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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
...alignments, profile hidden Markov models, and cross-references to G-quadruplex 3D structures. Examination of G-quadruplexes across functional genomic elements in different taxa indicates preferential orientation and positioning, with significant differences between individual taxonomic groups. For example...
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Method: Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC
- Byron J. Smith,
- Chunyu Zhao,
- Veronika Dubinkina,
- Xiaofan Jin,
- Liron Zahavi,
- Saar Shoer,
- Jacqueline Moltzau-Anderson,
- Eran Segal,
- and Katherine S. Pollard
Genome Res. May 2025 35: 1247-1260; Published in Advance April 10, 2025, doi:10.1101/gr.279543.124
...-pure gene content (StrainPGC), a computational method designed to accurately estimate the gene content of individual microbial strains. StrainPGC leverages modern strain tracking tools to separate samples into strain-pure subsets in order to combine data from pan profiling across multiple metas. We also...
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Resource: Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes
- Wenjuan Yu,
- Haohui Luo,
- Jinbao Yang,
- Shengchen Zhang,
- Heling Jiang,
- Xianjia Zhao,
- Xingqi Hui,
- Da Sun,
- Liang Li,
- Xiu-qing Wei,
- Stefano Lonardi,
- and Weihua Pan
Genome Res. February 2024 34: 326-340; Published in Advance March 1, 2024, doi:10.1101/gr.278232.123
..., Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; 2Fruit Research Institute, Fujian Academy of Agricultural Sciences...
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Research: Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets
- Matthew D. Pollard,
- Wynn K. Meyer,
- and Emily E. Puckett
Genome Res. December 2024 34: 2176-2189; Published in Advance November 22, 2024, doi:10.1101/gr.278930.124
...into lineage-specific dietary adaptations, studies that incorporate data encompassing a larger number of taxa can identify mechanisms shared across convergent changes in diet. To date, comparative genomic studies that sampled broadly within mammals have used coarse dietary classification systems...
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Research: Highly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversity
- Cory A. Weller,
- Ilya Andreev,
- Michael J. Chambers,
- Morgan Park,
- NISC Comparative Sequencing Program,
- Joshua S. Bloom,
- and Meru J. Sadhu
Genome Res. May 2023 33: 729-740; Published in Advance May 1, 2023, doi:10.1101/gr.277515.122
...for homology with reference genes using BLASTN. We removed highly repetitive ORFs, identified with TRF v. 4.09.1 (Benson 1999). Using custom R scripts (R. v. 4.1.2) (R Core Team 2023), ORFs were required to be >300 bp long, to begin with ATG, and to not overlap other genomic features (genes, transposable...
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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
...Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; 6McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA; 7Department of Life Sciences, Texas A&M University, Corpus Christi, Texas 78412, USA; 8Developmental Biochemistry, Biozentrum...
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Method: Accurate reconstruction of bacterial pan- and core genomes with PEPPAN
- Zhemin Zhou,
- Jane Charlesworth,
- and Mark Achtman
Genome Res. November 2020 30: 1667-1679; Published in Advance October 14, 2020, doi:10.1101/gr.260828.120
...cluster trees (Altenhoff et al. 2019). Branches with a paralogous score of greater than one are iteratively pruned until none remain. The remaining monophyletic subtrees are treated as putative orthologs.The genomic locations of multiple putative orthologs may overlap in some s owing to either...
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Research: Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize
- Baoxing Song,
- Edward S. Buckler,
- Hai Wang,
- Yaoyao Wu,
- Evan Rees,
- Elizabeth A. Kellogg,
- Daniel J. Gates,
- Merritt Khaipho-Burch,
- Peter J. Bradbury,
- Jeffrey Ross-Ibarra,
- Matthew B. Hufford,
- and M. Cinta Romay
Genome Res. July 2021 31: 1245-1257; Published in Advance May 27, 2021, doi:10.1101/gr.266528.120
...alignment pipeline to identify conserved noncoding sequences (CNSs) in the Andropogoneae tribe (multiple crop species descended from a common ancestor ∼18 million years ago). The Andropogoneae share similar physiology while being tremendously genomically diverse, harboring a broad range of ploidy levels...
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Resource: Using populations of human and microbial genomes for organism detection in metagenomes
- Sasha K. Ames,
- Shea N. Gardner,
- Jose Manuel Marti,
- Tom R. Slezak,
- Maya B. Gokhale,
- and Jonathan E. Allen
Genome Res. July 2015 25: 1056-1067; Published in Advance April 29, 2015, doi:10.1101/gr.184879.114
...Using populations of human and microbial genomes for organism detection in metagenomes Sasha K. Ames 1 , Shea N. Gardner 2 , Jose Manuel Marti 3 , Tom R. Slezak 2 , Maya B. Gokhale 1 and Jonathan E. Allen 2 1Center...
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Research: Evolutionary assembly patterns of prokaryotic genomes
- Maximilian O. Press,
- Christine Queitsch,
- and Elhanan Borenstein
Genome Res. June 2016 26: 826-833; Published in Advance April 14, 2016, doi:10.1101/gr.200097.115
...constraints.Finally, we demonstrate the predictability of genomic evolution by horizontal transfer from current genomic content. As stated above, this finding also suggests that such dependencies are fairly universal across the prokaryotic tree. Our approach was designed specifically to understand the PGCE...

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