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Method: FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data
- Can Luo,
- Zimeng Jamie Zhou,
- Yichen Henry Liu,
- and Xin Maizie Zhou
Genome Res. October 2025 35: 2252-2272; Published in Advance August 13, 2025, doi:10.1101/gr.280282.124
...abundant form of genetic variation in humans and can be efficiently detected using short-read sequencing technologies. Therefore, -wide association studies (GWASs) have primarily focused on SNVs to investigate the genetic basis of phenotypic traits. In contrast, structural variants (SVs)—larger genomic...
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Resource: Phenotypic diversity and genotypic flexibility of Burkholderia cenocepacia during long-term chronic infection of cystic fibrosis lungs
- Amy Huei-Yi Lee,
- Stephane Flibotte,
- Sunita Sinha,
- Adrianna Paiero,
- Rachel L. Ehrlich,
- Sergey Balashov,
- Garth D. Ehrlich,
- James E.A. Zlosnik,
- Joshua Chang Mell,
- and Corey Nislow
Genome Res. April 2017 27: 650-662; Published in Advance March 21, 2017, doi:10.1101/gr.213363.116
...genotypes, long-read sequencing by PacBio was carried out on 11 isolates as well as on the reference B. cenocepacia J2315 as a control. Genomic and phenotypic resource for Burkholderia Genome Research 651 www..org in lung function over time; 14 of 16 showed significant decreases for at least one of three...
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Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
.../or affected by high error rates, their underlying technology cannot be straightforwardly adapted to processing long reads. Therefore, several short-read-based tools, such as Kraken2, KrakenUniq, KMCP, and Ganon, can successfully process long read. However, they may encounter challenges in yielding...
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Method: Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration
- Zepu Miao and
- Jia-Xing Yue
Genome Res. February 2025 35: 296-310; Published in Advance January 13, 2025, doi:10.1101/gr.279461.124
...supports for integrating conventional linear--based feature annotations, enabling seamless examination of genomic variation in both graph-based and linear-based contexts. As further demonstrated with real world examples of yeast and human pan graphs as well as with benchmarking comparison with other tools...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...studies may overlook. On the other hand, analyses of genomic variation frequently reveal a complex interplay among sequence changes, including single-nucleotide polymorphisms (SNPs) and structural variations (SVs), which are associated with altered gene expression and phenotypic traits (Collins et al...
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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
..., independent of Hi-C data and scaffolding, will greatly enhance studies and overcome technical challenges in structural variation discovery. These advances are exemplified by long-read de novo assemblers such as hifiasm (UL) (Cheng et al. 2023) and Verkko (Rautiainen et al. 2023).To further investigate...
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Research: The human ribosomal DNA array is composed of highly homogenized tandem clusters
- Yutaro Hori,
- Akira Shimamoto,
- and Takehiko Kobayashi
Genome Res. November 2021 31: 1971-1982; Published in Advance August 18, 2021, doi:10.1101/gr.275838.121
...information on human rDNA. One reason is that the human rDNA unit (∼43 kb) is much larger than the yeast rDNA unit (∼9.2 kb), and it includes many small repetitive sequences in the noncoding region. Although the Human Genome Project declared its completion in 2003, it was difficult to assemble the r...
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