AUTHOR=Jonca Joanna , Pirhonen Minna , Waleron Michal Mateusz , Gawor Jan , Mrozik Agnieszka , Smoktunowicz Magdalena , Waleron Krzysztof , Waleron Malgorzata 

TITLE=Comprehensive phenomic and genomic studies of the species, Pectobacterium cacticida and proposal for reclassification as Alcorniella cacticida comb. nov

JOURNAL=Frontiers in Plant Science

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1323790

DOI=10.3389/fpls.2024.1323790

ISSN=1664-462X

ABSTRACT=<sec><title>Introduction</title><p><italic>Pectobacterium cacticida</italic> was identified as the causative agent of soft rot disease in cacti. Due to a high potential of spread in the face of global warming, the species poses a significant threat to horticultural and crop industry. The aim of this study was to revise the genomic, physiology and virulence characteristics of <italic>P. cacticida</italic> and update its phylogenetic position within the <italic>Pectobacterium</italic> genus.</p></sec><sec><title>Methods</title><p>Whole genome sequences of five <italic>P. cacticida</italic> strains were obtained and subjected to comprehensive genomic and phylogenomic data analyses. We assessed the presence of virulence determinants and genes associated with host and environmental adaptation. Lipidomic analysis, as well as biochemical and phenotypic assays were performed to correlate genomic findings.</p></sec><sec><title>Results</title><p>Phylogenomic analysis revealed that <italic>P. cacticida</italic> forms a distinct lineage within the <italic>Pectobacterium</italic> genus. Genomic evaluation uncovered 516 unique proteins, most of which were involved in cellular metabolism. They included genes of carbohydrate metabolism and transport and ABC transporters. The main differing characteristics from other <italic>Pectobacterium</italic> species were the lack of a myo-inositol degradation pathway and the presence of the malonate decarboxylase gene. All tested strains were pathogenic towards <italic>Opuntia</italic> spp., chicory, Chinese cabbage, and potato, but exhibited only mild pathogenicity towards carrot.</p></sec><sec><title>Discussion</title><p>This study sheds light into the genomic characteristics of <italic>P. cacticida</italic> and highlights the pathogenic potential of the species. Unique genes found in <italic>P. cacticida</italic> genomes possibly enhance the species’ survival and virulence. Based on phylogenomic analyses, we propose the reclassification of <italic>P. cacticida</italic> to a new genus, <italic>Alcorniella</italic> comb. nov.</p></sec>