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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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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: 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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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
.... Consequently, understanding the diversity in terms of strains in microbial communities is crucial, as variations between strains can lead to different phenotypic expressions or diverse biological functions. However, current methods for taxonomic classification from metagenomic sequencing data have several...
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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
...pangenomics: a tutorial on data structures and their applications. Nat Comput 21: 81–108. doi:10.1007/s11047-022-09882-6 ↵Bradbury PJ, Casstevens T, Jensen SE, Johnson L, Miller Z, Monier B, Romay M, Song B, Buckler ES. 2022. The practical haplotype graph, a platform for storing and using pans for imputation...
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Research: A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species
- Xuelei Dai,
- Peipei Bian,
- Dexiang Hu,
- Funong Luo,
- Yongzhen Huang,
- Shaohua Jiao,
- Xihong Wang,
- Mian Gong,
- Ran Li,
- Yudong Cai,
- Jiayue Wen,
- Qimeng Yang,
- Weidong Deng,
- Hojjat Asadollahpour Nanaei,
- Yu Wang,
- Fei Wang,
- Zijing Zhang,
- Benjamin D. Rosen,
- Rasmus Heller,
- and Yu Jiang
Genome Res. August 2023 33: 1284-1298; Published in Advance September 15, 2023, doi:10.1101/gr.277481.122
...A Chinese indicine pan reveals a wealth of novel structural variants introgressed from other Bos species Xuelei Dai1,8, Peipei Bian1,8, Dexiang Hu1,8, Funong Luo1,8, Yongzhen Huang1,8, Shaohua Jiao1, Xihong Wang1, Mian Gong1, Ran Li1, Yudong Cai1, Jiayue Wen1, Qimeng Yang1, Weidong Deng2, Hojjat...
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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
...Pan-genotyped structural variation improves molecular phenotype mapping in cattle Alexander S. Leonard, Xena M. Mapel and Hubert Pausch Animal Genomics, ETH Zurich, 8092 Zurich, Switzerland Corresponding authors: alleonard@ethz.ch, hubert.pausch@usys.ethz.chAbstractExpression and splicing...
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Resource: The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation
- Zhengcao Li,
- Xiaohong Liu,
- Chen Wang,
- Zhenyang Li,
- Bo Jiang,
- Ruifeng Zhang,
- Lu Tong,
- Youping Qu,
- Sheng He,
- Haifan Chen,
- Yafei Mao,
- Qingnan Li,
- Torsten Pook,
- Yu Wu,
- Yanjun Zan,
- Hui Zhang,
- Lu Li,
- Keying Wen,
- and Yaosheng Chen
Genome Res. October 2023 33: 1833-1847; Published in Advance November 1, 2023, doi:10.1101/gr.277638.122
...of structural variation have been challenging and elusive owing to the intricate and multifaceted features of SVs (Alkan et al. 2011). The advent of the pan expands the SV spectrum particularly by deciphering gene PAVs that underpin phenotypic diversity in bacteria, crops, and humans (Yu et al. 2022). However...
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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
...references. Consequently, two pangenomic aligners have been developed within the vg toolkit: vg map (Garrison et al. 2018; Sirén et al. 2020) and vg giraffe (Sirén et al. 2021). Both methods involve constructing and aligning to a variation graph. In this graph, nodes represent segments of DNA sequences...
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