Transcriptome of Ponkan mandarin (Citrus reticulata Blanco) in the early infection of Xylella fastidiosa

Mandarins are tolerant to Xylella fastidiosa (Xf), the causal agent of citrus variegated chlorosis (CVC) but the mechanism of tolerance is unknown. In this study we evaluated the global gene expression of Ponkan infected with Xf in preliminary stages of the infection (24 hours). RNAs were extracted from a pool of three biological replicates and sequenced using the Illumina platform. As results we obtained 35,344,265 library sequences for the non-infected library and 37,326,339 for the infected one. These transcripts were mapped in the whole reference genome of C. clementine by using TopHat software. An initial consensus of exon sequences was extracted from the mapped reads and used to measure the relative abundance of transcripts with Cufflinks. The transcripts quantitation was used to calculate the level of differential expression between mandarin inoculated with Xf, the control and their significance in Cuffdiff. A total of 27,888 coding sequences (cds) were obtained after mapping the reads in the reference genome sequence. From these cds, 349 were repressed and 225 significantly induced (fold ≥ 1.0) in the infected mandarin.  Among the induced cds we found sequences related to synthesis and cell wall organization, suggesting physical protection against Xf. Gene encoding a protein similar to a CC-NBS-LRR disease resistance protein was also expressed indicating perception of molecular signals from the bacteria that trigger a signaling cascade for expression of defense genes. However, the most interesting response was the induction of genes related to synthesis of auxin, as well as its receptor. Support: INCT Citrus (Fapesp/CNPq).