Draft Genome Sequence of a “ Candidatus Liberibacter europaeus” Strain Assembled from Broom Psyllids (Arytainilla spartiophila) from New Zealand

Abstract

Here, we report the draft genome sequence of “Candidatus Liberibacter europaeus” ASNZ1, assembled from broom psyllids (Arytainilla spartiophila) from New Zealand. The assembly comprises 15 contigs, with a total length of 1.33 Mb and a G+C content of 33.5%.

Comparative Phylogenomic Analysis Reveals Evolutionary Genomic Changes and Novel Toxin Families in Endophytic Liberibacter Pathogens

“…Liberibacter solanacearum” ( 33 ), one genome of “ Candidatus. Liberibacter europaeus” (which is a potential pathogen of Cytisus scoparius and vectored by Arytainilla spartiophila ) ( 34 , 35 ), and two genomes of Liberibacter crescens (which was isolated from papaya and represents the most basal lineage within the Liberibacter genus) ( 36 , 37 ). Maximum likelihood phylogenetic analyses of three conserved genes, 16S rRNA, 23S rRNA, and DNA polymerase I, support the same tree topology ( Fig.…”

Iodixanol density gradients as an effective phytoplasma enrichment approach to improve genome sequencing

“…This was expected as the plant organelles and bacterial cells are smaller and have a lower density than nuclei (Graham et al, 1994). Additionally, similar iodixanol-based density gradient centrifugation methods have been used to enrich for various subcellular components, such as mitochondria (Choi et al, 2021), as well as Gram-negative bacteria from human and animal cells (Henríquez et al, 2003;Beder et al, 2016) and from insect vectors (Frampton et al, 2018). Similar patterns of host-associated organismal and organellar enrichment was also observed for two phytoplasma enrichment methods recently investigated, one involving methylated DNA depletion (Nijo et al, 2021) and the other developed for phytoplasma-specific enrichment by immunoprecipitation (Tan et al, 2021).…”

“…Improving the specificity of current phytoplasma enrichment methods, combining multiple phytoplasma enrichment and/or host depletion methods, or developing host organellar DNA depletion methods would further enhance the efficiency and therefore the cost of phytoplasma whole genome sequencing in the absence of a phytoplasma culture system. Nevertheless, non-phytoplasma bacterial enrichment by the iodixanol density gradient method developed here is broadly useful, serving as a method that is suitable for genome sequencing of other unculturable and intracellular phytopathogenic bacteria, such as 'Candidatus Liberibacter' species (Frampton et al, 2018).…”

“…A 40% (v/v) iodixanol (Optiprep TM , Sigma-Aldrich, Missouri, MI, United States) working solution was prepared by diluting the 60% iodixanol stock solution with the diluent solution (0.15-M NaCl, 1-mM EDTA, 15-mM Tris; pH 7.6 at 4 • C; Frampton et al, 2018). Three subsequent iodixanol solutions [14, 22, and 30% (v/v)] were prepared by diluting the 40% (v/v) iodixanol working solution in a NaCl-EDTA-Tris buffer (0.15-M NaCl, 0.5-mM EDTA, 5-mM Tris; pH 7.6 at 4 • C; Frampton et al, 2018).…”

“…A 40% (v/v) iodixanol (Optiprep TM , Sigma-Aldrich, Missouri, MI, United States) working solution was prepared by diluting the 60% iodixanol stock solution with the diluent solution (0.15-M NaCl, 1-mM EDTA, 15-mM Tris; pH 7.6 at 4 • C; Frampton et al, 2018). Three subsequent iodixanol solutions [14, 22, and 30% (v/v)] were prepared by diluting the 40% (v/v) iodixanol working solution in a NaCl-EDTA-Tris buffer (0.15-M NaCl, 0.5-mM EDTA, 5-mM Tris; pH 7.6 at 4 • C; Frampton et al, 2018). The density gradient was prepared on ice and by first adding 3 ml 30% (v/v) iodixanol to a 13.2-ml open-top thin wall polypropylene centrifuge tube (Beckman Coulter Life Sciences, California, CA, United States) using a 20 gauge needle (Terumo Medical Corporation, Tokyo, Japan) and a 20-ml syringe, followed by gently adding 4 ml of the 22% (v/v) iodixanol solution, and 4 ml of the 14% (v/v) iodixanol.…”