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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 #348544

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: A new (type 3) prophage of "Candidatus Liberibacter asiaticus" in China

item ZHENG, Z - South China Agricultural University
item BAO, M - South China Agricultural University
item WU, F - South China Agricultural University
item Van Horn, Christopher
item Chen, Jianchi
item DENG, X - South China Agricultural University

Submitted to: Phytopathology
Publication Type: Abstract Only
Publication Acceptance Date: 3/27/2018
Publication Date: 7/28/2018
Citation: Zheng, Z., Bao, M., Wu, F., Van Horn, C.R., Chen, J., Deng, X. 2018. A new (type 3) prophage of "Candidatus Liberibacter asiaticus" in China. Phytopathology. 108:S1.107.

Interpretive Summary:

Technical Abstract: Prophages are important genetic entities of “Candidatus Liberibacter asiaticus” (CLas), a non-culturable a-proteobacterium associated with citrus Huanglongbing (HLB). Two CLas prophages have been described, SC1 (NC_019549.1, Type 1) and SC2 (NC_019550.1, Type 2). To explore the prophage repertoire, 523 CLas samples were collected from southern China and surveyed for Type 1 and Type 2 prophages by specific PCR. Eighteen samples were found lacking both prophages. One sample, JXGC, was sequenced using Illumina HiSeq and generated > 100 million short sequence reads (150 bp per read). Read mapping showed a sequence coverage of 46% to SC1 and 50% to SC2. BLAST search using SC1 and SC2 as queries identified three contigs from the JXGC de novo assembly that form a circular Type 3 prophage, P-JXGC-3 (31,449 bp, KY661963). P-JXGC-3 had 36 open reading frames, ten of which were not found in Type 1 or Type 2 prophages, including four genes that encoded a restriction-modification (R-M) system (hsdR, hsdS, hsdM1 and hsdM2). Typed by prophage specific PCR, the CLas strains in southern China contained all combinations of the three prophage types with the exception of a Type 2-Type 3 combination. Based on gene annotation, P-JXGC-3 is not capable of reproduction via lytic cycle. The R-M system was speculated to play a role against Type 1 prophage/phage invasion. The new prophage information will facilitate current research in HLB epidemiology and host-pathogen interactions.