Whole genome sequencing of citrus associated, plant pathogenic bacteria and further evaluation of the population structure in citrus orchards

Abstract

The Huanglongbing (HLB) is the most destructive citrus disease worldwide, associated to uncultivated Candidatus Liberibacter species, and spread in citrus orchards by the psyllid vector Diaphorina citri in main citriculture regions such as Brazil, China and Asia in general, the USA and Central America. Although HLB was first described in Brazil fifteen years ago and Candidatus Liberibacter asiaticus (Las) is the predominant species found in affected trees today, its incidence level is rising and currently close to 18%, which causes a lot of damage. HLB has spread unevenly in Sao Paulo state. Las is subject of intense research related to genomics. Las, an unculturable ±-proteobacterium associated with HLB, has been described three types of prophages, Type 1, represented by prophage SC1, Type 2, represented by prophage SC2 and Type 3. A new genomic organization in the junction of prophages SC2 and SC1 is prevalent found in Brazil, indicating gene rearrangement and a widespread occurrence of a type 1 prophage as well as the presence of a type 2-like prophage and with Las populations homogeneous (Silva et al. 2019). Three samples of sweet orange plants infected with Las kept in greenhouse Fundecitrus (Araraquara/SP/Brazil) were selected to conduct research on whole genome sequencing technology of Las strains from Brazil as an additional step on the selection of target genes for functional studies as alternatives to HLB control. All three Las strain samples of Brazil will be subject to Las genome Next Generation Sequencing (such as HiSeq) and genome assembly. Particular emphases will be on prophages characterizations, development of PCR procedures and identification of new targets (genes) for functional studies for HLB control. The complete genome sequencing of the Brazilian strains is of extreme importance because it will allow genomic knowledge, a new genomic organization in the junction of prophages SC2 and SC1 in Brazilian strains. The genetic features of Las strains from Brazil will be better evaluated with the genomic information generated and will contribute significantly to the advancement in Brazil Liberibacter genome analysis and biology of the causal agent of HLB. This genomic studies will allow to select new genes for functional studies that will be applied to determine the role of the Las genes in the interaction with their hosts, to apply biotechnological strategies and the generation of transgenic plants, and thus to search for alternatives for the control of HLB.