Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii

Abstract

Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart’s wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes, has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis. While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range.

Pantoea ananatis, A New Bacterial Pathogen Affecting Wheat Plants (Triticum L.) in Poland

“…Our results in this matter are congruent with the results obtained for onion-pathogenic P. ananatis strains [17]. Extensive genetic diversification of P. ananatis was described as a result of pan-genome analyses which revealed the significant role of an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements, and insertion elements [34] In conclusion, we state that the P. ananatis might pose a considerable threat to wheat crops on the whole area of CLB distribution which includes the whole Europe [35], Middle-East, North Asia, Africa, and eastern part of North America (https://gd.eppo.int/taxon/LEMAME/distribution). To our knowledge, this is the first report of P. ananatis affecting wheat plants.…”

Analysis of microbiomes in three traditional starters and volatile components of the Chinese rice wines

“…Lactobacillus and Acetobacter can produce abundant organic acids, which is one of the factors to impact the flavor and style of rice wine. Pantoea not only can produce yellow pigments, but also are the conditional pathogens (Maayer et al, 2017). The microbial communities of starter had a great significance for improving food safety of rice wine.…”

Pantoea ananatisdefeatsAlliumchemical defenses with a plasmid-borne virulence gene cluster

“…Pantoea ananatis is a broad-host-range pathogen able to cause disease in diverse monocot hosts including onion, pineapple, maize, rice, and sudangrass (17). P. ananatis is also a rare example of a gram negative plant pathogen that lacks both a virulence-associated Type III Secretion System (T3SS) used by many plant pathogenic bacteria to deliver immune-dampening effector proteins as well as a Type II Secretion System (T2SS) commonly used to deliver plant cell wall degrading enzymes associated with soft rot pathogens (18, 19). This surprising lack of the key pathogenicity factors, typically associated with gram negative bacterial plant pathogens, has left the primary molecular mechanisms by which P. ananatis causes disease an open question.…”