Transcriptome responses of alemow trees infected with a severe stem-pitting phenotype of Citrus tristeza virus

Citrus tristeza virus (CTV) stem-pitting (SP) disease which is a complex disease of citrus, reduces vigor and growth of trees. It also causes a reduction in fruit size which makes them unmarketable. Isolates of T68, T3, and VT are related to CTV SP syndrome. VT strain is present in infected trees throughout Florida, USA. The continued presence of this strain in Florida and the outcome of its interaction with other strain is a cause for concern. Yet there has been no study of the transcriptome responses of citrus trees to CTV severe SP infection and it remains to be determined. Recently we demonstrated the association between SP phenotypes and phloem regeneration using microscopy and comparative RNA-seq analyses of infected alemow (Citrus macrophylla) trees with CTV mutants exhibiting different SP symptoms from mild to severe in addition to the wild-type virus. We demonstrated that the severe SP phenotype has more phloem regeneration in symptomatic stems. In this study, transcriptome responses of infected C. macrophylla trees with severe phenotype of CTV SP syndrome were elucidated. We used RNA-seq analysis of trees infected with CTV∆p33∆p13 (CTV deletion of both p33 and p13 ORFs) which induces severe stem-pitting symptoms on experimental hosts. CTV severe SP infection resulted in 3115 up- and 1397 downregulated genes with the sum of 4512 differentially expressed genes (DEGs). Functional annotation analyses indicated that all DEGs are classified into three groups molecular function, biological process, and cellular component. Gene ontology analyses determined that genes associated with metabolic pathways and secondary metabolites biosynthesis were remarkably affected. Furthermore, transcriptome analyses identified some DEGs related to defense response pathways including proteins engaged in plant hormone signal transduction, plant-pathogen interaction, and mitogen-activated protein kinase (MAPK) signaling pathways. In addition, genes associated with secondary vascular tissue (SVT) regeneration were identified. Overall, the transcriptomic information obtained in this study improved our understanding of host-CTV SP interactions and it provides further support for phloem regeneration during symptom development.