Targeted genome reconstruction strategy for endosymbionts in eukaryotic genomes

Background The human microbiome project [1] is the first systematic and large-scale survey of microbial communities present in a eukaryotic metagenome. The availability of low-cost high-throughput next-generation sequencing technologies that enable us to sequence eukaryotes to a high depth of coverage presents an opportunity for in silico discovery of endosymbionts. We describe a method for mining a whole genome shotgun metagenome from an insect to identify members of the endosymbiont community, followed by reconstruction and validation of a highquality draft microbial genome. The Asian citrus psyllid (Diaphorina citri Kuwayama or ACP) is host to 7+ bacterial endosymbionts [2] and is the insect vector of Candidatus Liberibacter asiaticus (Las), which is the causal agent of citrus greening, a disease costing the Florida citrus industry US$3.63 billion and 6,611 jobs since 2006. Citrus greening is a complex patho-system that involves interactions between the psyllid vector, the citrus host, and Candidatus Liberibacter asiaticus.