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Huanglongbing (HLB) is a worldwide deadly citrus disease caused by the phloem-limited bacteria ‘ Candidatus  Liberibacter asiaticus’ ( C Las) vectored by Asian citrus psyllids. In order to effectively manage this disease, it is crucial to understand the relationship among the bacterial isolates from different geographical locations. Whole genome sequencing approaches will provide more precise molecular characterization of the diversity among populations. Due to the lack of  in vitro  culture, obtaining the whole genome sequence of  C Las is still a challenge, especially for medium to low titer samples. Hundreds of millions of sequencing reads are needed to get good coverage of  C Las from an HLB positive citrus sample. In order to overcome this limitation, we present here a new method, Agilent SureSelect  XT HS  target enrichment, which can specifically enrich  C Las from a metagenomic sample while greatly reducing cost and increasing whole genome coverage of the pathogen. In this study, the  C Las genome was successfully sequenced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equivalent to 28.52 Cq using Li 16 S qPCR). More importantly, this method also effectively captures regions of diversity in the  C Las genome, which provides precise molecular characterization of different strains.

SureSelect targeted enrichment, a new cost effective method for the whole genome sequencing of Candidatus Liberibacter asiaticus