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Whole Genome Sequence of Xylella fastidiosa ATCC 35879T and Detection of Genome Rearrangements Within Subsp. fastidiosa

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Abstract

Xylella fastidiosa is a Gram-negative and nutritionally fastidious bacterial pathogen causing Pierce’s disease (PD) of grapevine and other plant diseases. X. fastidiosa strain ATCC 35879T which originated from Florida is the designated type strain for the species and for subsp. fastidiosa. In bacterial taxonomy, type strains preserve the characters of the original descriptions. Whole genome sequence of a type strain not only provides a standard reference for bacterial taxonomy, but also facilitates research in other fields such as population diversity and genome evolution. In this study, the whole genome sequence of strain ATCC 35879T was determined using PacBio RSII format. The ATCC 35879T genome has a circular chromosome of 2,565,504 bp with 2,904 predicted protein coding genes and 55 RNA genes, and a circular plasmid of 41,753 bp. The chromosomal sequence of strain ATCC 35879T was compared to that of X. fastidosa subsp. fastidiosa strain M23 from California which causes both PD and almond leaf scorch disease. Genome rearrangements involving a ~ 1,200 K bp region were detected. Genome annotations showed clusters of phage-related genes around the rearrangement junctions, suggesting the likely involvement of phage activities. This is the first report on genome structure variations within strains of X. fastidiosa subsp. fastidiosa.

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Acknowledgements

This research used resources provided by the SCINet project of the USDA-ARS Project Number 0500–00093-001–00-D. We thank G. Phillips, and Y. Andrade for technical assistance. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture (USDA). USDA is an equal opportunity employer.

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Authors and Affiliations

  1. Agricultural Research Service, United States Department of Agriculture, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, USA

    J. Chen, M. O’Leary & L. Burbank

  2. Department of Plant Pathology, South China Agricultural University, Guangzhou, People’s Republic of China

    Z. Zheng & X. Deng

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  1. J. Chen
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  2. M. O’Leary
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  3. L. Burbank
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Correspondence to J. Chen.

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Chen, J., O’Leary, M., Burbank, L. et al. Whole Genome Sequence of Xylella fastidiosa ATCC 35879T and Detection of Genome Rearrangements Within Subsp. fastidiosa. Curr Microbiol 77, 1858–1863 (2020). https://doi.org/10.1007/s00284-020-01937-0

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  • DOI: https://doi.org/10.1007/s00284-020-01937-0

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