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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: 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
...and Salzberg 2020). These pans are frequently modeled as graphs (Garrison et al. 2018; Li et al. 2020), which work well to represent and detect structural variants (SVs), sequence alterations >50 bp, compared with reference-based short-read alignment (Mérot et al. 2020). Pangenomic approaches have proven...
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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
..., Markello C, Sibbesen JA, Hickey G, Chang PC, Carroll A, et al. 2021. Pangenomics enables genotyping of known structural variants in 5202 diverse s. Science 374: abg8871. doi:10.1126/science.abg8871 ↵Sirén J, Eskandar P, Ungaro MT, Hickey G, Eizenga JM, Novak AM, Chang X, Chang PC, Kolmogorov M, Carroll A...
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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
...al. 2022; Zheng et al. 2022). Therefore, to reveal the structure and function of microbial communities, we need to estimate their composition and abundance at finest resolution possible, that is, not only at the level of species, but also at the level of strains.For this study, we define a “strain...
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Corrigendum: Corrigendum: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. October 2025 35: 2375; doi:10.1101/gr.281340.125
...Corrigendum: A sheep pan reveals the spectrum of structural variations and their effects on tail phenotypes Ran Li, Mian Gong, Xinmiao Zhang, Fei Wang, Zhenyu Liu, Lei Zhang, Qimeng Yang, Yuan Xu, Mengsi Xu, Huanhuan Zhang, Yunfeng Zhang, Xuelei Dai, Yuanpeng Gao, Zhuangbiao Zhang, Wenwen Fang...
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Resource: Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle
- Alexander S. Leonard,
- Xena M. Mapel,
- and Hubert Pausch
Genome Res. February 2024 34: 300-309; Published in Advance February 14, 2024, doi:10.1101/gr.278267.123
...to comprehensively resolve structural variation. Here we build a pan from 16 HiFi haplotype-resolved cattle assemblies to identify small and structural variation and genotype them with PanGenie in 307 short-read samples. We find high (>90%) concordance of PanGenie-genotyped and DeepVariant-called small variation...
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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
...assembly path similarities within the graph to reveal an association between two most likely serial alleles of a complex structural variant (SV) 66 kb upstream of KIT and facial depigmentation. The complex SV contains a variable number of tandemly duplicated 14.3 kb repeats, consisting of LTRs, LINEs...
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Method: Accurate short-read alignment through r-index-based pangenome indexing
- Rahul Varki,
- Massimiliano Rossi,
- Eddie Ferro,
- Marco Oliva,
- Erik Garrison,
- Ben Langmead,
- and Christina Boucher
Genome Res. July 2025 35: 1609-1620; Published in Advance June 12, 2025, doi:10.1101/gr.279858.124
...the ground-truth GIAB HG005 MHC variants (https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/ChineseTrio/HG005_NA24631_son/NISTv4.2.1/GRCh38/) with Illumina's hap.py script (v0.3.15) (Krusche et al. 2019) and RTG's vcfeval (v3.12.1) (Cleary et al. 2015) as the comparison engine. The hap...
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Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. March 2023 33: 463-477; Published in Advance April 3, 2023, doi:10.1101/gr.277372.12
...A sheep pan reveals the spectrum of structural variations and their effects on tail phenotypes Ran Li1,15, Mian Gong1,15, Xinmiao Zhang1,15, Fei Wang1,15, Zhenyu Liu1,15, Lei Zhang1,15, Qimeng Yang1, Yuan Xu1, Mengsi Xu2, Huanhuan Zhang1, Yunfeng Zhang2, Xuelei Dai1, Yuanpeng Gao1, Zhuangbiao Zhang...
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Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. March 27, 2023 ; Published in Advance March 27, 2023, doi:10.1101/gr.277372.122
...A sheep pan reveals the spectrum of structural variations and their effects on tail phenotypes Ran Li,1,15 Mian Gong,1,15 Xinmiao Zhang,1,15 Fei Wang,1,15 Zhenyu Liu,1,15 Lei Zhang,1,15 Qimeng Yang,1 Yuan Xu,1 Mengsi Xu,2 Huanhuan Zhang,1 Yunfeng Zhang,2 Xuelei Dai,1 Yuanpeng Gao,1 Zhuangbiao Zhang...
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