Unraveling the First<i>Xylella fastidiosa</i>Subsp.<i>Fastidiosa</i>Genome from Texas

Schreiber, Henry L.; Koirala, M.; Lara, Adolfo; Louzao, M. Carmen; Dowd, Scot E.; Bextine, Blake; Morano, Lisa

doi:10.3958/059.035.0336

Cited by 28 publications

(11 citation statements)

References 9 publications

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“…The genome sequences are now available for 26 Xanthomonadales including 15 for Xanthomonas species/strains [5], [6], [29]–[33], [55], [56], 5 for different strains/pathovars of Xylella fastidiosa [10], [34], [35], [57], 3 for Stenotrophomonas species/strains [12], 2 for Pseudoxanthomonas species [58] and for the Rhodanobacter sp. 2APBS1.…”

Section: Resultsmentioning

confidence: 99%

Phylogenomics and Molecular Signatures for Species from the Plant Pathogen-Containing Order Xanthomonadales

Naushad

Gupta

2013

PLoS ONE

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The species from the order Xanthomonadales, which harbors many important plant pathogens and some human pathogens, are currently distinguished primarily on the basis of their branching in the 16S rRNA tree. No molecular or biochemical characteristic is known that is specific for these bacteria. Phylogenetic and comparative analyses were conducted on 26 sequenced Xanthomonadales genomes to delineate their branching order and to identify molecular signatures consisting of conserved signature indels (CSIs) in protein sequences that are specific for these bacteria. In a phylogenetic tree based upon sequences for 28 proteins, Xanthomonadales species formed a strongly supported clade with Rhodanobacter sp. 2APBS1 as its deepest branch. Comparative analyses of protein sequences have identified 13 CSIs in widely distributed proteins such as GlnRS, TypA, MscL, LysRS, LipA, Tgt, LpxA, TolQ, ParE, PolA and TyrB that are unique to all species/strains from this order, but not found in any other bacteria. Fifteen additional CSIs in proteins (viz. CoxD, DnaE, PolA, SucA, AsnB, RecA, PyrG, LigA, MutS and TrmD) are uniquely shared by different Xanthomonadales except Rhodanobacter and in a few cases by Pseudoxanthomonas species, providing further support for the deep branching of these two genera. Five other CSIs are commonly shared by Xanthomonadales and 1–3 species from the orders Chromatiales, Methylococcales and Cardiobacteriales suggesting that these deep branching orders of Gammaproteobacteria might be specifically related. Lastly, 7 CSIs in ValRS, CarB, PyrE, GlyS, RnhB, MinD and X001065 are commonly shared by Xanthomonadales and a limited number of Beta- or Gamma-proteobacteria. Our analysis indicates that these CSIs have likely originated independently and they are not due to lateral gene transfers. The Xanthomonadales-specific CSIs reported here provide novel molecular markers for the identification of these important plant and human pathogens and also as potential targets for development of drugs/agents that specifically target these bacteria.

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Section: Resultsmentioning

confidence: 99%

Phylogenomics and Molecular Signatures for Species from the Plant Pathogen-Containing Order Xanthomonadales

Naushad

Gupta

2013

PLoS ONE

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“…Other X. fastidiosa plasmids have been described and fully characterized, such as 25 kbp plasmids isolated from mulberry strains from California (Stenger et al 2010) and a similar plasmid sequence detected in a grapevine strain from Texas (Schreiber IV et al 2010). All showed a mosaic nature between plasmids from X. fastidiosa and from the earthworm symbiont Verminephrobacter eiseniae, a Betaproteobacterium (Stenger et al 2010).…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity of Xylella fastidiosa Plasmids Assessed by Comparative Genomics

Pierry

Uceda-Campos

Feitosa-Junior

et al. 2020

Trop. plant pathol.

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Plasmids are a major source of horizontal gene transfer among bacteria contributing to their evolution and ecology. The known collection of plasmids carried by the plant pathogen Xylella fastidiosa increases as new strains from different origins and hosts are sampled and sequenced. Here we performed an extensive comparison of 61 publicly available sequences annotated as plasmids belonging to 38 X. fastidiosa strains isolated from different plant species and distinct geographical locations. Twenty-six strains exhibited at least one plasmid and up to four plasmids were found in a single strain. Plasmids sizes varied widely from 1.3 kbp to 64.3 kbp, ranging from 1 to 70 protein-coding sequences (CDS) encompassing 324 orthologs. Based on the presence of specific mobility proteins such as relaxases and type 4 secretion system-related genes, respectively 40 and 8 of the X. fastidiosa plasmids were classified as conjugative and mobilizable, while 13 were classified as non-mobilizable. X. fastidiosa plasmids did not carry known antibiotic resistance or virulence genes, and their stability seems to take advantage of toxin/antitoxin systems. The comparative analyses described here revealed similarity among plasmids of X. fastidiosa from different subspecies, geographical regions, and hosts, as well as with sequences found in plasmids from other bacterial species. Altogether, our results provide an in silico analysis of X. fastidiosa plasmid content and their main features, with applications in future studies of epidemiology, ecology, and evolution of this phytopathogen.

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“…All STs 10 were run with 5 reference sequences in order to determine relatedness of strains from the District with strains representative of pre-defined subspecies. The reference strains included in the analysis were; Temecula 1 [ 37 ], GB514 (PD) [ 38 ], and M23 [ 4 ] represented subsp. fastidiosa ; M12 [ 4 ] represented subsp.…”

Section: Methodsmentioning

confidence: 99%

Population Structure of the Bacterial Pathogen Xylella fastidiosa among Street Trees in Washington D.C.

Harris

Balcì

2015

PLoS ONE

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Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely established and problematic disease of landscape ornamentals in Washington D.C. A multi-locus sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa strains in order to better understand the epidemiology of leaf scorch disease in this municipal environment. Samples were collected from 7 different tree species located throughout the District of Columbia, consisting of 101 samples of symptomatic and asymptomatic foliage from 84 different trees. Five strains of the bacteria were identified. Consistent with prior data, these strains were host specific, with only one strain associated with members of the red oak family, one strain associated with American elm, one strain associated with American sycamore, and two strains associated with mulberry. Strains found for asymptomatic foliage were the same as strains from the symptomatic foliage on individual trees. Cross transmission of the strains was not observed at sites with multiple species of infected trees within an approx. 25 m radius of one another. X. fastidiosa strain specificity observed for each genus of tree suggests a highly specialized host-pathogen relationship.

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Unraveling the FirstXylella fastidiosaSubsp.FastidiosaGenome from Texas

Cited by 28 publications

References 9 publications

Phylogenomics and Molecular Signatures for Species from the Plant Pathogen-Containing Order Xanthomonadales

Phylogenomics and Molecular Signatures for Species from the Plant Pathogen-Containing Order Xanthomonadales

Genetic Diversity of Xylella fastidiosa Plasmids Assessed by Comparative Genomics

Population Structure of the Bacterial Pathogen Xylella fastidiosa among Street Trees in Washington D.C.

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