Genome-wide Analyses of <i>Pectobacterium</i> and <i>Dickeya</i> Species

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Background

Plant pathogenic enterobacteria—Pectobacterium and Dickeya species—are responsible for devastating diseases, such as soft rot, blackleg, wilt and stem rot. Species within both genera cause enormous losses to vegetables (particularly potato) fruit, ornamental and field crops worldwide. The signs and symptoms produced by both genera are nearly identical, including slime production, wilting, black rot and foul odors. Bacterial pathogenicity determinants, including type secretion systems (TSS), suppress plant defense systems. The Pectobacterium and Dickeya genomes harbor different pathogenicity clusters, such as TSS, effector molecules, plant cell wall degrading enzymes (PCWDE), iron acquisition systems, cell attachment, and polysaccharides. However, noteworthy heterogeneity has been observed in their pathogenicity determinants and genomic constituents. Our understanding of processes regulating molecular interactions of Pectobacterium/Dickeya with their hosts and their host range is very restricted. Therefore, it is important to characterize the bacterial genomes and identify the genes and their functions that help such bacteria rapidly multiply in their hosts. Genome-based knowledge of these bacteria will enhance our ability to combat these soft rot diseases that unequivocally impact food security.

Rapidly developing sequencing technology (Illumina, Ion Torrent, Pacific Biosciences and Oxford Nanopore) has led to a sharp decrease in sequencing costs, which has enabled genome sequencing of plant bacterial strains on a vast scale. The amount of new ‘omics datasets—such as genome sequencing, RNA-seq, pan-genomics, metabolomics etc. is increasing rapidly. New bioinformatics pipelines and software also have become available. With the increasing numbers of datasets and bioinformatics pipelines and software, we can make more rapid progress in comparative and functional bacterial genomics.

This Research Topic welcomes—but is not limited to—submissions that cover a broad range of comparative and functional genomic studies on the soft rot pathogens Pectobacterium and Dickeya, and incorporate aspects of host plant physiology:
• Comparative genomics to understand genome constituents and heterogeneity
• Genome-based bacterial evolution, phylogenomics, and phylogenetics
• Genome-wide analyses of pathogenicity determinants and their roles in plant-bacterial interactions
• Genome-wide analyses of antimicrobial components and CRISPR-Cas systems
• Functional genomics

Descriptive studies, including those using 'omics approaches alone, will not be considered for review unless they address further functional insights into a relevant physiological process.

Keywords: Genome sequencing, comparative genomics, pathogenicity determinants, CRISPR, Functional genomics

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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