et al. 2019. A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD...
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Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
- Sheila Lutz,
- Megan Lawler,
- Samuel Amidon,
- and Frank W Albert
Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
...† equal contribution 9 * Corresponding authors: S.L. (lutz0006@umn.edu); F.W.A. (falbert@umn.edu) 10 11 Running title: Mapping of genetic variation with CRI-SPA-Map 12 ABSTRACT 13 Genetic variation within species shapes phenotypes, but identifying the specific genes and 14 variants that cause phenotypic...
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Method: Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
- Xuyan Liu,
- Lin Xia,
- Yixin Qiao,
- Yang Li,
- Yan Huang,
- Bingyan Yue,
- Xi Liang,
- Xin Yang,
- Honghui Zhang,
- Jiaxun Zhang,
- Xiao Chen,
- Dan Xie,
- and Jifeng Liu
Genome Res. April 8, 2026 gr.281046.125; Published in Advance April 8, 2026, doi:10.1101/gr.281046.125
...Enrichment Analysis) that were shared by three or 236 more samples from smokers. Using GREAT (McLean et al. 2010) , these loci were 237 mapped to 49 putative distal regulatory target genes. Pathway enrichment analysis 238 revealed that six of the top ten enriched pathways (q < 0.05) were immune-related, 239...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
.... 2023). Full haplotype resolution enables precise characterization of inter-haplotype variations predominantly shaped by heterozygosity, structural rearrangements, and transposable element (TE) movements (Gluck-Thaler et al. 2022; Hartmann 2022; Ferguson et al. 2024). Further, the complete picture...
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Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
- Michael K.B. Ford,
- Ananth Hari,
- Meredith Yeager,
- Lisa Mirabello,
- Stephen Chanock,
- Ibrahim Numanagić,
- COVNET Consortium,
- and S. Cenk Sahinalp
Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
.... 2016; Yacoob et al. 2016; Yeung et al. 2016; Lee et al. 2021). However, these tools require specialized, and therefore resource-intensive, sequencing and analysis protocols and cannot be applied to the extensive available databases of short-read WGS data. As a result, the human immune receptor loci...
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Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...Lake Malawi cichlid pan graph reveals extensive structural variation driven by transposable elements Fu Xiang Quah1,2, Miguel Vasconcelos Almeida1, Moritz Blumer2, Chengwei Ulrika Yuan1,2, Bettina Fischer2, Kirsten See1, Ben Jackson2, Richard Zatha3, Bosco Rusuwa3, George F. Turner4, M. Emília...
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Research: Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation
- Vanessa L. Porter,
- Michelle Ng,
- Kieran O'Neill,
- Signe MacLennan,
- Richard D. Corbett,
- Luka Culibrk,
- Zeid Hamadeh,
- Marissa Iden,
- Rachel Schmidt,
- Shirng-Wern Tsaih,
- Carolyn Nakisige,
- Martin Origa,
- Jackson Orem,
- Glenn Chang,
- Jeremy Fan,
- Ka Ming Nip,
- Vahid Akbari,
- Simon K. Chan,
- James Hopkins,
- Richard A. Moore,
- Eric Chuah,
- Karen L. Mungall,
- Andrew J. Mungall,
- Inanc Birol,
- Steven J.M. Jones,
- Janet S. Rader,
- and Marco A. Marra
Genome Res. April 2025 35: 653-670; Published in Advance December 5, 2024, doi:10.1101/gr.279041.124
...structures, methylation patterns, and transcriptional regulation associated with these loci. Our analysis revealed the extent of cis-linked genomic dysregulation resulting from HPV integration, including structural rearrangements and modulation of virus and host gene expression and epigenetic regulation...
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Research: Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii
- Frédéric Chaux,
- Nicolas Agier,
- Clotilde Garrido,
- Gilles Fischer,
- Stephan Eberhard,
- and Zhou Xu
Genome Res. September 2023 33: 1582-1598; Published in Advance August 14, 2023, doi:10.1101/gr.278043.123
.... The landscape of the ensuing rearrangements is not accessible by short-read sequencing. Here, we leverage Oxford Nanopore Technologies long-read sequencing to survey the extensive repertoire of rearrangements in telomerase mutants of the model green microalga Chlamydomonas reinhardtii. In telomerase...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...), NPC lines, and developmental timepoints, to generate a list of putative enhancer regions to investigate using the phNPC model. Whereas other enhancer mapping tools such as massively parallel reporter assays (MPRAs) have been used to identify putative enhancer regions in primary human cortical cells...
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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
...loci. Synteny can become disrupted by the loss, gain, duplication, rearrangement, or divergence of existing sequences. Rearrangements can occur as inversions, translocations, and duplications, altering the order of sequences within chromosomes while maintaining gene content, and are often labeled...
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