engleski

Comparative genomics of bacteria from 'Canididatus Phytoplasma' genus: from genome instability to host adaptation

Wall-less bacteria from the genus 'Candidatus Phytoplasma' belong to the class Mollicutes along with mycoplasmas, spiroplasmas and acholeplasmas. They are associated with numerous plant species worldwide causing significant economic losses in agriculture, viticulture and fruit production. Phytoplasmas induce dramatic perturbations in plant development ; however, the understanding of all mechanisms underlying phytoplasma pathogenicity is far from complete. These intracellular pathogens have a unique life-style successfully manipulating their plant and insect hosts and needing both hosts for survival and dispersal in nature. Through their dynamic co-evolution with both hosts from different domains of life, they experienced specific gene losses and gains which resulted in unsuccessful axenic cultivation of these bacteria. Due to that fact, and their repeat-rich nature they are challenging experimental models and difficult to study. Nevertheless, 5 annotated genomes are available together with a number of genome draft assemblies. Among the later, ‘Ca. P. solani’ possesses one of the largest chromosomes with a known heterogeneity between the strains. In this work ‘Ca. P. solani’ strains were used for genome sequencing. Upon library construction, Illumina MiSeq platform was used for generation of short reads. De novo assembly pipeline produced a genome draft in 39 contigs of ~ 590 bp in total, compared to 128 contigs and 298 contigs of 574 kb and 545 kb, respectively, from two reference drafts. Obtained results, with difficulties in assembling the complete genome suggest the presence of distinct features and the abundance of repetitive sequences. Thus, the high plasticity of ‘Ca. P. solani’ genome is also implied which is in agreement with the wide host range and its adaptability to different plant and insect hosts. Previously, comparative analyses of phytoplasma genomes revealed the presence of unique repetitive features termed potential mobile units (PMUs) that have characteristics of replicative transposons. Moreover, recent breakthroughs in phytoplasma functional genomics are findings on the secreted effector molecules and virulence factors proved for ‘Ca. P. asteris’ subclade members. Detailed characterization of PMUs and the potential effectors are the further step in the analyses of the hereby presented ‘Ca. P. solani’ genome sequencing results.

plant hosts; insect hosts; genome draft assembly; MiSeq; 'Candidaus Phytoplasma solani'; potential mobile units; effectors

Istraživanje je ostvareno u okviru HRZZ uspostavnog istraživačkog projekta "Komparativna i funkcionalna genomika fitoplazmi-emergentnih biljnih patogena u Hrvatskoj" (GenoPhyto), voditeljica Martina Šeruga Musić.