An Introduced Crop Plant Is Driving Diversification of the Virulent Bacterial Pathogen Erwinia tracheiphila

Coexistence of Multiple Endemic and Pandemic Lineages of the Rice Blast Pathogen

(2018) Pierre Gladieux et al.   mBio

Crop-associated virus infection in a native perennial grass: reduction in plant fitness and dynamic patterns of virus detection

(2017) Helen M. Alexander et al.   JOURNAL OF ECOLOGY

Karyotype Stability and Unbiased Fractionation in the Paleo-Allotetraploid Cucurbita Genomes

(2017) Honghe Sun et al.   Molecular Plant

Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management

(2017) Elizabeth A Savory et al.   eLife

Horizontal Gene Acquisitions, Mobile Element Proliferation, and Genome Decay in the Host-Restricted Plant PathogenErwinia Tracheiphila

(2016) Lori R. Shapiro et al.   Genome Biology and Evolution

The first phase of PREDICT: Surveillance for emerging infectious zoonotic diseases of wildlife origin (2009-2014)

(2016) D. Joly et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Rapid emergence of pathogens in agro-ecosystems: global threats to agricultural sustainability and food security

(2016) Bruce A. McDonald et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Differential Colonization Dynamics of Cucurbit Hosts by Erwinia tracheiphila

(2016) Cláudio M. Vrisman et al.   PHYTOPATHOLOGY

Integrative Analyses of Nontargeted Volatile Profiling and Transcriptome Data Provide Molecular Insight into VOC Diversity in Cucumber Plants ( Cucumis sativus )

(2016) Guo Wei et al.   PLANT PHYSIOLOGY

Pseudomonas syringaetype III effector HopAF1 suppresses plant immunity by targeting methionine recycling to block ethylene induction

(2016) Erica J. Washington et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origins of food crops connect countries worldwide

(2016) Colin K. Khoury et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Crop domestication facilitated rapid geographical expansion of a specialist pollinator, the squash beePeponapis pruinosa

(2016) Margarita M. López-Uribe et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A global map of genetic diversity in Babesia microti reveals strong population structure and identifies variants associated with clinical relapse

(2016) Jacob E. Lemieux et al.   Nature Microbiology

Crop domestication, global human-mediated migration, and the unresolved role of geography in pest control

(2016) Yolanda H. Chen   Elementa-Science of the Anthropocene

micropan: an R-package for microbial pan-genomics

(2015) Lars Snipen et al.   BMC BIOINFORMATICS

Insights from 20 years of bacterial genome sequencing

(2015) Miriam Land et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Bacterial Wilt of Cucurbits: Resurrecting a Classic Pathosystem

(2015) Erika Saalau Rojas et al.   PLANT DISEASE

Gourds and squashes (Cucurbitaspp.) adapted to megafaunal extinction and ecological anachronism through domestication

(2015) Logan Kistler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The biogeography of viral emergence: rice yellow mottle virus as a case study

(2015) Agnès Pinel-Galzi et al.   Current Opinion in Virology

Ecosystem simplification, biodiversity loss and plant virus emergence

(2015) Marilyn J Roossinck et al.   Current Opinion in Virology

Harnessing Population Genomics to Understand How Bacterial Pathogens Emerge, Adapt to Crop Hosts, and Disseminate

(2014) Boris A. Vinatzer et al.   Annual Review of Phytopathology

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Prochlorococcus: the structure and function of collective diversity

(2014) Steven J. Biller et al.   NATURE REVIEWS MICROBIOLOGY

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

Dynamics of short- and long-term association between a bacterial plant pathogen and its arthropod vector

(2014) L. R. Shapiro et al.   Scientific Reports

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Insect resistance to Bt crops: lessons from the first billion acres

(2013) Bruce E Tabashnik et al.   NATURE BIOTECHNOLOGY

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Genetic and Virulence Variability AmongErwinia tracheiphilaStrains Recovered from Different Cucurbit Hosts

(2013) E. Saalau Rojas et al.   PHYTOPATHOLOGY

Disease Interactions in a Shared Host Plant: Effects of Pre-Existing Viral Infection on Cucurbit Plant Defense Responses and Resistance to Bacterial Wilt Disease

(2013) Lori R. Shapiro et al.   PLoS One

Tempo and mode of evolutionary radiation in Diabroticina beetles (genera Acalymma, Cerotoma, and Diabrotica)

(2013) Astrid Eben et al.   ZooKeys

Correction: Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Provides Insight into the Origins of an Emergent Plant Disease

(2013) Honour C. McCann et al.   PLoS Pathogens

Pathogen effects on vegetative and floral odours mediate vector attraction and host exposure in a complex pathosystem

(2012) Lori Shapiro et al.   ECOLOGY LETTERS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Emergence and global spread of epidemic healthcare-associated Clostridium difficile

(2012) Miao He et al.   NATURE GENETICS

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs

(2012) Martin T Swain et al.   Nature Protocols

Genetic Diversity and Population Structure of Cucumber (Cucumis sativus L.)

(2012) Jing Lv et al.   PLoS One

A Population Genomics Perspective on the Emergence and Adaptation of New Plant Pathogens in Agro-Ecosystems

(2012) Eva H. Stukenbrock et al.   PLoS Pathogens

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Pseudomonas syringae pv. phaseolicola effector HopF1 inhibits pathogen-associated molecular pattern-triggered immunity in a RIN4-independent manner in common bean (Phaseolus vulgaris)

(2011) Shuguo Hou et al.   FEMS MICROBIOLOGY LETTERS

HopX1 in Erwinia amylovora Functions as an Avirulence Protein in Apple and Is Regulated by HrpL

(2011) A. M. Bocsanczy et al.   JOURNAL OF BACTERIOLOGY

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

First Report of Bacterial Wilt Caused by Erwinia tracheiphila on Pumpkin and Watermelon in New Mexico

(2011) S. Sanogo et al.   PLANT DISEASE

Field-Evolved Resistance to Bt Maize by Western Corn Rootworm

(2011) Aaron J. Gassmann et al.   PLoS One

The Plant Pathogen Pseudomonas syringae pv. tomato Is Genetically Monomorphic and under Strong Selection to Evade Tomato Immunity

(2011) Rongman Cai et al.   PLoS Pathogens

Citrobacter rodentium is an Unstable Pathogen Showing Evidence of Significant Genomic Flux

(2011) Nicola K. Petty et al.   PLoS Pathogens

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Floral Transmission ofErwinia tracheiphilaby Cucumber Beetles in a WildCucurbita pepo

(2010) M. A. Sasu et al.   ENVIRONMENTAL ENTOMOLOGY

Cucumber (Cucumis sativus) and melon (C. melo) have numerous wild relatives in Asia and Australia, and the sister species of melon is from Australia

(2010) P. Sebastian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Spread of Tomato Yellow Leaf Curl Virus from the Middle East to the World

(2010) Pierre Lefeuvre et al.   PLoS Pathogens

Salicylic Acid, a Multifaceted Hormone to Combat Disease

(2009) A. Corina Vlot et al.   Annual Review of Phytopathology

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Indirect costs of a nontarget pathogen mitigate the direct benefits of a virus-resistant transgene in wildCucurbita

(2009) Miruna A. Sasu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution, Population Structure, and Phylogeography of Genetically Monomorphic Bacterial Pathogens

(2008) Mark Achtman   Annual Review of Microbiology

ThePseudomonas syringaeType III Effector HopAM1 Enhances Virulence on Water-Stressed Plants

(2008) Ajay K. Goel et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Global trends in emerging infectious diseases

(2008) Kate E. Jones et al.   NATURE

Molecular phylogeny of rootworms and related galerucine beetles (Coleoptera: Chrysomelidae)

(2008) Joseph J. Gillespie et al.   ZOOLOGICA SCRIPTA