The Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool

BMC Genomics

Sandra Smit¹  Dick de Ridder¹  Eef M. Jonkheer²  Ilse M. Houwers³  Jan M. van der Wolf³  Peter J. M. Bonants³  Balázs Brankovics³  Theo A. J. van der Lee³  Lidija Berke⁴  Jorn R. de Haan⁴  Robert Bollema⁵  Robert A. M. Vreeburg⁵ 

[1] Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands;Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands;Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands;Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands;Genetwister Technologies B.V, Nieuwe Kanaal 7b, 6709 PA, Wageningen, The Netherlands;Nederlandse Algemene Keuringsdienst voor zaaizaad en pootgoed van landbouwgewassen, Randweg 14, 8304 AS, Emmeloord, The Netherlands;

关键词: Pectobacterium;    Pectobacteriaceae;    Plant pathogen;    Comparative genomics;    Pangenome;    Gene repertoire;    Phylogeny;    Virulence;    Pectobacterium brasiliense;   

DOI  :  10.1186/s12864-021-07583-5

来源: Springer

【 摘 要 】

BackgroundBacterial plant pathogens of the Pectobacterium genus are responsible for a wide spectrum of diseases in plants, including important crops such as potato, tomato, lettuce, and banana. Investigation of the genetic diversity underlying virulence and host specificity can be performed at genome level by using a comprehensive comparative approach called pangenomics. A pangenomic approach, using newly developed functionalities in PanTools, was applied to analyze the complex phylogeny of the Pectobacterium genus. We specifically used the pangenome to investigate genetic differences between virulent and avirulent strains of P. brasiliense, a potato blackleg causing species dominantly present in Western Europe.ResultsHere we generated a multilevel pangenome for Pectobacterium, comprising 197 strains across 19 species, including type strains, with a focus on P. brasiliense. The extensive phylogenetic analysis of the Pectobacterium genus showed robust distinct clades, with most detail provided by 452,388 parsimony-informative single-nucleotide polymorphisms identified in single-copy orthologs. The average Pectobacterium genome consists of 47% core genes, 1% unique genes, and 52% accessory genes. Using the pangenome, we zoomed in on differences between virulent and avirulent P. brasiliense strains and identified 86 genes associated to virulent strains. We found that the organization of genes is highly structured and linked with gene conservation, function, and transcriptional orientation.ConclusionThe pangenome analysis demonstrates that evolution in Pectobacteria is a highly dynamic process, including gene acquisitions partly in clusters, genome rearrangements, and loss of genes. Pectobacterium species are typically not characterized by a set of species-specific genes, but instead present themselves using new gene combinations from the shared gene pool. A multilevel pangenomic approach, fusing DNA, protein, biological function, taxonomic group, and phenotypes, facilitates studies in a flexible taxonomic context.

【 授权许可】

CC BY