Anatomical and dual transcriptomic analysis reveals the interaction of “Candidatus Liberibacter asiaticus” and citrus host in new shoots at different growth stage

“Candidatus Liberibacter asiaticus” (CLas), the causal agent of citrus Huanglongbing (HLB), poses a significant threat to citrus production worldwide. New shoots play a crucial role in the HLB pathosystem, serving as key sites for CLas acquisition and transmission by insect vector. However, CLas-host interactions in newly developing shoots remain poorly understood. This study investigated CLas population dynamic, anatomical change and dual transcriptomic profiles in new shoots at different growth stage after pruning two-years-old CLas-infected citrus plants. CLas population increased rapidly within 2 weeks after pruning (WAP), peaked at 4 WAP and subsequently declined between 6 WAP and 8 WAP. CLas infection inhibited the shoots growth and induced severe phloem collapse, particularly at 8 WAP. Transcriptomic analyses revealed that CLas genes involved in transcription/translation, lipid transport and metabolism, energy production, and resilience to host immune response were highly expressed at 4 WAP and 8 WAP, indicating active bacterial adaptation. In citrus, CLas infection primary affected metabolism, hormone signal transduction, cell wall metabolism, and transcription factors, particularly trihelix and bHLH families. The activation of citrus genes related to α-linolenic acid, WRKY and MYB transcription factors, pathogenesis-related proteins, and Ca2+-mediated signaling suggested potential defense response against in new shoots. These finding provide a comprehensive transcriptome landscape of CLas and its host in developing shoots, offering new insights into CLas-host interactions and potential defense mechanisms in citrus.