Genomic Acquisitions in Emerging Populations ofXanthomonas vasicolapv.vasculorumInfecting Corn in the United States and Argentina

Abstract

Xanthomonas vasicola pv. vasculorum is an emerging bacterial plant pathogen that causes bacterial leaf streak on corn. First described in South Africa in 1949, reports of this pathogen have greatly increased in the past years in South America and in the United States. The rapid spread of this disease in North and South America may be due to more favorable environmental conditions, susceptible hosts and/or genomic changes that favored the spread. To understand whether genetic mechanisms exist behind the recent spread of X. vasicola pv. vasculorum, we used comparative genomics to identify gene acquisitions in X. vasicola pv. vasculorum genomes from the United States and Argentina. We sequenced 41 genomes of X. vasicola pv. vasculorum and the related sorghum-infecting X. vasicola pv. holcicola and performed comparative analyses against all available X. vasicola genomes. Time-measured phylogenetic analyses showed that X. vasicola pv. vasculorum strains from the United States and Argentina are closely related and arose from two introductions to North and South America. Gene content comparisons identified clusters of genes enriched in corn X. vasicola pv. vasculorum that showed evidence of horizontal transfer including one cluster corresponding to a prophage found in all X. vasicola pv. vasculorum strains from the United States and Argentina as well as in X. vasicola pv. holcicola strains. In this work, we explore the genomes of an emerging phytopathogen population as a first step toward identifying genetic changes associated with the emergence. The acquisitions identified may contain virulence determinants or other factors associated with the spread of X. vasicola pv. vasculorum in North and South America and will be the subject of future work.

SNP‐based genotyping and whole‐genome sequencing reveal previously unknown genetic diversity in Xanthomonas vasicola pv. musacearum, causal agent of banana xanthomonas wilt, in its presumed Ethiopian origin

“…Collectively, these findings further reinforce the hypothesis that Ethiopia is the centre of diversity of Xvm, and possibly its area of origin. Nevertheless, this pathovar remains apparently relatively monomorphic, with no more than a few hundred SNPs distinguishing any two isolates, significantly fewer than that observed in another pathovar of the same species (Aritua et al, 2007; Wasukira et al, 2014; Perez‐Quintero et al, 2020).…”

Bacterium-Enabled Transient Gene Activation by Artificial Transcription Factor for Resolving Gene Regulation in Maize

“…The Xvv strain Xv1601, a pathogen of maize, was used for delivery, and, based on previous sequence analysis, is free of TALe genes (Perez-Quintero et al, 2020). Phylogenetic analysis of 10 Xanthomonas species indicated that Xvv is genetically close to Xanthomonas oryzae (Xo) ( Supplemental Figure 1 ).…”

“…Here, we used TALe-mediated targeting activation of transcription as delivered by the maize pathogen Xanthomonas vasicola pv. vascularum (Xvv) (Perez-Quintero et al, 2020) to characterize the regulation of cuticular wax development. Cuticular waxes are derivatives of very-long-chain fatty acids (VLCFAs), which are produced through cyclic reactions that add two carbons per cycle (Kunst and Samuels, 2003; Lee and Suh, 2013).…”

Factorial estimating assembly base errors using k-mer abundance difference (KAD) between short reads and genome assembled sequences

“…We previously produced a genome assembly of an Xvv isolate Xvv1601 that was isolated from a Kansas corn adult leaf showing the symptoms characteristic of bacterial leaf streak in 2016 ( 33 ). PacBio long reads were used for the genome assembly with the assembler Canu ( 26 ).…”