Characterization of bacterial endosymbionts and systems biology resources for Diaphorina citri, insect vector for the citrus greening disease
The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Ca. Liberibacter asiaticus (CLas), the causal agent for citrus greening or Huanglongbing disease which threatens the citrus industry worldwide. There is evidence that CLas interacts with the known endosymbionts of D. citri: Wolbachia, Ca. Profftella armatura, and Ca. Carsonella ruddii. Profftella and Carsonella are primary endosymbionts present in the bacteriome of the psyllid, while Wolbachia is present in the bacteriome as well as other tissues, notably in the gut. Profftella likely plays a defensive role in D. citri, while Carsonella is associated with amino acid synthesis and nutrition. Wolbachia is commonly found in insects and has been reported to have various roles, including reproductive effects. Wolbachia, Profftella, and Carsonella are all known to be inherited vertically through the eggs; however, there is also evidence in other insects of Wolbachia being transmitted horizontally.
A previous version of the D. citri genome, v1.1, was contaminated with bacterial contigs. We sequenced the 450Mb psyllid genome to 80X coverage with Pacbio long reads. The Canu assembler followed by Dovetail Chicago-based scaffolding was used to create an improved assembly (v2.0) with a contig N50 of 758.7kb and 1906 contigs. Endosymbiont sequences were extracted from the new D. citri genome assembly and verified for coverage against Pacbio and Illumina data, as well as against published reference genomes. Scaffolds from SSPACE were annotated with prokka and analyzed using Orthofinder and BRIG for gene copy number and conserved synteny.
Annotation and subsequent orthology analysis of the Profftella genome shows that all orthogroups conserved among the published reference genomes are also present in our assembly. Orthology analysis of the Carsonella genome shows >90% of conserved orthogroups to be present. We have 10 scaffolds that represent multiple Wolbachia strains, and together cover 557/559 conserved orthogroups. We have also assembled the mitochondrial organellar genome. This is the first report of the genomes of the primary endosymbionts and the mitochondria from D. citri sourced from Florida.
We have designed a web portal with genomics and bioinformatics resources for the vector D. citri including endosymbionts, the host citrus (C. clementina and C. sinensis) and multiple pathogens including CLas for the citrus greening disease. We have used Biocyc Pathway Tools databases to model biochemical pathways within each organism that can be used to explore the entire disease complex. All tools like JBrowse, Biocyc, Blast and Psyllid Expression Network connect to a central database containing gene models for citrus, ACP and multiple Ca. Liberibacter pathogens. The portal can be accessed at https://citrusgreening.org/.