Transcriptome wide identification of CDR family in Citrus latifolia and its expression during HLB infection

Abstract

Abstract Huanglongbing (HLB) is the most important disease in citrus production around the world. Currently, there are not HLB-resistant citrus species or genotypes, however, Persian lime (Citrus latifolia Tan.) has been reported as the most tolerant citrus species to this disease, but their molecular mechanisms of tolerance has not being characterized yet. In other citrus species, Poncirus trifoliate, it has been suggested that the overexpression of CDR genes is associated to HLB tolerance, therefore, the aim of this work was to identify CDR gene family members in the Persian lime transcriptome and to determine if the HLB infection induces their expression. A Bayesian approach was used to search transcripts with one or two catalytic domains, then, a non-weighted parsimony phylogeny for CDR genes was carried out with the selected transcripts from C latifolia, P. trifoliata and C. sinensis, to identify phylogenetic homologous. The corresponding encoded proteins were obtained from the selected genes, and the similarity among them was estimated using alignments, identity matrix, UPGMA and conserved motifs analysis. Once the ClCDR genes were identified, their expression was determined with the transcriptome data and validated by RT-PCR and qRT-PCR in tissues of asymptomatic and HBL-symptomatic leaves. 146 sequences with one or two catalytic domains, were found, and 7 CDR clades were recovered. Similarity analysis demonstrated that there is a complex relationship among CDR genes and proteins in the species used in the present study. Moreover, the transcriptome and qRT-PCR data showed that none of the ClCDRgenes were expressed, neither in healthy nor in HLB-infected Persian lime plants, except for the ClCDR8a gene, which showed high expression. However, no significant differences were found between the ClCDR8a REL values from symptomatic or non-symptomatic leaves. Our results demonstrated the presence of CDR genes in the Persian lime genome, however, they suggest that HLB tolerance is not correlated with the overexpression of this gene family in this species.