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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
...symptoms across the wheat heads (Fig. 3G). Deoxynivalenol (DON), a critical virulence factor, is essential for fungal spread within a spike. Given the mutants’ restricted spread or complete loss of pathogenicity, we quantified DON production. Cultivation in trichothecene biosynthesis induction (TBI) medium...
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Research: Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States
- Greta Bellinzona,
- Tiago Nardi,
- Michele Castelli,
- Gherard Batisti Biffignandi,
- Karim Adjou,
- Martha Betson,
- Yannick Blanchard,
- Ioana Bujila,
- Rachel Chalmers,
- Rebecca Davidson,
- Nicoletta D'Avino,
- Tuulia Enbom,
- Jacinto Gomes,
- Gregory Karadjian,
- Christian Klotz,
- Emma Östlund,
- Judith Plutzer,
- Ruska Rimhanen-Finne,
- Guy Robinson,
- Anna Rosa Sannella,
- Jacek Sroka,
- Christen Rune Stensvold,
- Karin Troell,
- Paolo Vatta,
- Barbora Zalewska,
- Claudio Bandi,
- Davide Sassera,
- and Simone M. Cacciò
Genome Res. June 2024 34: 877-887; Published in Advance July 8, 2024, doi:10.1101/gr.278830.123
...(s) for the successful spread of population 3 remain elusive, although genes under selective pressure uniquely in this population were identified.The genus Cryptosporidium (phylum Apicomplexa) currently comprises at least 46 species and more than 120 genotypes of uncertain taxonomic status (Innes et al. 2020; Ryan et al...
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Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
- Marin Volarić,
- Evelin Despot-Slade,
- Damira Veseljak,
- Brankica Mravinac,
- and Nevenka Meštrović
Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
...Long-read assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events Marin Volarić1,2, Evelin Despot-Slade1,2, Damira Veseljak1, Brankica Mravinac1 and Nevenka Meštrović1 1Ruđer Bošković Institute, 10000 Zagreb, Croatia...
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Research: Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains
- Vivek Hari Sundar G,
- Chenna Swetha,
- Debjani Basu,
- Kannan Pachamuthu,
- Steffi Raju,
- Tania Chakraborty,
- Rebecca A. Mosher,
- and P.V. Shivaprasad
Genome Res. May 2023 33: 715-728; Published in Advance June 5, 2023, doi:10.1101/gr.277353.122
...loci, thus implicating the spread of this mark into both PCGs and non-PCGs in kd (Fig. 2D). Moreover, the activation mark H3K4me3 also showed differential enrichment and overabundance over the PCGs and non-PCGs in kd (Supplemental Fig. 10B,C). Because monocot s are relatively enriched with repeats...
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Research: Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans
- Christopher A. Desjardins,
- Charles Giamberardino,
- Sean M. Sykes,
- Chen-Hsin Yu,
- Jennifer L. Tenor,
- Yuan Chen,
- Timothy Yang,
- Alexander M. Jones,
- Sheng Sun,
- Miriam R. Haverkamp,
- Joseph Heitman,
- Anastasia P. Litvintseva,
- John R. Perfect,
- and Christina A. Cuomo
Genome Res. July 2017 27: 1207-1219; Published in Advance June 13, 2017, doi:10.1101/gr.218727.116
...of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; 5Mycotic Diseases Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30329, USA Cryptococcus neoformans is an opportunistic fungal pathogen...
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Research: Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting
- Steven Y.C. Tong,
- Matthew T.G. Holden,
- Emma K. Nickerson,
- Ben S. Cooper,
- Claudio U. Köser,
- Anne Cori,
- Thibaut Jombart,
- Simon Cauchemez,
- Christophe Fraser,
- Vanaporn Wuthiekanun,
- Janjira Thaipadungpanit,
- Maliwan Hongsuwan,
- Nicholas P. Day,
- Direk Limmathurotsakul,
- Julian Parkhill,
- and Sharon J. Peacock
Genome Res. January 2015 25: 111-118; Published in Advance December 9, 2014, doi:10.1101/gr.174730.114
...levels in a hospital where transmission was common.We repeatedly screened all patients on two intensive care units for MRSA carriage over a 3-mo period. All MRSA belonged to multilocus sequence type 239 (ST 239). We defined the population structure and charted the spread of MRSA by sequencing 79 isolates...
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Research: Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection
- Simon R. Harris,
- Carl Robinson,
- Karen F. Steward,
- Katy S. Webb,
- Romain Paillot,
- Julian Parkhill,
- Matthew T.G. Holden,
- and Andrew S. Waller
Genome Res. September 2015 25: 1360-1371; Published in Advance July 9, 2015, doi:10.1101/gr.189803.115
...diversity and mechanisms underlying the evolution of S. equi as a host-restricted pathogen remain poorly understood. Here, we define the global population structure of this important pathogen and reveal a population replacement in the late 19th or early 20th Century. Our data reveal a dynamic that continues...
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Research: A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia
- Sivaranjani Namasivayam,
- Rodrigo P. Baptista,
- Wenyuan Xiao,
- Erica M. Hall,
- Joseph S. Doggett,
- Karin Troell,
- and Jessica C. Kissinger
Genome Res. May 2021 31: 852-865; Published in Advance April 27, 2021, doi:10.1101/gr.266403.120
...A novel fragmented mitochondrial in the protist pathogen Toxoplasma gondii and related tissue coccidia Sivaranjani Namasivayam1,2, Rodrigo P. Baptista2,3, Wenyuan Xiao1,2, Erica M. Hall1, Joseph S. Doggett4,5, Karin Troell6 and Jessica C. Kissinger1,2,3 1Department of Genetics, University...
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Research: Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response
- Ariadna Picart-Picolo,
- Stefan Grob,
- Nathalie Picault,
- Michal Franek,
- Christel Llauro,
- Thierry Halter,
- Tom R. Maier,
- Edouard Jobet,
- Julie Descombin,
- Panpan Zhang,
- Vijayapalani Paramasivan,
- Thomas J. Baum,
- Lionel Navarro,
- Martina Dvořáčková,
- Marie Mirouze,
- and Frédéric Pontvianne
Genome Res. November 2020 30: 1583-1592; Published in Advance October 8, 2020, doi:10.1101/gr.261586.120
...on 3D organization, gene expression, and cytosine methylation. We found that duplicated genes often accumulate more transcripts. Among them, several are involved in plant–pathogen response, which could explain why the 20rDNA line is hyper-resistant to both bacterial and nematode infections. Finally, we...
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Method: Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid
- Steve Miller,
- Samia N. Naccache,
- Erik Samayoa,
- Kevin Messacar,
- Shaun Arevalo,
- Scot Federman,
- Doug Stryke,
- Elizabeth Pham,
- Becky Fung,
- William J. Bolosky,
- Danielle Ingebrigtsen,
- Walter Lorizio,
- Sandra M. Paff,
- John A. Leake,
- Rick Pesano,
- Roberta DeBiasi,
- Samuel Dominguez,
- and Charles Y. Chiu
Genome Res. May 2019 29: 831-842; Published in Advance April 16, 2019, doi:10.1101/gr.238170.118
...; 9Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, California 94143, USA ↵10 These authors contributed equally to this work. Corresponding author: charles.chiu@ucsf.eduAbstractMetagenomic next-generation sequencing (mNGS) for pan-pathogen...
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