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ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #373141

Research Project: Identification of Novel Management Strategies for Key Pests and Pathogens of Grapevine with Emphasis on the Xylella Fastidiosa Pathosystem

Location: Crop Diseases, Pests and Genetics Research

Title: Metagenomic analyses of ACP and citrus samples infected with “Candidatus Liberibacter asiaticus” in California

item HUANG, J - South China Agricultural University
item DAI, Z - South China Agricultural University
item ZHENG, Z - South China Agricultural University
item SILVIA, P.A. - Fundecitrus - Brazil
item KUMAGAI, L - California Department Of Food And Agriculture
item Chen, Jianchi
item DENG, X - South China Agricultural University

Submitted to: American Phytopathological Society Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 8/3/2020
Publication Date: 12/30/2020
Citation: Huang, J., Dai, Z., Zheng, Z., Silvia, P., Kumagai, L., Chen, J., Deng, X. 2020. Metagenomic analyses of ACP and citrus samples infected with “Candidatus Liberibacter asiaticus” in California. American Phytopathological Society Meeting. 125:S2.53.

Interpretive Summary:

Technical Abstract: Huanglongbing (HLB) is a highly destructive disease in citrus production. The disease is associated with an unculturable proteobacterium “Candidatus Liberibacter asiaticus” (CLas), transmitted by Asian citrus psyllid (ACP, Diaphorina citri). HLB was first discovered in Southern California in 2012. Since then, the disease has been found in multiple locations. Understanding the microbiome associated with HLB has important impact for disease management. In this study, citrus and ACP CLas samples recently collected from County of San Bernardino were analyzed. A metagenomics pipeline was developed that included DNA extraction, a next-generation-sequencing (NGS) Illumina NextSeq format, and bacterial sequence grouping using a metagenomic tool (Kaiju) along with appropriate validation. In addition to CLas, sequence groups of Bradyrhizobium, Burkholderia, Mesorhizobium, Paraburkholderia, and Pseudomonas were found in both the citrus and ACP samples. Some groups had relatively high abundance. Draft genome sequences of the ACP and citrus CLas strains were obtained. Based on terL locus, the two CLas strains were in the Asiatic group with Type 1 prophages, i.e. PGT-1 group. In the sequence groups of Bradyrhizobium and Mesorhizobium, sequences highly similar to the 16S rRNA gene of CLas were detected. These sequences could potentially impact the accuracy of CLas detection using 16S rRNA gene-based PCR. Characterization of Burkholderia, Paraburkholderia and Pseudomonas groups are currently underway.