Transcriptome analysis of sweet orange trees infected with ‘Candidatus Liberibacter asiaticus’ and two strains of Citrus Tristeza Virus

Abstract

BackgroundHuanglongbing (HLB) and tristeza, are diseases of citrus caused by a member of the α-proteobacteria, ‘Candidatus Liberibacter asiaticus’ (CaLas), and Citrus tristeza virus (CTV) respectively. HLB is a devastating disease, but CTV strains vary from very severe to very mild. Both CaLas and CTV are phloem-restricted. The CaLas-B232 strain and CTV-B6 cause a wide range of severe and similar symptoms. The mild strain CTV-B2 doesn’t induce significant symptoms or damage to plants.ResultsTranscriptome profiles obtained through RNA-seq revealed 611, 404 and 285 differentially expressed transcripts (DETs) after infection with CaLas-B232, CTV-B6 and CTV-B2. These DETs were components of a wide range of pathways involved in circadian rhythm, cell wall modification and cell organization, as well as transcription factors, transport, hormone response and secondary metabolism, signaling and stress response. The number of transcripts that responded to both CTV-B6 and CaLas-B232 was much larger than the number of transcripts that responded to both strains of CTV or to both CTV-B2 and CaLas-B232. A total of 38 genes were assayed by RT-qPCR and the correlation coefficients between Gfold and RT-qPCR were 0.82, 0.69, 0.81 for sweet orange plants infected with CTV-B2, CTV-B6 and CaLas-B232, respectively.ConclusionsThe number and composition of DETs reflected the complexity of symptoms caused by the pathogens in established infections, although the leaf tissues sampled were asymptomatic. There were greater similarities between the sweet orange in response to CTV-B6 and CaLas-B232 than between the two CTV strains, reflecting the similar physiological changes caused by both CTV-B6 and CaLas-B232. The circadian rhythm system of plants was perturbed by all three pathogens, especially by CTV-B6, and the ion balance was also disrupted by all three pathogens, especially by CaLas-B232. Defense responses related to cell wall modification, transcriptional regulation, hormones, secondary metabolites, kinases and stress were activated by all three pathogens but with different patterns. The transcriptome profiles of Citrus sinensis identified host genes whose expression is affected by the presence of a pathogen in the phloem without producing symptoms (CTV-B2), and host genes whose expression leads to induction of symptoms in the plant (CTV-B6, CaLas-B232).Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2663-9) contains supplementary material, which is available to authorized users.

Co-infection of Sweet Orange with Severe and Mild Strains of Citrus tristeza virus Is Overwhelmingly Dominated by the Severe Strain on Both the Transcriptional and Biological Levels

“…In a previous study, transcriptional changes in sweet orange separately infected with CTV-B2 and CTV-B6 revealed a disturbance of circadian rhythm and ionic homeostasis, as well as activation of defense responses including modification of cell walls. The regulation of transcription, hormone, and secondary metabolism, are also affected by infection by CTV, but with differing patterns depending on the strain of CTV (Fu et al, 2016 ). In this study, transcriptome data were collected from sweet orange co-infected with both mild strain CTV-B2 and severe strain CTV-B6.…”

An Overview on Citrus Mal Secco Disease: Approaches and Strategies to Select Tolerant Genotypes in C. limon

“…Huanglongbing (HLB) Proteomics [142] Proteomics; nutrient analysis [143] Proteomics; enzyme activity; reverse genetic [144] Transcriptomics ( Microarray) [145] Transcriptomics (RNASeq) [137,138,146] Transcriptomics (RNASeq); proteomics; FISH [147] Transcriptomics (qPCR); physiology; hormone content [148,149] Phytophthora spp Metabolomics [150] Transcriptomics (RNASeq) [151] Xanthomonas citri Metabolomics [152] Proteomics [153,154] Proteomics; structural study; enzyme activity; reverse genetic [155] Citrus Tristeza Virus Metabolomics; physiology; hormone content [156,157] Proteomics; enzyme activity [158] Reverse genetic [159,160] Transcriptomics (qPCR) [161,162] Transcriptomics (RNASeq) [146,163] Mal secco Proteomics; metabolomics; physiology [164] Transcriptomics (SSH) [40] Unlike to other citrus diseases, such as Phytophthora spp., [137,138,142,145], sometimes together with multidisciplinary approaches [139,165,166], identifying many candidates and regulated genes. Other works are focused to identify potential genotypes tolerant to CTV by qPCR [162] or to highlight the differentially expressed transcripts (DETs) after combined infection with different virus (HLB and CTV) [146]. Chiesa et al [167] avoided when the leaves were shaded [64...…”

Transcriptome landscape of the developing olive fruit fly embryo delineated by Oxford Nanopore long-read RNA-Seq

“…Using our time-course data, we performed differential expression between successive timepoints using GFOLD [24] which is designed for samples without biological replicates. GFOLD log2 fold change has been shown to correlate well with qPCR-determined fold change [25]. Genes were coded as upregulated or downregulated using a Gfold cutoff of ±0.5.…”