Species Boundaries and Molecular Markers for the Classification of 16SrI Phytoplasmas Inferred by Genome Analysis

SignalP 5.0 improves signal peptide predictions using deep neural networks

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Genomic diversity and recombination among Xylella fastidiosa subspecies

(2019) Mathieu Vanhove et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Patterns of inter- and intrasubspecific homologous recombination inform eco-evolutionary dynamics of Xylella fastidiosa

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Genomic Characterization of the Periwinkle Leaf Yellowing (PLY) Phytoplasmas in Taiwan

(2019) Shu-Ting Cho et al.   Frontiers in Microbiology

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Updating the 97% identity threshold for 16S ribosomal RNA OTUs

(2018) Robert C Edgar   BIOINFORMATICS

A multi-layered mechanistic modelling approach to understand how effector genes extend beyond phytoplasma to modulate plant hosts, insect vectors and the environment

(2018) Melissa Tomkins et al.   CURRENT OPINION IN PLANT BIOLOGY

Draft genome sequence of the New Jersey aster yellows strain of ‘Candidatus Phytoplasma asteris’

(2018) Michael E. Sparks et al.   PLoS One

Comparative genome analysis of jujube witches’-broom Phytoplasma, an obligate pathogen that causes jujube witches’-broom disease

(2018) Jie Wang et al.   BMC GENOMICS

Convergent Evolution among Ruminant-Pathogenic Mycoplasma Involved Extensive Gene Content Changes

(2018) Wen-Sui Lo et al.   Genome Biology and Evolution

Alterations of plant architecture and phase transition by the phytoplasma virulence factor SAP11

(2018) Shu Heng Chang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Phytoplasma effector SWP1 induces witches’ broom symptom by destabilizing the TCP transcription factor BRANCHED1

(2018) Nan Wang et al.   MOLECULAR PLANT PATHOLOGY

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

The genome of ‘Candidatus Phytoplasma solani’ strain SA-1 is highly dynamic and prone to adopting foreign sequences

(2018) Martina Seruga Music et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Biological Species Are Universal across Life’s Domains

(2017) Louis-Marie Bobay et al.   Genome Biology and Evolution

Uncultivated microbes in need of their own taxonomy

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GenBank

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Identification of wheat blue dwarf phytoplasma effectors targeting plant proliferation and defence responses

(2017) N. Wang et al.   PLANT PATHOLOGY

Criteria for phytoplasma 16Sr group/subgroup delineation and the need of a platform for proper registration of new groups and subgroups

(2016) Yan Zhao et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A Bacterial Parasite Effector Mediates Insect Vector Attraction in Host Plants Independently of Developmental Changes

(2016) Zigmunds Orlovskis et al.   Frontiers in Plant Science

Decreasing Global Transcript Levels over Time Suggest that Phytoplasma Cells Enter Stationary Phase during Plant and Insect Colonization

(2015) D. Pacifico et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Multilocus sequence analysis (MLSA) in prokaryotic taxonomy

(2015) Stefanie P. Glaeser et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Molecular Diagnostic Tools for Detection and Differentiation of Phytoplasmas Based on Chaperonin-60 Reveal Differences in Host Plant Infection Patterns

(2015) Tim J. Dumonceaux et al.   PLoS One

Recognition of floral homeotic MADS domain transcription factors by a phytoplasmal effector, phyllogen, induces phyllody

(2014) Kensaku Maejima et al.   PLANT JOURNAL

Transgenic Plants That Express the Phytoplasma Effector SAP11 Show Altered Phosphate Starvation and Defense Responses

(2014) Y.-T. Lu et al.   PLANT PHYSIOLOGY

Comparative Genome Analysis of Wheat Blue Dwarf Phytoplasma, an Obligate Pathogen That Causes Wheat Blue Dwarf Disease in China

(2014) Wang Chen et al.   PLoS One

The phytoplasmal virulence factor TENGU causes plant sterility by downregulating of the jasmonic acid and auxin pathways

(2014) Nami Minato et al.   Scientific Reports

Comparative genome analysis of Spiroplasma melliferum IPMB4A, a honeybee-associated bacterium

(2013) Wen-Sui Lo et al.   BMC GENOMICS

A Multiplex-PCR Method for Strain Identification and Detailed Phylogenetic Analysis of AY-Group Phytoplasmas

(2013) Shigeyuki Kakizawa et al.   PLANT DISEASE

The Alteration of Plant Morphology by Small Peptides Released from the Proteolytic Processing of the Bacterial Peptide TENGU

(2013) K. Sugawara et al.   PLANT PHYSIOLOGY

Comparative Analysis of the Peanut Witches'-Broom Phytoplasma Genome Reveals Horizontal Transfer of Potential Mobile Units and Effectors

(2013) Wan-Chia Chung et al.   PLoS One

Genome wide sequence analysis grants unbiased definition of species boundaries in “Candidatus Phytoplasma”

(2013) Giuseppe Firrao et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R

(2012) Andrei-Alin Popescu et al.   BIOINFORMATICS

Comparative Analysis of Gene Content Evolution in Phytoplasmas and Mycoplasmas

(2012) Ling-Ling Chen et al.   PLoS One

The groEL gene as an additional marker for finer differentiation of ‘Candidatus Phytoplasma asteris'-related strains

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Diverse Targets of Phytoplasma Effectors: From Plant Development to Defense Against Insects

(2011) Akiko Sugio et al.   Annual Review of Phytopathology

Phytoplasma Effector SAP54 Induces Indeterminate Leaf-Like Flower Development in Arabidopsis Plants

(2011) A. M. MacLean et al.   PLANT PHYSIOLOGY

Phytoplasma protein effector SAP11 enhances insect vector reproduction by manipulating plant development and defense hormone biosynthesis

(2011) A. Sugio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

genoPlotR: comparative gene and genome visualization in R

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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

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

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

The consequences of genetic drift for bacterial genome complexity

(2009) C.-H. Kuo et al.   GENOME RESEARCH

Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII)

(2009) Y. Zhao et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A unique virulence factor for proliferation and dwarfism in plants identified from a phytopathogenic bacterium

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

The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali'

(2008) Michael Kube et al.   BMC GENOMICS

Automated RFLP pattern comparison and similarity coefficient calculation for rapid delineation of new and distinct phytoplasma 16Sr subgroup lineages

(2008) W. Wei et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Comparative Genome Analysis of "Candidatus Phytoplasma australiense" (Subgroup tuf-Australia I; rp-A) and "Ca. Phytoplasma asteris" Strains OY-M and AY-WB

(2008) L. T. T. Tran-Nguyen et al.   JOURNAL OF BACTERIOLOGY

Phytoplasmas: bacteria that manipulate plants and insects

(2008) SASKIA A. HOGENHOUT et al.   MOLECULAR PLANT PATHOLOGY

AY-WB Phytoplasma Secretes a Protein That Targets Plant Cell Nuclei

(2008) Xiaodong Bai et al.   MOLECULAR PLANT-MICROBE INTERACTIONS