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ARS Home » Pacific West Area » Wapato, Washington » Temperate Tree Fruit and Vegetable Research » Research » Research Project #440856

Research Project: Profiling Pathogenic Genome Variation in Novel Haplotypes of 'Candidatus Liberibacter Solanacearum' Isolated from Psyllid Species from Potato

Location: Temperate Tree Fruit and Vegetable Research

Project Number: 2092-21220-003-027-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: May 21, 2021
End Date: Apr 30, 2024

Project objectives are two-fold. 1) Using a comparative genomics approach, assess the genome differences between Lso haplotypes that induce ZC symptoms in potato and those that are only asymptomatic in potato upon infection. 2) Use a targeted approach to profile the above-identified pathogenicity factors or prophage loci in the novel Lso haplotypes isolated from non-potato psyllids.

Objective 1. We will utilize several computational strategies to identify the genome difference between Lso haplotypes, including whole genome comparisons, ortholog analysis, gene neighborhood analysis, phylogenetic inference and conservation analysis. Seven genomes of Lso haplotypes are available in NCBI GenBank database, including Lso haplotype A (NZ1, GCA_000968085.1; HenneA, GCA_000968075.1 ), haplotype B (ZC1,GCA_000183665.1), and haplotype C (FIN114; GCA_001983675.1). We aim to identify the pathogenicity-related genes or prophage regions that are present in Lso haplotypes A and B, which induce ZC symptoms, but are absent in haplotype C, which is asymptomatic in potato upon infection. We will also utilize the domain-centric protein sequence and structural analyses to understand the potential functions of the identified genes. Objective 2. Following the successful identification of genomic factors present in Lso haplotypes that are associated with ZC symptom development in potato, specific primers will be designed for use in targeted polymerase chain reaction (PCR) assays. Standard PCR using a high fidelity, proof reading polymerase will then be conducted using DNA previously isolated from Lso-infected non-potato psyllid species collected in the Klamath Basin of Oregon. DNA extracted from potato psyllid specimens containing either Lso haplotype A or B will be used as a control to verify that the primers and PCR thermal cycler conditions are successful. Following PCR validation, any PCR products that are produced from the novel Lso haplotypes using the targeted primers will then be subjected to sequence analysis. Sequencing results will be further incorporated into comparative genomics and phylogenetic analyses (approaches in Objective 1) to correlate genotypic data with our phenotypic knowledge.