Comparative genomics of Spiraeoideae‐infecting Erwinia amylovora strains provides novel insight to genetic diversity and identifies the genetic basis of a low‐virulence strain

Abstract

Summary Erwinia amylovora is the causal agent of fire blight, one of the most devastating diseases of apple and pear. Erwinia amylovora is thought to have originated in North America and has now spread to at least 50 countries worldwide. An understanding of the diversity of the pathogen population and the transmission to different geographical regions is important for the future mitigation of this disease. In this research, we performed an expanded comparative genomic study of the Spiraeoideae‐infecting (SI) E. amylovora population in North America and Europe. We discovered that, although still highly homogeneous, the genetic diversity of 30 E. amylovora genomes examined was about 30 times higher than previously determined. These isolates belong to four distinct clades, three of which display geographical clustering and one of which contains strains from various geographical locations (‘Widely Prevalent’ clade). Furthermore, we revealed that strains from the Widely Prevalent clade displayed a higher level of recombination with strains from a clade strictly from the eastern USA, which suggests that the Widely Prevalent clade probably originated from the eastern USA before it spread to other locations. Finally, we detected variations in virulence in the SI E. amylovora strains on immature pear, and identified the genetic basis of one of the low‐virulence strains as being caused by a single nucleotide polymorphism in hfq, a gene encoding an important virulence regulator. Our results provide insights into the population structure, distribution and evolution of SI E. amylovora in North America and Europe.

Survey of Toxin–Antitoxin Systems in Erwinia amylovora Reveals Insights into Diversity and Functional Specificity

“…We selected E. amylovora strain CTBT3-1, a sequenced high-virulence strain [3], to perform functional validation studies of protein–protein TA systems. While most known roles of TA systems have been attributed to those of type II, the single type IV family identified has a similar operon structure and is incorporated into the training sets of multiple TA system prediction programs [6,7].…”

“…The plant pathogen Erwinia amylovora causes fire blight, an economically important disease of apple and pear that poses a significant threat to rosaceous fruit tree cultivation globally [2]. E. amylovora is divided into two genetically homogeneous groups based on host specificity: Spiraeoideae-infecting (SI) strains can cause disease on apple and pear, while Rubus -infecting strains are limited to bramble hosts [3]. Although no TA systems have previously been studied in E. amylovora , it is a species with well-characterized virulence mechanisms, ample genomic resources, standardized protocols for genetic manipulation and close genetic relatedness to the enteric human pathogens that have served as models for TA system function.…”

Shotgun sequencing decades-old lichen specimens to resolve phylogenomic placement of type material

“…For all specimens with inferred identity in the R. haydenii/idahoensis group (Keuler et al 2019), we generated a nuclear phylogenomic alignment using REALPHY v1.12 (Bertels et al 2014), which has empirically been shown to construct genome-scale datasets (Leavitt et al 2016;Zeng et al 2018). New data were combined with metagenomic reads from previous studies (Leavitt et al 2016) and mapped to BUSCO gene regions > 1 kb from a pure fungal culture of R. melanophthalma (see Keuler et al 2019) in REALPHY v1.12, implementing Bowtie 2.1.0 (Langmead & Salzberg 2012) for read mapping with the following parameters: -readLength 75 -perBaseCov 5 -gapThreshold 0.2 with the remaining parameters set to default values.…”

Genome-scale data reveal the role of hybridization in lichen-forming fungi

“…The nuclear phylogenomic alignment was created with REALPHY v1.12 63 , which has previously been shown to construct robust genome-scale datasets 55,64 . Metagenomic reads were mapped to contigs >5 kb from a previously published draft genome assembly for R. melanophthalma sensu stricto 55 in REALPHY v1.12, implementing Bowtie 2.1.0 65 for read mapping using the following parameters: -readLength 75 -perBaseCov 5 -gapThreshold 0.2 with the remaining parameters set at default values.…”