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Title: Identification of a novel 1033-nucleotide deletion polymorphism in the prophage region of ‘Candidatus Liberibacter asiaticus’: potential applications for bacterial epidemiology

Author
item WANG, X - Southwest University
item SU, H - Southwest University
item HUANG, L - Southwest University
item DENG, X - South China Agricultural University
item Chen, Jianchi
item ZHOU, C - Southwest University
item LI, Z - Southwest University

Submitted to: Journal of Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/25/2014
Publication Date: 8/27/2014
Citation: Wang, X., Su, H., Huang, L., Deng, X., Chen, J., Zhou, C., Li, Z. 2014. Identification of a novel 1033-nucleotide deletion polymorphism in the prophage region of ‘Candidatus Liberibacter asiaticus’: potential applications for bacterial epidemiology. Journal of Phytopathology. 163:681-685. doi: 10.1111/jph.12307.

Interpretive Summary: Huanglongbing (HLB, also known as yellow shoot disease or greening disease) is a highly destructive disease threatening the citrus industry in the U.S. and other citrus producing countries. The pathogen, “Candidatus Liberibacter asiaticus”, is not culturable, and information on the bacterium is limited. China has a long history of HLB, providing an ideal location to study the population biology of the pathogen. This study examined the HLB pathogen genome using 267 samples from eight provinces in southern China. A unique DNA sequence was found in southwestern regions. While the true nature of the DNA sequence needs further investigation, discovery helps current research efforts in differentiating and tracking the origin and movement of the pathogen, which will benefit both regional and global HLB control efforts.

Technical Abstract: The prophage/phage region in the genome of ‘Candidatus Liberibacter asiaticus’, an alpha-proteobacterium associated with citrus Huanglongbing, includes loci useful for genetic diversity studies. Previously, a mosaic genomic region (CLIBASIA_05640 to CLIBASIA_05650) was characterized and revealed inter- and intra-continental variations of ‘Ca. L. asiaticus’ (Wang et al., BMC Microbiol 12:18). In this study, 267 ‘Ca. L. asiaticus’ isolates collected from eight provinces in China were analyzed with a primer set flanking the same mosaic region plus downstream sequence. While most amplicon sizes ranged from 1,400 to 1,800 bp, an amplicon of 550 bp (S550) was found in 14 samples collected from southwestern China. Sequence analyses showed that S550 was the result of a 1,033 bp deletion including the previously known mosaic region. Genetic nature of the deletion event remains unknown. The regional restriction of S550 suggests that ‘Ca. L. asiaticus’ populations from southwestern China are different from those in eastern China. The small and easy-to-detect S550 amplicon could make it a molecular marker for ‘Ca. L. asiaticus’ epidemiology.