Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

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ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

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Pacbio sequencing of copper-tolerant Xanthomonas citri reveals presence of a chimeric plasmid structure and provides insights into reassortment and shuffling of transcription activator-like effectors among X. citri strains

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Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Genomics of the origin and evolution of Citrus

(2018) Guohong Albert Wu et al.   NATURE

A Xanthomonas citri subsp citri hypothetical protein related to virulence contains a non-functional HD domain and is implicated in flagellar motility

(2017) F.C.F. Vieira et al.   GENETICS AND MOLECULAR RESEARCH

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

First Report of Copper-resistant Xanthomonas citri pv. citri Pathotype A Causing Asiatic Citrus Canker in Réunion, France

(2017) D. Richard et al.   PLANT DISEASE

Phylogenetic rooting using minimal ancestor deviation

(2017) Fernando Domingues Kümmel Tria et al.   Nature Ecology & Evolution

The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography

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(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Examining the sensitivity of molecular species delimitations to the choice of mitochondrial marker

(2016) Andrew M. Ritchie et al.   ORGANISMS DIVERSITY & EVOLUTION

Whole-Genome Sequences of Xanthomonas euvesicatoria Strains Clarify Taxonomy and Reveal a Stepwise Erosion of Type 3 Effectors

(2016) Jeri D. Barak et al.   Frontiers in Plant Science

Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges

(2015) Jonathan L. Gordon et al.   BMC GENOMICS

Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts

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Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer

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Positive selection is the main driving force for evolution of citrus canker-causing Xanthomonas

(2015) Yunzeng Zhang et al.   ISME Journal

A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the GenusCitrus

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RASP (Reconstruct Ancestral State in Phylogenies): A tool for historical biogeography

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A Novel Periplasmic Protein, VrpA, Contributes to Efficient Protein Secretion by the Type III Secretion System inXanthomonasspp.

(2015) Xiaofeng Zhou et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

A MLVA Genotyping Scheme for Global Surveillance of the Citrus Pathogen Xanthomonas citri pv. citri Suggests a Worldwide Geographical Expansion of a Single Genetic Lineage

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GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

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Evolutionary History of the Plant Pathogenic Bacterium Xanthomonas axonopodis

(2013) Nadia Mhedbi-Hajri et al.   PLoS One

The gpsX gene encoding a glycosyltransferase is important for polysaccharide production and required for full virulence in Xanthomonas citri subsp. citri

(2012) Jinyun Li et al.   BMC MICROBIOLOGY

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

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Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Short-distance dispersal of splashed bacteria of Xanthomonas citri subsp. citri from canker-infected grapefruit tree canopies in turbulent wind

(2012) C. H. Bock et al.   PLANT PATHOLOGY

High-Throughput Screening and Analysis of Genes ofXanthomonas citrisubsp.citriInvolved in Citrus Canker Symptom Development

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Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

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Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

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FASconCAT: Convenient handling of data matrices

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progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

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Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection

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Effects of Substitution Models on Divergence Time Estimates: Simulations and an Empirical Study of Model Uncertainty Using Cornales

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Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria

(2009) Chih-Horng Kuo et al.   Biology Direct

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

New genes of Xanthomonas citri subsp. citri involved in pathogenesis and adaptation revealed by a transposon-based mutant library

(2009) Marcelo L Laia et al.   BMC MICROBIOLOGY

Amplified fragment length polymorphism and multilocus sequence analysis-based genotypic relatedness among pathogenic variants of Xanthomonas citri pv. citri and Xanthomonas campestris pv. bilvae

(2009) L. Bui Thi Ngoc et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Phylogenetic structure of Xanthomonas determined by comparison of gyrB sequences

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Identification ofXanthomonas citrissp.citrihost specificity genes in a heterologous expression host

(2009) MYRIAN RYBAK et al.   MOLECULAR PLANT PATHOLOGY

First Report of Xanthomonas citri pv. citri-A* Causing Citrus Canker on Lime in Ethiopia

(2009) E. Derso et al.   PLANT DISEASE

The Last Glacial Maximum

(2009) P. U. Clark et al.   SCIENCE

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

A comparison of homologous recombination rates in bacteria and archaea

(2008) Michiel Vos et al.   ISME Journal

Identification of Novel Type III Secretion Effectors inXanthomonas oryzaepv.oryzae

(2008) Ayako Furutani et al.   MOLECULAR PLANT-MICROBE INTERACTIONS