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A New (Type 3) Prophage of “Candidatus Liberibacter asiaticus” in China

Zheng Zheng: South China Agricultural University

<div>Prophages are important genetic entities of “<em>Candidatus </em>Liberibacter asiaticus” (CLas), a non-culturable α-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 <em>de novo</em> 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 (<em>hsdR</em>, <em>hsdS</em>, <em>hsdM1</em> and<em> hsdM2</em>). 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.</div>