Potential habitat suitability of Candidatus Liberibacter asiaticus and genetic diversity of its prophages across China

Huanglongbing (HLB) is a severe citrus disease in China caused by Candidatus Liberibacter asiaticus (CLas). Since its initial identification, the pathogen has spread to 10 mainland provinces in China and caused devastating loss. Three distinct prophage types have been identified in CLas; however, their distribution and diversity in China remain inadequately understood. In this study, we collected 500 CLas samples from 10 provinces in China, employing three specific genomic loci to identify prophage types. Subsequently, Sanger sequencing was employed to analyze the genetic diversity of prophage within populations of CLas in China. In addition, the MaxEnt model optimized by the ENMeval software package, was used to predict the habitat suitability of populations of CLas and assess the potential impact of future climate change on its distribution in China. Our analysis revealed that type 2 prophage is the most prevalent, accounting for 55% in China. Among the 10 provinces tested, CLas populations in Yunnan and Sichuan demonstrated higher genetic diversity. Further analysis reveals that CLas populations harboring type 1 prophage remain relatively stable, whereas those carrying type 2 and type 3 prophages undergo population expansion. Furthermore, our predictive models indicate that the presently suitable habitat for CLas populations is concentrated in the southern and certain central regions of China, with an anticipated expansion under future climate change conditions. Presently, the center of populations of CLas characterized by favorable living conditions is situated in Zunyi City, Guizhou Province. Nevertheless, a projected trend indicates a shift toward the northeast, particularly targeting Tongren City in the foreseeable future.