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Research: Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
- Peter O. Mulhair,
- Liam Crowley,
- Douglas H. Boyes,
- Amber Harper,
- Owen T. Lewis,
- Darwin Tree of Life Consortium,
- and Peter W.H. Holland
Genome Res. January 2023 33: 32-44; Published in Advance December 8, 2022, doi:10.1101/gr.277118.122
....5281/zenodo.7274111). To place our analyses in an evolutionary context, we also constructed a phylogenetic tree of the species analyzed using 2262 BUSCO genes (see Methods; Fig. 1A; Supplemental Fig. S1). Homeobox sequences were then classified using the characteristic homeodomain and a combination...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...and Rademakers 2023). In this context, SAMtools can be used to calculate alignment metrics such as the percentage of mapped reads, the presence of split-read alignments, or high numbers of soft-clipped bases. For a typical human realignment, one might expect >90% of reads to align successfully, with only a small...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...to formulate hypotheses about what regulates your GOI, it is indispensable for validating potential regulators in a physiologically relevant context of the cell or organism. Specifically, fluorescence microscopy has emerged as a leading technique for studying gene regulation owing to its unique capabilities...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...-C alignments (MAPQ ≥ 20), which were analyzed using scripts from GitHub (https://github.com/RunpengLuo/HiC-Analysis) to quantify cis- and trans-chromosome contacts.TE and gene annotationsTE and gene annotations were performed for each haplotype separately. We predicted and annotated TEs using the REPET...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...on the array (Dover et al. 1993; Elder and Turner 1995; Lower et al. 2018). Untangling patterns of concerted evolution on tandem arrays experiencing different forces requires a comprehensive map of genetic variation spanning such clusters.The cluster of highly conserved histone genes on Chromosome arm 2L...
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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
...constitute a principal driver of evolution, shaping its architecture and regulatory networks. In this context, Tuberaceae can become an important model system to study their genomic impact; however, the family lacks high-quality assemblies. Here, we investigate the interplay between TEs and Tuberaceae...
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Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
- Yang Liu,
- João Botelho,
- and Jaime Iranzo
Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
...opposite scenarios by quantifying the association between defense systems, MGE abundance, and gene acquisition rates in a phylogeny-aware comparative study of 197 prokaryotic species.Our results shed light on previous, apparently contradictory findings concerning the effect of CRISPR-Cas on evolution...
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Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
- Dmitry Antipov,
- Mikko Rautiainen,
- Sergey Nurk,
- Brian P. Walenz,
- Steven J. Solar,
- Adam M. Phillippy,
- and Sergey Koren
Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
...for heterogametic samples, missing genes were also counted for the autosomal sequences as identified by MashMap3 alignment to the existing reference s (CHM13 for human [Nurk et al. 2022], GCA_024206055.1 [Huang et al. 2023] for chicken, and GCF_016772045.2 [Davenport et al. 2022] for sheep).View this table...
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Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
- Charles Plessy,
- Michael J. Mansfield,
- Aleksandra Bliznina,
- Aki Masunaga,
- Charlotte West,
- Yongkai Tan,
- Andrew W. Liu,
- Jan Grašič,
- María Sara del Río Pisula,
- Gaspar Sánchez-Serna,
- Marc Fabrega-Torrus,
- Alfonso Ferrández-Roldán,
- Vittoria Roncalli,
- Pavla Navratilova,
- Eric M. Thompson,
- Takeshi Onuma,
- Hiroki Nishida,
- Cristian Cañestro,
- and Nicholas M. Luscombe
Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
...that operon-switching can occur. As such, an operon system such as exists in O. dioica might in fact help to maintain gene expression in the context of scrambling. Although operons may facilitate scrambling, they may not directly cause scrambling; operons are found in the short-lived nematode Caenorhabditis...
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Method: Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics
- Etienne Routhier,
- Edgard Pierre,
- Ghazaleh Khodabandelou,
- and Julien Mozziconacci
Genome Res. February 2021 31: 317-326; Published in Advance December 18, 2020, doi:10.1101/gr.264416.120
...) and predicted (blue) nucleosome densities in a region of Chromosome 16. Genes are shown in blue on top of the two tracks (data from Hughes et al. 2012). (B) Density plot of the predicted nucleosome density in function of the experimental nucleosome density. The correlation between the two signals is 0...

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