Pan-Genome Analysis of Wolbachia , Endosymbiont of Diaphorina citri , Reveals Independent Origin in Asia and North America.

Wolbachia , a group of Gram-negative symbiotic bacteria, infects nematodes and a wide range of arthropods. Diaphorina citri Kuwayama, the vector of Candidatus Liberibacter asiaticus ( C Las) that causes citrus greening disease, is naturally infected with Wolbachia ( w Di). However, the interaction between wDi and D. citri remains poorly understood. In this study, we performed a pan-genome analysis using 65 w Di genomes to gain a comprehensive understanding of w Di. Based on average nucleotide identity (ANI) analysis, we classified the w Di strains into Asia and North America strains. The ANI analysis, principal coordinates analysis (PCoA), and phylogenetic tree analysis supported that the D. citri in Florida did not originate from China. Furthermore, we found that a significant number of core genes were associated with metabolic pathways. Pathways such as thiamine metabolism, type I secretion system, biotin transport, and phospholipid transport were highly conserved across all analyzed w Di genomes. The variation analysis between Asia and North America w Di showed that there were 39,625 single-nucleotide polymorphisms (SNPs), 2153 indels, 10 inversions, 29 translocations, 65 duplications, 10 SV-based insertions, and 4 SV-based deletions. The SV-based insertions and deletions involved genes encoding transposase, phage tail tube protein, ankyrin repeat (ANK) protein, and group II intron-encoded protein. Pan-genome analysis of w Di contributes to our understanding of the geographical population of w Di, the origin of hosts of D. citri , and the interaction between w Di and its host, thus facilitating the development of strategies to control the insects and huanglongbing (HLB).