Genomic Comparisons and Phenotypic Diversity of Dickeya zeae Strains Causing Bacterial Soft Rot of Banana in China

Abstract

Bacterial soft rot of banana, caused by Dickeya zeae, is spreading rapidly in important banana growing areas in China and seriously threatens banana production. In this study, we sequenced the high-quality complete genomes of three typical banana strains, MS1 (size: 4,831,702-bp; genome coverages: 538x), MS_2014 (size: 4,740,000-bp; genome coverages: 586x) and MS_2018 (size: 4,787,201-bp; genome coverages: 583x), isolated in 2009, 2014, and 2018, respectively. To determine their genomic and phenotypic diversity with respect to their hosts of origin, they were compared with other D. zeae strains, including another representative banana strain MS2 from China. The sequenced strains were similar in utilization of carbon source and chemical substrates, and general genomic features of GC content, and tRNA and rRNA regions. They were also conserved in most virulence determinants, including gene-encoding secretion systems, plant cell wall degrading enzymes, and exopolysaccharides. We further explored their genomic diversity in the predicted genomic islands (GIs). These GIs were rich in integrases and transposases, where some genomic dissimilarity was observed in the flagellar gene cluster and several secondary metabolite gene clusters. Different constituents of core biosynthetic modules were found within the bacteriocin and aryl polyene (APE) pigment gene clusters, and the strains from banana showed different phenotypes with respect to antibiosis effects and colony pigmentation. Additionally, clustered regularly interspaced short palindromic repeat (CRISPR) and prophage elements, such as type I-F and III-A CRISPR arrays and an intact prophage of MS1-P5, contributed to bacterial diversity. Phylogenetic tree analysis and genome-genome nucleotide comparison confirmed the genomic divergence among the strains isolated from banana. Considering these characteristics, MS2 and MS_2014 probably diverged later than MS1, while MS_2018 was different and more similar to foreign strains isolated from other hosts in several characteristics. Strain MS_2018 caused severe symptoms on banana varieties previously considered moderately resistant or moderately susceptible, including varieties of Cavendish (Musa AAA) and Plantain (Musa ABB). Our study of genomic and phenotypic diversity raises public attention to the risk of spreading new pathogenic variants within banana growing regions and supports development of predictive strategies for disease control.

Morpho-physiological and molecular characteristics of bacteria causing stalk rot disease on corn in Gorontalo, Indonesia

“…The alignment of the BGO4 DNA sequences with the bacterial strains in GeneBank showed very high genetic variation in the nucleotide sequence or loci. In addition, Zhang et al (2022) reported the sequencing genomes of three D. zeae strains isolated from banana plants showed phenotypic diversity in antibiotic effects, colony pigments, and virulence levels between strains. Therefore, studies of the genetic diversity of bacterial strains need to be carried out to suppress the spread of new virulent strains.…”

Genomic and phenotypic biology of a novel Dickeya zeae WH1 isolated from rice in China: Insights into pathogenicity and virulence factors

“…Although there are some differences in isolated hosts, SRP shares many virulence factors, including PCWDE, secretion systems, motility, and plant responses to SRP infections ( Davidsson et al, 2013 ; Reverchon et al, 2016 ). In Dickeya genus, D. zeae strains and their genomes were used for references to study virulence factors and pathogenicity of the genus ( Zhang et al, 2014 , 2022 ; Zhou et al, 2015 ; Lv et al, 2022 ). However, there is a relatively small amount of research on the above diseases in rice ( Van Gijsegem et al, 2021 ).…”

“…The soft rot bacteria within Dickeya genus macerate the plant tissue and acquire nutrients from the dead cells. Most pathogenicity determinants related encoding genes, including PCWDEs, type secretion systems (types I–VI), extracellular polysaccharides (such as CPS and EPS), bacterial attachment operons (type IV pili), flagella and chemotaxis, zeamine synthesis, quorum sensing systems, and biofilm formation, have been described in strains EC1, EC2, MS1, or MS2 ( Feng et al, 2019 ; Zhang et al, 2020 , 2022 ; Liu et al, 2022 ). In this study, we mainly analyzed and compared the similarities, differences, or absence of gene encoding virulence determinants between WH1 and these four D. zeae strains.…”

“…Generally, D. zeae strains infect plants through three main steps: (1) adhesion to plant surface and penetration in the plant tissues, either via wound sites or through natural openings such as stomata; (2) invasion of apoplasts; and (3) plant cell wall degradation ( Reverchon and Nasser, 2013 ). Some typical virulence factors are involved in these processes, such as type I–VI secretion systems (T1SS–T6SS), PCWDEs, flagella, and flagella-mediated motility, quorum sensing signal molecules acylhomoserine lactone (AHL) and Vfm, and biofilms ( Zhang et al, 2022 ). A previous study showed that the zeamines produced by D. zeae EC1 were important virulence factors for rice, but antagonists for many bacteria and fungi ( Liao et al, 2014 ).…”