Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families

Authors: Murray P. Cox, Yanan Guo, David J. Winter, Diya Sen, Nicholas C. Cauldron, Jason Shiller, Ellie L. Bradley, Austen R. Ganley, Monica L. Gerth, Randy F. Lacey, Rebecca L. McDougal, Preeti Panda, Nari M. Williams, Niklaus J. Grunwald, Carl H. Mesarich, Rosie E. Bradshaw

Source: Frontiers in Microbiology, Vol 13 (2022)

Subject Terms: Phytophthora, oomycete, kauri dieback, forest disease, chromosome-level genome assembly, chromatin conformation capture, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2022.1038444/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/01390332fb02429695084cf6f33e539f

Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria

Authors: Edward W. Davis II, Alexandra J. Weisberg, Javier F. Tabima, Niklaus J. Grunwald, Jeff H. Chang

Source: PeerJ, Vol 4, p e2222 (2016)

Subject Terms: Taxonomy, Genomes, Molecular diagnostics, Multilocus sequence analysis, Average nucleotide identity, Agrobacterium, Medicine, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://peerj.com/articles/2222.pdf; https://peerj.com/articles/2222/; https://doaj.org/toc/2167-8359

Access URL: https://doaj.org/article/cc89770f2c904d20b35ca9a2f80df1d4

Phylogeography and population structure of the global, wide host-range hybrid pathogen Phytophthora × cambivora

Authors: Martin S. Mullett, Kris Van Poucke, Annelies Haegeman, Fran Focquet, Nicholas C. Cauldron, Brian J. Knaus, Marilia Horta Jung, Koji Kageyama, Ayaka Hieno, Hayato Masuja, Seiji Uematsu, Joan F. Webber, Clive M. Brasier, József Bakonyi, Kurt Heungens, Niklaus J. Grünwald, Thomas Jung

Source: IMA Fungus, Vol 14, Iss 1, Pp 1-18 (2023)

Subject Terms: Invasive pathogen, Hybridization, Polyploidy, Population genetics, Botany, QK1-989

File Description: electronic resource

Relation: https://doaj.org/toc/2210-6359

Access URL: https://doaj.org/article/251b0a79296a4f7f8f03b208e74035d1

Comparative Genomic Analysis of 31 Phytophthora Genomes Reveals Genome Plasticity and Horizontal Gene Transfer

Authors: Brent A. Kronmiller, Nicolas Feau, Danyu Shen, Javier F. Tabima, Shahin S. Ali, Andrew D. Armitage, Felipe Arredondo, Bryan A. Bailey, Stephanie R. Bollmann, Angela Dale, Richard J. Harrison, Kelly Hrywkiw, Takao Kasuga, Rebecca McDougal, Charlotte F. Nellist, Preeti Panda, Sucheta Tripathy, Nari M. Williams, Wenwu Ye, Yuanchao Wang, Richard C. Hamelin, Niklaus J. Grünwald

Source: Molecular Plant-Microbe Interactions, Vol 36, Iss 1, Pp 26-46 (2023)

Subject Terms: effectors, horizontal gene transfer, oomycete plant pathogens, Phytophthora, Microbiology, QR1-502, Botany, QK1-989

File Description: electronic resource

Relation: https://doaj.org/toc/0894-0282; https://doaj.org/toc/1943-7706

Access URL: https://doaj.org/article/060644a863b149059fa77e3dc237ec40

A New Oomycete Metabarcoding Method Using the rps10 Gene

Authors: Zachary S. L. Foster, Felipe E. Albornoz, Valerie J. Fieland, Meredith M. Larsen, F. Andrew Jones, Brett M. Tyler, Hai D. T. Nguyen, Treena I. Burgess, Carolyn Riddell, Hermann Voglmayr, Frank N. Martin, Niklaus J. Grünwald

Source: Phytobiomes Journal, Vol 6, Iss 3, Pp 214-226 (2022)

Subject Terms: amplicon metagenomics, detection, DNA, ecology, Illumina, ITS1, Plant culture, SB1-1110, Microbial ecology, QR100-130, Plant ecology, QK900-989

File Description: electronic resource

Relation: https://doaj.org/toc/2471-2906

Access URL: https://doaj.org/article/a6a5c53ccffa4f4699203184ded518bf

Genomic biosurveillance detects a sexual hybrid in the sudden oak death pathogen

Authors: Richard C. Hamelin, Guillaume J. Bilodeau, Renate Heinzelmann, Kelly Hrywkiw, Arnaud Capron, Erika Dort, Angela L. Dale, Emilie Giroux, Stacey Kus, Nick C. Carleson, Niklaus J. Grünwald, Nicolas Feau

Source: Communications Biology, Vol 5, Iss 1, Pp 1-8 (2022)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/2399-3642

Access URL: https://doaj.org/article/d8f308a73ba343dc827ba7ea333854bd

High-Quality, Phased Genomes of Phytophthora ramorum Clonal Lineages NA1 and EU1

Authors: Nicholas C. Carleson, Caroline M. Press, Niklaus J. Grünwald

Source: Molecular Plant-Microbe Interactions, Vol 35, Iss 4, Pp 360-363 (2022)

Subject Terms: oak, tanoak, sudden oak death, Microbiology, QR1-502, Botany, QK1-989

File Description: electronic resource

Relation: https://doaj.org/toc/0894-0282; https://doaj.org/toc/1943-7706

Access URL: https://doaj.org/article/c657f0bd9f934c95b68417c7cad5b23d

Growth, infection and aggressiveness of Phytophthora pathogens on Rhododendron leaves

Authors: Clare R. Taylor, Niklaus J. Grünwald

Source: CABI Agriculture and Bioscience, Vol 2, Iss 1, Pp 1-15 (2021)

Subject Terms: Ecology, Epidemiology, Fitness, Ornamentals, Oomycetes, Agriculture (General), S1-972

File Description: electronic resource

Relation: https://doaj.org/toc/2662-4044

Access URL: https://doaj.org/article/5bdffb304b6045d39d74df48a8f728a8

Entering the international year of fruits and vegetables: tradeoffs between food production and the environment

Authors: Niklaus J. Grünwald

Source: CABI Agriculture and Bioscience, Vol 2, Iss 1, Pp 1-3 (2021)

Subject Terms: Agriculture (General), S1-972

File Description: electronic resource

Relation: https://doaj.org/toc/2662-4044

Access URL: https://doaj.org/article/8b5f031cd4c1434d8f8d20f1ae0cd610

Launching CABI Agriculture and Bioscience: ensuring that today’s research meets tomorrow’s global challenges in agriculture and the environment

Authors: Niklaus J. Grünwald, Pablo A. Marquet, Andrew Robinson

Source: CABI Agriculture and Bioscience, Vol 1, Iss 1, Pp 1-3 (2020)

Subject Terms: Agriculture (General), S1-972

File Description: electronic resource

Relation: https://doaj.org/toc/2662-4044

Access URL: https://doaj.org/article/8460ba0fed2e43db85245b3b62a15c9e

effectR: An Expandable R Package to Predict Candidate RxLR and CRN Effectors in Oomycetes Using Motif Searches

Authors: Javier F. Tabima, Niklaus J. Grünwald

Source: Molecular Plant-Microbe Interactions, Vol 32, Iss 9, Pp 1067-1076 (2019)

Subject Terms: crinkler (CRN), effector, oomycete, plant-pathogen interactions, R package, RxLR, Microbiology, QR1-502, Botany, QK1-989

File Description: electronic resource

Relation: https://doaj.org/toc/0894-0282; https://doaj.org/toc/1943-7706

Access URL: https://doaj.org/article/ca5dc5ced97d44c09fb2af6f32be32f8

Genome-Wide Increased Copy Number is Associated with Emergence of Dominant Clones of the Irish Potato Famine Pathogen Phytophthora infestans

Authors: Brian J. Knaus, Javier F. Tabima, Shankar K. Shakya, Howard S. Judelson, Niklaus J. Grünwald

Source: mBio, Vol 11, Iss 3 (2020)

Subject Terms: Irish famine, Phytophthora, copy number variation, oomycetes, plant pathogen, plant pathology, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2150-7511

Access URL: https://doaj.org/article/f0506aa211534f23ba1c8a973d8b10fc

Stable predictive markers for Phytophthora sojae avirulence genes that impair infection of soybean uncovered by whole genome sequencing of 31 isolates

Authors: Geneviève Arsenault-Labrecque, Humira Sonah, Amandine Lebreton, Caroline Labbé, Geneviève Marchand, Allen Xue, François Belzile, Brian J. Knaus, Niklaus J. Grünwald, Richard R. Bélanger

Source: BMC Biology, Vol 16, Iss 1, Pp 1-16 (2018)

Subject Terms: Avr genes, Effectors, Genomics, Haplotype analysis, Oomycete, Phytophthora sojae, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12915-018-0549-9; https://doaj.org/toc/1741-7007

Access URL: https://doaj.org/article/c69052c34c4347e4a1f936de79c0c1df

Welcoming PhytoFrontiers™ into Our APS Family of Journals

Authors: Niklaus J. Grünwald, Steven J. Klosterman

Source: PhytoFrontiers, Vol 1, Iss 1, Pp 2-3 (2021)

Subject Terms: open access, broad scope, negative results, scientific rigor, Plant culture, SB1-1110, Botany, QK1-989

File Description: electronic resource

Relation: https://doaj.org/toc/2690-5442

Access URL: https://doaj.org/article/23f14ca0a34e432286a3855a2bfbac55

Survey and analysis of microsatellites from transcript sequences in Phytophthora species: frequency, distribution, and potential as markers for the genus.

Authors: Diana P Garnica, Andres M Pinzon, Lina M Quesada-Ocampo, Adriana J Bernal, Emiliano Barreto, Niklaus J Grunwald, Silvia Restrepo

Source: BMC Genomics; 2006, Vol. 7, p1-11, 11p, 6 Charts, 3 Graphs

Subject Terms: MICROSATELLITE repeats, NUCLEOTIDE sequence, PHYTOPHTHORA, BIOMARKERS, GENES, GENOMICS

Genomic Investigation of the Strawberry Pathogen Phytophthora fragariae Indicates Pathogenicity Is Associated With Transcriptional Variation in Three Key Races

Authors: Thomas M. Adams, Andrew D. Armitage, Maria K. Sobczyk, Helen J. Bates, Javier F. Tabima, Brent A. Kronmiller, Brett M. Tyler, Niklaus J. Grünwald, Jim M. Dunwell, Charlotte F. Nellist, Richard J. Harrison

Source: Frontiers in Microbiology, Vol 11 (2020)

Subject Terms: red core, oomycete, RNA-Seq, host–microbe interactions, nanopore sequencing, population resequencing, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fmicb.2020.00490/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/16486536e90043abb99bea0e25e8e69f

Whole Genome Sequences of the Raspberry and Strawberry Pathogens Phytophthora rubi and P. fragariae

Authors: Javier F. Tabima, Brent A. Kronmiller, Caroline M. Press, Brett M. Tyler, Inga A. Zasada, Niklaus J. Grünwald

Source: Molecular Plant-Microbe Interactions, Vol 30, Iss 10, Pp 767-769 (2017)

Subject Terms: genome, Phytophthora, raspberry, strawberry, Microbiology, QR1-502, Botany, QK1-989

File Description: electronic resource

Relation: https://doaj.org/toc/0894-0282; https://doaj.org/toc/1943-7706

Access URL: https://doaj.org/article/341bd43b86e44ae7adfebc67c4fe080d

Mitotic Recombination and Rapid Genome Evolution in the Invasive Forest Pathogen Phytophthora ramorum

Authors: Angela L. Dale, Nicolas Feau, Sydney E. Everhart, Braham Dhillon, Barbara Wong, Julie Sheppard, Guillaume J. Bilodeau, Avneet Brar, Javier F. Tabima, Danyu Shen, Clive M. Brasier, Brett M. Tyler, Niklaus J. Grünwald, Richard C. Hamelin

Source: mBio, Vol 10, Iss 2 (2019)

Subject Terms: forest health, genome evolution, oomycetes, sudden larch death, sudden oak death, tree pathogen, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2150-7511

Access URL: https://doaj.org/article/7ed7ecba6ade42a4a23f9b0a8a03f8c3

Expansion and Divergence of Argonaute Genes in the Oomycete Genus Phytophthora

Authors: Stephanie R. Bollmann, Caroline M. Press, Brett M. Tyler, Niklaus J. Grünwald

Source: Frontiers in Microbiology, Vol 9 (2018)

Subject Terms: Phytophthora, argonaute, Chromalveolate, evolution, small RNA, stramenopiles, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fmicb.2018.02841/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/508e704751fd4ea0b19d52cf4fead7fd

Taxa: An R package implementing data standards and methods for taxonomic data [version 2; referees: 2 approved, 2 approved with reservations]

Authors: Zachary S.L. Foster, Scott Chamberlain, Niklaus J. Grünwald

Source: F1000Research, Vol 7 (2018)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/7-272/v2; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/7e0ecd4c75e34000bcfefd20a9d3955d