engleski

Next-generation sequencing and comparative genomics of 'Candidatus Phytoplasma solani' strains: towards understanding of versatile pathogens

Endocellular wall-less bacteria known as phytoplasmas (genus ‘Candidatus Phytoplasma’) encompass a diverse group of pathogens affecting numerous plant species and causing significant damage in agriculture worldwide. While economic importance is increasing, studies related to their pathogenicity mechanisms are still hindered due to the inability of cultivation in vitro. Nevertheless, the rise of metagenomic era delivered new tools in finding potential virulence factors and effectors enabling phytoplasmas successful manipulation of their plant and insect hosts. ‘Ca. P. solani’ is a cosmopolitan pathogen with a broad host range transmitted by various polyphagous insect-vectors, and one of the common phytoplasmas found in Croatia. In our previous work, we sequenced a genome of ‘Ca. P. solani’ SA-1 strain. The aim of this study was to obtain more genomic data by sequencing two ‘Ca. P. solani’ strains originating from different plant hosts in order to get insight into the pathogenic potential and the repertoire of putative effectors of this versatile phytoplasma species. Whole plant samples of periwinkle infected with two different ‘Ca. P. solani’ strains (ST19 and STOL) maintained by grafting, were used for generation of libraries sequenced on Illumina MiSeq and MinION nanopore sequencing platforms. Raw reads were mapped to the reference genome and reads originating from periwinkle were filtered out. Moreover, de novo assembly was performed by using Unicycler v0.4.9b followed by annotation of genome drafts and prediction of putative effectors. Whole genome alignment and comparative analyses were also performed. Two draft genomes of 17 (ST19) and 22 (STOL) contigs were generated. Total size of drafts obtained were 647, 316 bp (ST19) and 668, 749 bp (STOL) with longest contigs of 140, 634 bp and 158, 078 bp, respectively. Whole genome alignment with reference SA-1 genome revealed synteny and conserved gene order. However, the abundant presence of repetitive sequences and potential mobile units disabled completion of the assembly. Prediction and search for putative effectors showed the presence of homologues of SAP11 and SAP54 effectors as well as some putative effectors that were specific for each of the strains. Nonetheless, sequencing and comparative genome analyses of ‘Ca. P. solani’ genomes confirmed their highly repetitive nature and the presence of diverse putative effectors as a mechanism for successful adaptation and pathogenicity of this versatile pathogen.

bois noir ; effectors ; genom ; phytoplasma ; stolbur

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