Dataset Information

Draft Whole-Genome Sequences of Xylella fastidiosa subsp. fastidiosa Strains TPD3 and TPD4, Isolated from Grapevines in Hou-li, Taiwan.

ABSTRACT: We report the draft assemblies of TPD3 and TPD4, two Xylella fastidiosa subsp. fastidiosa isolates infecting grapevines in Hou-li, Taiwan. TPD3 and TPD4 showed similar characteristics regarding genome size (2,483,503?bp and 2,491,539?bp, respectively), GC content (51.49% and 51.47%, respectively), and number of protein-coding sequences (2,394 and 2,413, respectively).

SUBMITTER: Castillo AI

PROVIDER: S-EPMC6872878 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Draft Whole-Genome Sequences of Xylella fastidiosa subsp. fastidiosa Strains TPD3 and TPD4, Isolated from Grapevines in Hou-li, Taiwan.

Castillo Andreina I AI Tuan Shu-Jen SJ Retchless Adam C AC Hu Fei-Ting FT Chang Hsun-Yin HY Almeida Rodrigo P P RPP

Microbiology resource announcements 20191121 47

We report the draft assemblies of TPD3 and TPD4, two <i>Xylella fastidiosa</i> subsp. <i>fastidiosa</i> isolates infecting grapevines in Hou-li, Taiwan. TPD3 and TPD4 showed similar characteristics regarding genome size (2,483,503 bp and 2,491,539 bp, respectively), GC content (51.49% and 51.47%, respectively), and number of protein-coding sequences (2,394 and 2,413, respectively). ...[more]

PMID: 31753936

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Project description:BackgroundThe xylem-inhabiting bacterium Xylella fastidiosa (Xf) is the causal agent of Pierce's disease (PD) in vineyards and citrus variegated chlorosis (CVC) in orange trees. Both of these economically-devastating diseases are caused by distinct strains of this complex group of microorganisms, which has motivated researchers to conduct extensive genomic sequencing projects with Xf strains. This sequence information, along with other molecular tools, have been used to estimate the evolutionary history of the group and provide clues to understand the capacity of Xf to infect different hosts, causing a variety of symptoms. Nonetheless, although significant amounts of information have been generated from Xf strains, a large proportion of these efforts has concentrated on the study of North American strains, limiting our understanding about the genomic composition of South American strains - which is particularly important for CVC-associated strains.ResultsThis paper describes the first genome-wide comparison among South American Xf strains, involving 6 distinct citrus-associated bacteria. Comparative analyses performed through a microarray-based approach allowed identification and characterization of large mobile genetic elements that seem to be exclusive to South American strains. Moreover, a large-scale sequencing effort, based on Suppressive Subtraction Hybridization (SSH), identified 290 new ORFs, distributed in 135 Groups of Orthologous Elements, throughout the genomes of these bacteria.ConclusionResults from microarray-based comparisons provide further evidence concerning activity of horizontally transferred elements, reinforcing their importance as major mediators in the evolution of Xf. Moreover, the microarray-based genomic profiles showed similarity between Xf strains 9a5c and Fb7, which is unexpected, given the geographical and chronological differences associated with the isolation of these microorganisms. The newly identified ORFs, obtained by SSH, represent an approximately 10% increase in our current knowledge of the South American Xf gene pool and include new putative virulence factors, as well as novel potential markers for strain identification. Surprisingly, this list of novel elements include sequences previously believed to be unique to North American strains, pointing to the necessity of revising the list of specific markers that may be used for identification of distinct Xf strains.

Project description:Bacterial leaf scorch (BLS), caused by Xylella fastidiosa (Xf), is a prevalent disease of blueberries in the southeastern United States. Initially, this disease was reported to be caused by X. fastidiosa subsp. multiplex (Xfm). However, a recent survey revealed the presence of another subspecies, X. fastidiosa subsp. fastidiosa (Xff), within naturally infected blueberry plantings in Georgia. Since knowledge regarding the origins of isolates causing Xf outbreaks can impact management recommendations, a routine method for identifying the pathogen at the subspecies level can be beneficial. Several detection strategies are available to identify Xf infection at the subspecies level. However, none of these have been developed for the routine and rapid differentiation of the blueberry-infecting Xf subspecies. Here, we developed two separate straightforward and rapid detection techniques, a cleaved amplified polymorphic sequence (CAPS) marker, and a loop-mediated isothermal amplification (LAMP) assay, targeting the RNA polymerase sigma-70 factor (rpoD) gene sequence of Xfm to discriminate between the two Xf subspecies infecting blueberry. With the CAPS marker, specific detection of Xfm isolates was possible from pure cultures, inoculated greenhouse-grown plant samples, and field infected blueberry samples by restriction digestion of the rpoD gene PCR product (amplified with primers RST31 and RST33) using the BtsI enzyme. The LAMP assay allowed for specific real-time amplification of a 204-bp portion of the XfmrpoD gene from both pure bacterial cultures and infected plant material using the Genie® III system, a result further affirmed by gel electrophoresis and SYBR™ Green I DNA staining for visual observation. These detection strategies have the potential to greatly aid existing diagnostic methods for determining the distribution and prevalence of these Xf subspecies causing bacterial leaf scorch (BLS) in blueberries in the southeastern United States.

Dataset Information

Draft Whole-Genome Sequences of Xylella fastidiosa subsp. fastidiosa Strains TPD3 and TPD4, Isolated from Grapevines in Hou-li, Taiwan.

Publications

Draft Whole-Genome Sequences of Xylella fastidiosa subsp. fastidiosa Strains TPD3 and TPD4, Isolated from Grapevines in Hou-li, Taiwan.

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