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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Molecular Plant Pathology Laboratory » Research » Research Project #432646

Research Project: Exotic Pathogens of Citrus: Curation, Diagnostics, and Interactions

Location: Molecular Plant Pathology Laboratory

2019 Annual Report

Objective 1: Evaluate patterns of gene expression in mixed infections between CTV and HLB in citrus, with the goal of discovering both cross-protecting strains and potential synergistic interactions. Objective 2: Develop new diagnostic reagents for emerging citrus pathogens and evaluate them as research reagents for the citrus community.

Host gene expression with two phloem limited pathogens - We intend to define citrus genes expressed in response to infection by phloem limited pathogens Citrus tristeza virus (CTV) and 'Ca. Liberibacter asiaticus' (CaLas). RNA Seq: Asymptomatic, young leaf tissue will be ground to a powder in liquid nitrogen and RNA will be isolated using a Trizol protocol. RNA will be used for RNA sequencing (Illumina 2500). Paired-end reads will be mapped to Citrus sinensis ‘Valencia’ reference genome. Differentially expressed transcripts will be identified. P < 0.01 and log2 fold change (log2FC) =¦1¦will be set as cut-off values. Curation of Exotic Pathogens of Citrus Collection: Each CTV isolate is composed of different genotypes, and we do not have detailed information on the CTV strain composition within each isolate. We will obtain this information by extracting RNA, preparing cDNA and performing multiplex PCR to identify mixed genotypes to characterize the CTV isolates. We will then extract dsRNA and use it as template for single read RNASeq and CTV genome assembly of CTV isolates of interest. ‘Ca. Liberibacter asiaticus’: We will determine the genome sequence of the 14 strains of ‘CaLas’ present in the EPPC. The parasitic plant dodder, Cuscuta indecora, is itself parasitized by ‘Ca. Liberibacter asiaticus’. The original genomic sequence data for ‘Ca. Liberibacter asiaticus’ was obtained from a single super-infected psyllid that provided a high ratio of CaLas to psyllid DNA required for shotgun sequencing. We can’t use psyllids under the conditions of our permit from USDA APHIS. We have shown that 2 cm segments of dodder stem infected with CaLas vary greatly in the concentration of CaLas, reaching concentrations of 109/g. We will infest citrus inoculated with CaLas from our collection with dodder and allow it to establish. We will harvest the dodder, cut them in 2 cm segments, and extract DNA. The extracts will be tested for the CaLas using our standard assay. We expect to find segments which have very high concentrations of CaLas (Cq<16). These will be sent to Jianchi Chen at Parlier for sequencing following amplification using his established protocol. We have recombinant antibodies that recognize surface antigens of CaLas. We have MTRAs with USDA APHIS CPHST and PathSensors, Inc (Baltimore, MD) to use our antibodies to develop a ‘CANARY’ assay for ‘Ca. Liberibacter asiaticus’. CANARY enables serologically based detection of pathogens in three minutes starting from an environmental sample. Direct tissue blot immunoassay (DTBIA) – The DTBIA is a well established technique for localizing proteins in plant tissue. We have used a rabbit polyclonal antibody for DTBIA of CaLas. We therefore expressed and purified the same antigens used to generate scFv to immunize New Zealand white rabbits to produce conventional polyclonal antisera. The DTBIA format preserves the localized concentration of CaLas observed in phloem cells and works in leaf midribs as well as in fruit petioles and peduncles, seed, stem and root tissues. These new antibodies will be used in DTBIA and the results compared with those obtained with anti-OmpA antibodies.

Progress Report
The goal of this project ’Invasive Citrus Pathogens’ is to prevent the introduction or spread within the citrus industry of a number of graft-transmissible and invasive pathogens of citrus. Due to quarantine considerations this work is carried out at Beltsville, Maryland. MPPL has continued their study of how several of the diseases of interest effect the expression of genes in infected citrus, and have identified families of genes that are differentially expressed in sweet orange trees infected by Citrus tristeza virus and ‘Ca. Liberibacter asiaticus’. We have moved on from assays with trees infected by pathogens one by one and continued with ‘deep sequencing’ of RNA in trees simultaneously infected with Citrus tristeza virus and ‘Ca. Liberibacter asiaticus. We have analyzed the data which will give a more precise understanding of how gene expression varies in trees infected by these two important citrus pathogens. Gene expression analysis of the doubly-infected plants will provide information on the specificity of gene expression in response to different pathogens, and is also reflective of real-world conditions. Because these genes are plant genes, expression is likely to be more uniform than is the distribution of the pathogens themselves, and the resulting assays to reveal the pattern of plant gene expression in response to the pathogen may be more reliable. The data have been analyzed and the manuscripts have been published. We have also documented a beneficial protective effect of prior inoculation with a mild strain of CTV against subsequent infection by ‘Ca. Liberibacter asiaticus’. A manuscript on this topic has been submitted for publication. We have also worked with an antibody against the critically important pathogen that causes citrus greening disease, ‘Ca. Liberibacter asiaticus’. We have raised and purified this antibody from rabbits and have used them in ‘tissue print’ assays to reveal the presence of the pathogen in infected citrus tissues. This has never been done before with this pathogen, and allows us to both detect the pathogen and study its distribution in infected citrus trees. Several manuscripts using the ‘tissue print’ method have been published, including a manuscript in which the tissue print method is combined with PCR- and qPCR based methods. MPPL has also worked on projects to identify novel pathogens of citrus and establish the causes of diseases of citrus. In cooperation with researchers at the University of Florida and at Ft. Detrick, Maryland, we have characterized a group of novel pararetroviruses that are associated with citrus blight disease. Citrus blight has been a serious problem for Florida citrus growers since at least the 1880's but the cause has always eluded researchers. We have developed evidence that an endogenous pararetrovirus is associated with the disease. This group of viruses may be integrated in the genome of citrus and under certain environmental or stress conditions may become active and cause disease. We continue to work on this important disease problem. We are also working with RNA library sequencing methodology to characterize gene expression in trees affected by citrus blight.


Review Publications
Fu, S., Liu, H., Liu, Q.H., Zhou, C., Hartung, J.S. 2019. Detection of ‘Candidatus Liberibacter asiaticus’ in citrus by concurrent tissue print based qPCR and Immunoassay. Plant Disease.