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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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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...sequencing (De Roeck et al. 2019).Recent studies highlighted the need for LRS-specific algorithms for analysis of LRS data (DeJesus-Hernandez et al. 2021; Guo et al. 2021; Miller et al. 2021). While various combinations of base-caller algorithms and tandem-genotypes could provide estimates for the ABCA7 VNTR...
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Research: Interplay between coding and exonic splicing regulatory sequences
- Nicolas Fontrodona,
- Fabien Aubé,
- Jean-Baptiste Claude,
- Hélène Polvèche,
- Sébastien Lemaire,
- Léon-Charles Tranchevent,
- Laurent Modolo,
- Franck Mortreux,
- Cyril F. Bourgeois,
- and Didier Auboeuf
Genome Res. May 2019 29: 711-722; Published in Advance April 8, 2019, doi:10.1101/gr.241315.118
...equally to this work. ↵5 Present address: INSERM UMR 861, I-STEM, 91100 Corbeil-Essonnes, France Corresponding author: didier.auboeuf@inserm.frAbstractThe inclusion of exons during the splicing process depends on the binding of splicing factors to short low-complexity regulatory sequences...
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Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
- Rodrigo P. Baptista,
- Yiran Li,
- Adam Sateriale,
- Mandy J. Sanders,
- Karen L. Brooks,
- Alan Tracey,
- Brendan R.E. Ansell,
- Aaron R. Jex,
- Garrett W. Cooper,
- Ethan D. Smith,
- Rui Xiao,
- Jennifer E. Dumaine,
- Peter Georgeson,
- Bernard J. Pope,
- Matthew Berriman,
- Boris Striepen,
- James A. Cotton,
- and Jessica C. Kissinger
Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
...IA are mapped to the CpIA Chr 1 long-read assembly subtelomeric region to identify read pileups and estimates of sequence copy number by normalizing against the average genomics Illumina read depth. Vertical gray areas indicate regions with annotated genes. Annotated genes are represented below the shaded...
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Research: Direct estimate of the rate of germline mutation in a bird
- Linnéa Smeds,
- Anna Qvarnström,
- and Hans Ellegren
Genome Res. September 2016 26: 1211-1218; Published in Advance July 13, 2016, doi:10.1101/gr.204669.116
.... 1998]), in which phenotypic effects are recorded at the end of the experiment after line propagation. A shift in the way mutation rate could be estimated came about with DNA sequencing technology and by the appreciation that the rate of neutral sequence divergence is equal to the rate of mutation...
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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
...proportion of s of a given taxon to the total s detected) (Simon et al. 2019). Note that none of these tools aims to assemble the individual s prior to raising the relevant estimates. Rather, they put the reads of a meta into context with existing reference sequences and derive the corresponding conclusions...
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Method: Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II
- Paul J. Norman,
- Steven J. Norberg,
- Lisbeth A. Guethlein,
- Neda Nemat-Gorgani,
- Thomas Royce,
- Emily E. Wroblewski,
- Tamsen Dunn,
- Tobias Mann,
- Claudia Alicata,
- Jill A. Hollenbach,
- Weihua Chang,
- Melissa Shults Won,
- Kevin L. Gunderson,
- Laurent Abi-Rached,
- Mostafa Ronaghi,
- and Peter Parham
Genome Res. May 2017 27: 813-823; Published in Advance March 30, 2017, doi:10.1101/gr.213538.116
...assembly (Horton et al. 2004). The most significant of these is the haplotype from APD, which we have raised from an estimated completion of 45% to 98% (Fig. 3B). Consistent with expectations, the longest final sequence, of 5.2Mbp, was obtained from theDEU cell line, which has an HLA-DRB1∗04 (DR4...
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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
...with their estimated condition (i.e., mesic or arid). (3) We also added a commercially available mouse strain, as a reference. In all cases, whole kidneys were preserved in RNAlater and stored at −20°C.Kidney dissection, RNA extraction, and sequencingTo obtain representative expression levels, we removed fat tissue...
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Method: Genome-wide identification of conserved regulatory function in diverged sequences
- Leila Taher,
- David M. McGaughey,
- Samantha Maragh,
- Ivy Aneas,
- Seneca L. Bessling,
- Webb Miller,
- Marcelo A. Nobrega,
- Andrew S. McCallion,
- and Ivan Ovcharenko
Genome Res. July 2011 21: 1139-1149; Published in Advance May 31, 2011, doi:10.1101/gr.119016.110
...pairs with an estimated false-positive rate (FPR) of 5%. Putative human/ zebrafish orthologs were tested in transgenic zebrafish assays, confirming enhancer activity of 7/8 (88%) of the zebrafish sequences for which the human counterpart also showed enhancer activity. Furthermore, 5/7 (71...
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Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
...), and FISH results in this work reveal a comparable situation in T. freemani. Such abundance raises questions about what enables a sequence to become a centromere-dominant satellite and whether a sequence or a structure is more important. In T. freemani, the long-range organization of (peri)centromeric sat...

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