Comparative analysis of 16S/23S intergenic region of Candidatus Liberibacter asiaticus associated with citrus greening disease in different citrus cultivars of Assam

Citrus greening, also known as Huanglongbing (HLB) is one of the most destructive diseases to commercial citrus plantations in India. Among the three different species of the causal bacterium reported worldwide, Candidatus Liberibacter asiaticus is the only species prevalent with HLB throughout the country. Though HLB has long been observed in different citrus cultivars and insect vectors (citrus psylla, Diaphorina citri Kuwayama) from North eastern territory of India, knowledge on the molecular variability in ' Ca . L. asiaticus' populations from this geographical region is limited. In this study, HLB was detected and identified by symptomatology, biological indexing on indicator plants and PCR (polymerase chain reaction) with ' Ca . L. asiaticus' specific 16S rDNA primers. Comparative analysis of 16S/23S intergenic region sequences of six representative ' Ca . L. asiaticus' isolates infecting three different citrus cultivars in Assam viz. Khasi  mandarin ( Citrus reticulata ), Assam lemon ( Citrus limon )  and  Sweet orange ( Citrus sinensis ) revealed  that  sequences were 99-100% similar to the published sequences of  ' Ca. L. asiaticus'  from Brazil, Taiwan, USA and some Indian (Poona) strains. However, approximately 88% sequence identity was seen with an Africanas strain (JF819885). Phylogenetic analysis with various published Candidatus Liberibacter species sequences revealed that all asiaticus isolates remained in one group while AsL-i isolate was quite distinct from other strains and close to a Chinese strain of the pathogen. The data also reveals that the genomic region can be used for HLB detection but not for strain differentiations.