Genetic Characterization of ‘Candidatus Liberibacter solanacearum’ Haplotypes Associated with Apiaceous Crops in France

Abstract

‘Candidatus Liberibacter solanacearum’ (Lso) is an emerging phytopathogenic bacterium that causes significant crop losses worldwide. This bacterium has been identified in association with diseases of several solanaceous crops in the United States and New Zealand, and with carrot and celery crops in several European countries. Five Lso haplotypes (LsoA, LsoB, LsoC, LsoD, and LsoE) have now been described worldwide. In France, symptoms of Lso were observed on plants of the Apiaceae family in several regions. One hundred and ninety-two samples of apiaceous plants were collected from 2012 to 2016 in different geographical regions and were tested for the occurrence of Lso by real-time PCR assay. In addition to carrot and celery, Lso was detected in four other apiaceous crops: chervil, fennel, parsley, and parsnip. These new findings suggest that Lso has a wider natural host range within the Apiaceae family than expected. To identify the Lso haplotypes present in France, we sequenced and analyzed the 16S rRNA gene and the 50S ribosomal protein rpIJ-rpIL gene region from a representative bacterial collection of 44 Lso-positive samples. Our SNP analysis revealed the occurrence of two distinct bacterial lineages that correspond to haplotypes D and E. Then, we assessed the phylogenetic relationships between strains isolated from France and a worldwide collection of Lso isolates by using the rpIJ-rpIL gene region sequences. The neighbor-joining tree constructed delineated five clusters corresponding to the five Lso haplotypes, with LsoD and LsoE being closely related phylogenetically. Altogether, the data presented here constitute a first step toward a better understanding of the genetic diversity among Lso haplotypes in France, and provide new insights into the host range of this emerging bacterial species.

New Insights into the Genetic Diversity of the Bacterial Plant Pathogen ‘Candidatus Liberibacter solanacearum’ as Revealed by a New Multilocus Sequence Analysis Scheme

“…Indeed, LsoD and LsoE, which appeared to be very close phylogenetically, share the same insect vector ( B. trigonica ) (Alfaro-Fernández et al, 2012b; Teresani et al, 2014; Tahzima et al, 2017), whereas LsoC which forms a more distant cluster, is associated with a different psyllid species ( T. apicalis ) (Munyaneza et al, 2010b). The genetic relatedness of LsoD and LsoE was reported previously based on sequence analysis of the 50S rpIJ - rpIL gene (Hajri et al, 2017). For solanaceous haplotypes, this is not true since LsoA and LsoB, which are both associated with B. cockerelli , did not cluster together on the basis of our phylogenetic analysis.…”

“…To determine the haplotype affiliation of tested Lso strains, the sequenced genomes of strains from LsoA (strains NZ1, HenneA and RSTM), LsoB (strain ZC1), LsoC (strains FIN111 and FIN114) and LsoD (strain haplotype D1) were included in the analysis. For LsoE for which no published genome sequence is available, we used as reference, strain 14/235 that was previously determined as belonging to LsoE using the 16S rRNA gene and the 50S ribosomal protein rpIJ-rpIL gene region (Hajri et al, 2017).…”

“…LsoC is vectored by the carrot psyllid Trioza apicalis , and is associated with carrot in northern Europe (Munyaneza et al, 2010a,b; 2012a,b; 2015; Nissinen et al, 2014). LsoD and LsoE are associated with the carrot psyllid Bactericera trigonica , and with vegetative disorders on several apiaceous crops in southwestern Europe and the Mediterranean area (Alfaro-Fernández et al, 2012a,b; Nelson et al, 2013; Loiseau et al, 2014; Tahzima et al, 2014, 2017; Teresani et al, 2014; Hajri et al, 2017; Mawassi et al, 2018). A best understanding of the relationships between Lso strains isolated from a set of various host plants in different geographical locations may help to better explain the increasing spread and extended host range of Lso.…”

“…For Lso, few studies have been attempted to investigate its population structure and genetic diversity, in particular due to its fastidious nature (Lin and Gudmestad, 2013). Sequencing of the 16S rRNA, 16S/23S ISR and 50S rpIJ - rpIL ribosomal gene loci has become the method of choice for the study of the genetic diversity of the bacterium (Lin et al, 2009; Wen et al, 2009; Nelson et al, 2011, 2013; Teresani et al, 2014; Alfaro-Fernández et al, 2017; Haapalainen et al, 2017; Hajri et al, 2017; Monger and Jeffries, 2018). However, genetic variation within these genes does not generally allow differentiation of closely related strains due to their high degree of conservation (Lin and Gudmestad, 2013).…”

PM 9/25 (1) Bactericera cockerelli and ‘Candidatus Liberibacter solanacearum’

“…Haplotypes C, D and E have been found in several EPPO countries (see details in the EPPO Global Database) in plants from the family Apiaceae. They are associated with diseased carrots (Daucus carota) (C, D, E) as well as diseased celery (Apium graveolens), chervil (Anthriscus cerefolium), fennel (Foeniculum vulgare), parsley (Petroselinum crispum) and parsnip (Pastinaca sativa) (haplotypes D, E) (Alfaro-Fern andez et al, 2017;Hajri et al, 2017). Zebra chip symptoms have been reported from a few commercial potato lots in Spain, and haplotype E was detected in the symptomatic tubers (Cambra, 2014).…”