Comparative genomics of Xanthomonas fragariae and Xanthomonas arboricola pv. fragariae reveals intra- and interspecies variations

Michael Gétaz,Joël F. Pothier,Theo H. M. Smits,Jochen Blom

doi:10.1186/s42483-020-00061-y

Michael Gétaz, Joël F. Pothier + Show 2 more

Open Access

https://doi.org/10.1186/s42483-020-00061-y

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Abstract

The quarantine bacterium Xanthomonas fragariae causes angular leaf spots on strawberry. Its population structure was recently found to be divided into four (sub)groups resulting from two distinct main groups. Xanthomonas arboricola pv. fragariae causes bacterial leaf blight, but the bacterium has an unclear virulence status on strawberry. In this study, we use comparative genomics to provide an overview of the genomic variations of a set of 58 X. fragariae and five X. arboricola pv. fragariae genomes with a focus on virulence-related proteins. Structural differences within X. fragariae such as differential plasmid presence and large-scale genomic rearrangements were observed. On the other hand, the virulence-related protein repertoire was found to vary greatly at the interspecies level. In three out of five sequenced X. arboricola pv. fragariae strains, the major part of the Hrp type III secretion system was lacking. An inoculation test with strains from all four X. fragariae (sub)groups and X. arboricola pv. fragariae resulted in an interspecies difference in symptom induction since no symptoms were observed on the plants inoculated with X. arboricola pv. fragariae. Our analysis suggests that all X. fragariae (sub)groups are pathogenic on strawberry plants. On the other hand, the first genomic investigations of X. arboricola pv. fragariae revealed a potential lack of certain key virulence-related factors which may be related to the difficulties to reproduce symptoms on strawberry and could question the plant-host interaction of the pathovar.

Highlights

Strawberry is a small fruit crop of great economic importance in the world (Amil-Ruiz et al 2011)
X. fragariae is considered as quarantine organism by the European and Mediterranean Plant Protection Organization (OEPP/EPPO 1986), and the symptoms it caused are defined as angular leaf spots (ALS) affecting strawberry plant leaves
Genome sequences As the genome sequences of X. fragariae and X. arboricola pv. fragariae strains included in this study were resulted from different sequencing technologies with different read lengths, the genomes vary in their total numbers of contigs and genome size (Table 1)

Summary

Introduction

Strawberry is a small fruit crop of great economic importance in the world (Amil-Ruiz et al 2011). Strawberry became a part of the major fruit industry for several countries (Kim et al 2016). Strawberry cultivars exhibit diverse susceptibilities to a large variety of harmful organisms, reducing fruit quality and plant yield (2020) 2:17. X. fragariae is considered as quarantine organism by the European and Mediterranean Plant Protection Organization (OEPP/EPPO 1986), and the symptoms it caused are defined as angular leaf spots (ALS) affecting strawberry plant leaves. The bacterium was first described in 1960 from the USA (Kennedy and King 1960), and was subsequently found in most major strawberry producing regions worldwide (Zimmermann et al 2004; OEPP/EPPO 2006). The artificial infection of X. fragariae displayed different disease incidences on strawberry cultivars indicated by variably severe symptoms on plant leaves (Bestfleisch et al 2015)

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