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ARS Home » Southeast Area » Fort Pierce, Florida » U.S. Horticultural Research Laboratory » Subtropical Plant Pathology Research » Research » Publications at this Location » Publication #381688

Research Project: Mitigating High Consequence Domestic, Exotic, and Emerging Diseases of Fruits, Vegetables, and Ornamentals

Location: Subtropical Plant Pathology Research

Title: Draft Genome Sequence Resource for Two Xanthomonas fragariae Strains

Author
item HERBERT, AUSTIN - Clemson University
item WANG, HEHE - Clemson University
item SASKI, CHRIS - Clemson University
item Turechek, William

Submitted to: Microbiology Resource Announcements
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/24/2021
Publication Date: 4/22/2021
Citation: Herbert, A., Wang, H., Saski, C., Turechek, W. 2021. Draft Genome Sequence Resource for Two Xanthomonas fragariae Strains. Microbiology Resource Announcements. 10:e00138-21. https://doi.org/10.1128/MRA.00138-21.
DOI: https://doi.org/10.1128/MRA.00138-21

Interpretive Summary: Xanthomonas fragariae is the causal agent of angular leaf spot of strawberry. Short read sequences were generated for two X. fragariae strains with different virulence phenotypes on an Illumina Hiseq 2000 platform. The genome sequences will contribute to a better understanding of pathogen evolution and genes contributing to virulence in Xf.

Technical Abstract: Xanthomonas fragariae is the causal agent of angular leaf spot of strawberry. Short read sequences were generated for two X. fragariae strains with different virulence phenotypes (Xf100 and Xf1431) on an Illumina Hiseq 2000 platform and de novo genome assembly was performed with SOAP. Gene prediction and annotations were accomplished with PROKKA. Xf100 and Xf1431 are 99.8% similar in genome size, GC content, gene number, and protein sequences to the reference strain LMG-25863. Similar to with LMG-25863, Xf100 and Xf1431 lack several genes present in other Xanthomonas species that are critical for pathogen-host interactions, including the xcs genes in the type II secretion system, phenolics degradation I & II, glyoxylate shunt, and xylan degradation clusters I-III. All three strains share the same proteins in the type II-xps, III, IV, and VI secretion systems, except for the ClpB T6SS protein which is present in Xf100 and Xf1431 but highly fragmented in LMG-25863. Some genes in the TA system were different between strains; Xf1431 harbors two copies of RelB and RelE, while Xf100 and LMG-25863 only have one each; DinJ and YafO in Xf100 only shared 44% and 88% identity to the homologs in Xf1431 and LMG-25863. While only 148 variant sites were found between Xf100 and Xf1431, they shared a total of 749 variant sites from LMG-25863. Our two strains were grouped in a distinct clade from LMG-25863 on the phylogenomic tree, which supports the delineation of strains based on the previous multiple loci VNTR analysis. The genome sequences of Xf100 and Xf1431 will be important resources for future genomic analyses for a better understanding of pathogen evolution and genes responsible for virulence in X. fragariae.