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Three complete genome sequences of novel Xanthomonas citri strains from Texas carry atypical PthA alleles and unusual large plasmids
Alejandra Munoz Bodnar: University of Florida; Vessela Mavrodieva: USDA-APHIS-PPQ-S&T-CPHST; Dean Gabriel: University of Florida; Zhaowei Liu: USDA APHIS PPQ; Mark Nakhla: USDA-APHIS-PPQ-S&T-CPHST; Gem Santillana: APHIS
<div>In 2015, backyard lime (<i>Citrus </i>spp.) trees in Texas showing typical citrus canker symptoms were confirmed positive for <i>Xanthomonas citri </i>subsp. <i>citri</i>. This confirmation triggered a regulatory response since the disease has been absent from the state since 1940s. The complete genomes of three strains from Texas were determined by PacBio Single Molecule, Real-Time (SMRT) sequencing. The genomes were 5,330,822 bp, 5,341,733 bp and 5,337,252 bp in size with an average read length of 15,756 bp, 15,261 bp and 16,590 bp, respectively. Bioinformatic analyses indicated that the new strains were related to the Florida A<sup>w</sup> strain. However, all three strains carried nearly identical and unusual large plasmids (123557bp, 123557bp, and 129139bp, respectively), that matched contigs in the NCBI Whole Genome Shotgun (WGS) database from some <i>X. citri subsp citri, X. fuscans</i> pv. fuscans and <i>X. axonopodis</i> pv. manihotis strains. These plasmids contain a region of ca. 39 kB similar to Type 4 conjugational transfer genes, indicating recent horizontal transfer into <i>X. citri</i>. All three Texas strains carried predicted functional <i>pthA</i> homologs with 18.5 tandem repeats each instead of the typical 17.5 repeats and a second homolog predicted to be nonfunctional. Atypically for citrus canker causing strains, two of the Texas strains carried both <i>pthA</i> homologs on the chromosome. Specific primers to distinguish the Texas strains from other canker-causing strains were designed and evaluated.</div>

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