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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...High-quality assembly of the Chinese white truffle and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae Jacopo Martelossi1,2,8, Jacopo Vujovic3,8, Yue Huang3,4,8, Alessia Tatti2,5, Kaiwei Xu4, Federico Puliga3, Yuanxue Chen4, Omar Rota Stabelli2...
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Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
...and reverse strands in each genomic bin and observed highly biased distributions when comparing the relative enrichment between the two strands across the (Fig. 6A–C; Supplemental Fig. 11). These biases reflect a preference for G4s in the leading strand and a dearth in the lagging strand. At individual phyla...
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Resource: Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
- Cory Gardner,
- Junhao Chen,
- Christina Hadfield,
- Zhaolian Lu,
- David Debruin,
- Yu Zhan,
- Maureen J. Donlin,
- Tae-Hyuk Ahn,
- and Zhenguo Lin
Genome Res. November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124
...Chromosome-level sub-aware de novo assembly provides insight into Saccharomyces bayanus divergence after hybridization Cory Gardner1,2,5, Junhao Chen3,5, Christina Hadfield2, Zhaolian Lu3, David Debruin2, Yu Zhan3, Maureen J. Donlin2,4, Tae-Hyuk Ahn1,2 and Zhenguo Lin2,3 1Department of Computer...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...of transposable element origination and high inactivity compared to other vertebrates. Beyond providing a reference point for comparative vertebrate genomic studies, the new gar s illuminate a structural component of slow genomic evolution in living fossils and molecular mechanisms that may underlie exceptional...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...to a karyotypically normal reference . This needs to be addressed if further progress in understanding the 3D cancer is to be achieved.In conclusion, our findings provide new insights into the complex genomic structural changes that underlie breast cancer metastatic progression. The interplay between subcompartment...
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Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
- Paras Verma,
- Deeksha Thakur,
- Deepanshi Awasthi,
- and Shashi Bhushan Pandit
Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
..., particularly indels and substitution among isoforms from its coalescence of exon's splicing information and their isoform protein sequences, is discussed below.Inferring protein sequence indel and substitution from Block-I attributesEUID's Block-I attributes provide insights into coding scope of exons...
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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
...The pig pan provides insights into the roles of coding structural variations in genetic diversity and adaptation Zhengcao Li1, Xiaohong Liu1, Chen Wang1, Zhenyang Li1, Bo Jiang1, Ruifeng Zhang1, Lu Tong1, Youping Qu1, Sheng He1, Haifan Chen1, Yafei Mao2, Qingnan Li1, Torsten Pook3, Yu Wu1, Yanjun...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
..., TF binding for each factor is highly variable across genotypes, as shown for two loci for Twist and Mef2 occupancy (Fig. 1F).Effects of genetic variation on TF binding are extensive and preferably detected in genomic regions with less bufferingTo disentangle the impact of genetic variation on TF...
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Method: A new compression strategy to reduce the size of nanopore sequencing data
- Kavindu Jayasooriya,
- Sasha P. Jenner,
- Pasindu Marasinghe,
- Udith Senanayake,
- Hassaan Saadat,
- David Taubman,
- Roshan Ragel,
- Hasindu Gamaarachchi,
- and Ira W. Deveson
Genome Res. July 2025 35: 1574-1582; Published in Advance May 15, 2025, doi:10.1101/gr.280090.124
..., this provides the basis to evaluate and/or develop alternative lossless or lossy compression strategies, which may be applied on top of bit-reduction to deliver greater savings. For example, our preliminary observations suggest the Free Lossless Audio Codec (FLAC) algorithm, commonly used for audio...
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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
...have been under artificial selection for purely aesthetic or other cultural reasons. These results provide insights into the adaptive introgression of coat color in Chinese indicine at the SV level.View larger version: In this window In a new window Figure 5. Candidate introgressed SV of Chinese...
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