Comparative Genomic Analysis and Rapid Molecular Detection of Xanthomonas euvesicatoria Using Unique ATP-Dependent DNA Helicase recQ, hrpB1, and hrpB2 Genes Isolated from Physalis pubescens in China

Abstract

Ground cherry (<i>Physalis pubescens</i>) is the most prominent species in the <i>Solanaceae</i> family due to its nutritional content, and prospective health advantages. It is grown all over the world, but notably in northern China. In 2019 firstly bacterial leaf spot (BLS) disease was identified on <i>P. pubescens</i> in China that caused by both BLS pathogens <i>Xanthomonas euvesicatoria</i> pv. <i>euvesicatoria</i> resulted in substantial monetary losses. Here, we compared whole genome sequences of <i>X. euvesicatoria</i> to other <i>Xanthomonas</i> species that caused BLS diseases for high similarities and dissimilarities in genomic sequences through average nucleotide identity (ANI) and BLAST comparison. Molecular techniques and phylogenetic trees were adopted to detect <i>X. euvesicatoria</i> on <i>P. pubescens</i> using <i>recQ</i>, <i>hrpB1</i>, and <i>hrpB2</i> genes for efficient and precise identification. For rapid molecular detection of <i>X. euvesicatoria</i>, loop-mediated isothermal amplification, polymerase chain reaction (PCR), and real-time PCR techniques were used. Whole genome comparison results showed that the genome of <i>X. euvesicatoria</i> was more closely relative to <i>X. perforans</i> than <i>X. vesicatoria</i>, and <i>X. gardneri</i> with 98%, 84%, and 86% ANI, respectively. All infected leaves of <i>P. pubescens</i> found positive amplification, and negative controls did not show amplification. The findings of evolutionary history revealed that isolated strains XeC10RQ, XeH9RQ, XeA10RQ, and XeB10RQ that originated from China were closely relative and highly homologous to the <i>X. euvesicatoria</i>. This research provides information to researchers on genomic variation in BLS pathogens, and further molecular evolution and identification of <i>X. euvesicatoria</i> using the unique target <i>recQ</i> gene through advance molecular approaches.