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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
...compelling causal candidates.MethodsHiFi sequencingWe extracted high-molecular-weight DNA from blood of two animals with the Qiagen MagAttract HMW kit, following the manufacturer's protocols. PacBio HiFi libraries were generated and sequenced on three SMRT cells each by the Functional Genomic Center Zurich...
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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
...from markedly larger interspecific unaligned regions in C. nigoni, which overlap significantly with C. nigoni intraspecific unaligned segments that are also substantially larger than those in C. briggsae. Moreover, the increased gene number in C. nigoni is largely owing to the expansion of species...
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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
..., gene absence/presence, etc. (Computational Pan-Genomics Consortium 2018).Recent works propose the use of pan references to improve genotyping accuracy from short-read sequencing data (Eggertsson et al. 2017; Sibbesen et al. 2018; Hickey et al. 2020; Letcher et al. 2021; Bradbury et al. 2022; Ebler et...
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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
...technologies, long-read sequencing (PacBio and ONT) avoids the generation of PCR duplicates common to short-read sequencing, which avoids the corresponding biases during taxonomic profiling. Third, portable long-read sequencing sequencers, such as ONT Flongle and MinION, enable cost-effective, in...
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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
...), such as pathogen immunity in cattle (Crysnanto et al. 2021), body development in ducks (Wang et al. 2024) and sheep (Li et al. 2023), fruit flavor in tomatoes (Gao et al. 2019), and flowering time in cucumbers (Li et al. 2022). In wild populations, the use of pans is gaining attention, as they can uncover key...
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Resource: Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
- Yang Zhou,
- Lv Yang,
- Xiaotao Han,
- Jiazheng Han,
- Yan Hu,
- Fan Li,
- Han Xia,
- Lingwei Peng,
- Clarissa Boschiero,
- Benjamin D. Rosen,
- Derek M. Bickhart,
- Shujun Zhang,
- Aizhen Guo,
- Curtis P. Van Tassell,
- Timothy P.L. Smith,
- Liguo Yang,
- and George E. Liu
Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
...). One example of an SV-affecting phenotype is a chromosomal translocation and subsequent duplication encompassing the KIT gene, leading to characteristic coat-color phenotypes in Belgian Blue and Brown Swiss cattle (Durkin et al. 2012). Another example is a 660-kb deletion found to be at high frequency...
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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
...to the Illumina library preparation protocol and was sequenced on the Illumina HiSeq platform to generate 150-bp paired-end reads (Supplemental Tables S1, S21). The RNA of 19 PiNan cattle was extracted with a Qiagen RNeasy mini kit for transcriptome sequencing, and a total of 19 paired-end libraries were prepared...
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Research: Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression
- Sudeshna Majumdar,
- Lakshmi Sowjanya Bammidi,
- Hemant C. Naik,
- Avinchal Manhas,
- Runumi Baro,
- Akash Kalita,
- Amlan Jyoti Naskar,
- Sundarraj Nidharshan,
- Girija S. Bariha,
- Dimple Notani,
- and Srimonta Gayen
Genome Res. September 2025 35: 1992-2010; Published in Advance August 6, 2025, doi:10.1101/gr.279822.124
...and clones with paternal D1 deletion. P values (Mann–Whitney U test): (****) P ≤ 0.0001. n = 113, 100, 110, 100, 103.Next, to further explore, we generated XEN cell lines with two segmental deletions (D2: near to Xist, and D3: near to Jpx) of the Xist upstream region using CRISPR-Cas9 (Fig. 3A). We generated...
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Method: Genetic complexity of killer-cell immunoglobulin-like receptor genes in human pangenome assemblies
- Tsung-Kai Hung,
- Wan-Chi Liu,
- Sheng-Kai Lai,
- Hui-Wen Chuang,
- Yi-Che Lee,
- Hong-Ye Lin,
- Chia-Lang Hsu,
- Chien-Yu Chen,
- Ya-Chien Yang,
- Jacob Shujui Hsu,
- and Pei-Lung Chen
Genome Res. August 2024 34: 1211-1223; Published in Advance September 9, 2024, doi:10.1101/gr.278358.123
...gene with an African high-frequency KIR3DL1 allele resulting from a deletion between KIR3DL1 and KIR3DL2. Purple represents framework genes; red, duplicated genes; blue, nonframework genes; and gray, pseudogenes. (#) An allele having nonsynonymous variant(s) in CDS, segmental deletion, or fusion...
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Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
- Yuwei Cao,
- Lauren Patel,
- Lauren Alcoser,
- Eric Mendenhall,
- Christopher Benner,
- Sven Heinz,
- and Alon Goren
Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
...buffer.Library construction, reverse cross-linking, and library cleanupFor the IP and input samples, libraries were constructed with the NEBNext Ultra II DNA library prep kit (Illumina E7645L). Indexing adapters were from NEXTflex DNA barcodes 48 (NOVA-514104) and NEXTflex unique dual index barcodes (8NT...

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