Genetic Diversity of " Candidatus Liberibacter asiaticus" Based on Four Hypervariable Genomic Regions in China.

Huanglongbing (HLB; greening disease), caused by Candidatus Liberibacter asiaticus ( C Las), is the most damaging citrus disease worldwide. The disease has spread throughout the citrus-producing regions of Guangxi, Guangdong, Fujian, and others in China. A total of 1,788 HLB-like symptomatic or asymptomatic samples were collected from the Guangxi and Fujian provinces of China to decipher the genetic diversity of C Las and its correlation with geographic region and host plant. The disease was the most severe in orange and the least in pomelo. C Las bacteria associated with the specific geographical and citrus variety infected more than 50% of the HLB-like symptomatic samples. We identified 6,286 minor variations by comparing 35 published C Las genomes and observed a highly heterogeneous variation distribution across the genome, including four highly diverse nonprophages and three prophage segments. Four hypervariable genomic regions (HGRs) were identified to determine the genetic diversity among the C Las isolates collected from Guangxi and Fujian, China. A phylogenetic tree constructed from four HGRs showed that 100 C Las strains could be separated into four distinct clades. Ten new strains with high variations of prophage regions were identified in the mandarin and tangerine grown in new plantation areas of Guangxi. Characterizing these HGR variations in the C Las bacteria may provide insight into their evolution and adaptation to host plants and insects. IMPORTANCE The hypervariable genomic regions derived from 35 published C Las genomes were used to decipher the genetic diversity of C Las strains and identify 10 new strains with high variations in prophage regions. Characterizing these variations in the C Las bacteria might provide insight into their evolution and adaptation to host plants and insects in China.