Identification of a Novel 1033‐Nucleotide Deletion Polymorphism in the Prophage Region of ‘ Candidatus Liberibacter asiaticus’: Potential Applications for Bacterial Epidemiology

The prophage/phage region in the genome of ‘ Candidatus Liberibacter asiaticus’, an alpha‐proteobacterium associated with citrus Huanglongbing, included many valuable loci for genetic diversity studies. Previously, a mosaic genomic region ( CLIBASIA _05640 to CLIBASIA _05650) was characterized, and this revealed inter‐ and intracontinental variations of ‘ Ca . L. asiaticus’. In this study, 267 ‘ Ca . L. asiaticus’ isolates collected from eight provinces in China were analysed with a primer set flanking the same mosaic region plus downstream sequence. While most amplicon sizes ranged from 1400 to 2000 bp, an amplicon of 550 bp ( S 550) was found in 14 samples collected from south‐western China. Sequence analyses showed that S 550 was the result of a 1033 bp deletion which included the previously known mosaic region. The genetic nature of the deletion event remains unknown. The regional restriction of S550 suggests that the ‘ Ca . L. asiaticus’ population from south‐western China is different from those in eastern China. The small and easy‐to‐detect S550 amplicon could serve as a molecular marker for ‘ Ca . L. asiaticus’ epidemiology.