A recently collected Xanthomonas translucens isolate encodes TAL effectors distinct from older, less virulent isolates

Xanthomonas translucens, the causal agent of bacterial leaf streak disease (BLS) in cereals, is a re-emerging pathogen that is becoming increasingly destructive across the world. While BLS has caused yield losses in the past, there is anecdotal evidence that newer isolates may be more virulent. We observed that two Xanthomonas translucens isolates collected from two sites in Colorado are more aggressive on current wheat and barley varieties compared to older isolates, and we hypothesize that genetic changes between recent and older isolates contribute to the differences in isolate aggressiveness. To test this, we phenotyped and genetically characterized two X. translucens isolates collected from Colorado in 2018, which we designated CO236 (from barley) and CO237 (from wheat). Using pathovar-specific phenotyping and PCR primers, we determined that CO236 belongs to pathovar translucens and CO237 belongs to pathovar undulosa. We sequenced the full genomes of the isolates using Oxford Nanopore long-read sequencing, and compared their whole genomes against published X. translucens genomes. This analysis confirmed our pathovar designations for Xtt CO236 and Xtu CO237, and showed that, at the whole-genome level, there were no obvious genomic structural changes between Xtt CO236 and Xtu CO237 and other respective published pathovar genomes. Focusing on pathovar undulosa (Xtu CO237), we then compared putative Type III effectors among all available Xtu isolate genomes and found that they were highly conserved. However, there were striking differences in the presence and sequence of various transcription activator-like effectors (TALE) between Xtu CO237 and published undulosa genomes, which correlate with isolate virulence. Here, we explore the potential implications of the differences in these virulence factors, and provide possible explanations for the increased virulence of recently-emerged isolates. Data SummaryA list of all Xanthomonas accessions used in this study can be found in Supplemental Table S1. Xtt CO236 and Xtu CO237 genomic sequences are deposited in GenBank (Accession: PRJNA1017868 and PRJNA1017870, respectively). Software packages for the custom Conda environment used in this analysis can be found in Supplemental Table S4. The dataset from the MinION reads from CO236 and CO237 can be found in Dryad, https://doi.org/10.5061/dryad.d51c5b06q. Custom bash and Python scripts for the effector analysis are available in (https://github.com/robertslabcsu/xanthanalysis.git). Impact statementXanthomonas translucens is a destructive, re-emerging pathogen of cereal crops with no known resistance or methods for chemical control. Recent isolates have increased virulence compared to older isolates, which emphasizes the need to understand how virulence evolves, and how the pathogen interacts with its host, to find new ways to manage the disease. Here, we identify potential virulence factors that contribute to the increased aggressiveness observed in two recently collected Colorado isolates, with potential impacts on understanding pathogen host range and evolution.