Transcriptomic analyses reveal physiological changes in sweet orange roots affected by citrus blight

Changyong Zhou,Shimin Fu,Ronald H Brlansky,John S Hartung,Jonathan Shao,Avijit Roy

doi:10.1186/s12864-019-6339-0

Abstract

BackgroundCitrus blight is a very important progressive decline disease of commercial citrus. The etiology is unknown, although the disease can be transmitted by root grafts, suggesting a viral etiology. Diagnosis is made by demonstrating physical blockage of xylem cells that prevents the movement of water. This test was used to identify symptomatic trees from four commercial groves in Florida. Total RNA extracts of phloem-enriched scaffold root tissues were prepared from seven trees that failed to take up water and from one healthy tree. These RNA extracts were used for transcriptomic analyses using paired end RNA-Seq from an Illumina 2500 system. The expression of transcripts annotated as polyprotein of citrus endogenous pararetrovirus were estimated by both RT-qPCR and RNA-Seq.ResultsTranscripts from seven RNA-Seq libraries from trees affected by citrus blight were compared to a control tree. 129–148 million RNA fragments (two paired-end reads/fragment) were generated per library and were mapped to the sweet orange reference genome. In response to citrus blight stress, genes encoding aquaporins, proteins with water channel activity and several cellulose synthase genes were down-regulated, whereas genes involved in lignin and glucosinolate biosynthesis were up-regulated. Transcripts encoding proteins in pathways of carbohydrate metabolism, nucleotide synthesis, signaling, hormone metabolism, secondary metabolism, transport, and biotic stress pathways were overwhelmingly down regulated in all libraries.ConclusionReduced water intake and xylem plugging were observed in the trees tested and the changes in their transcriptome were analyzed. Plants adapted to reduced water flow by regulating primary and secondary metabolism, nuclear transport and hormone associated pathways. The patterns of energy generation, transcription, translation and protein degradation were consistent with irreversible decline. The down regulation of cellulose synthase transcripts and up regulation of transcripts related to lignin production likely lead to an imbalance in the pathways leading to wood formation, and may lead to the blockage of the xylem vessels seen as the cardinal symptom of citrus blight. Transcripts of a pararetrovirus were elevated in the transcriptome of roots used in this study.

Highlights

Citrus blight (CB) was described in Florida more than a century ago and 50 years of research on CB was reviewed in 1936 [41] and more recently [16]
Demonstration of xylem plugging in blight-affected trees Symptoms observed on the CB affected trees included severe twig dieback and defoliation, as seen on Hamlin sweet orange grafted on citrumelo rootstock (X Citroncirus spp.) (Fig. 1a)
The ability of the trees to take up water into their trunks by syringe injection was measured to select trees from which root samples were taken to prepare RNA extracts

Summary

Introduction

Citrus blight (CB) was described in Florida more than a century ago and 50 years of research on CB was reviewed in 1936 [41] and more recently [16]. Diagnosis is made by demonstrating physical blockage of xylem cells that prevents the movement of water. This test was used to identify symptomatic trees from four commercial groves in Florida. Total RNA extracts of phloem-enriched scaffold root tissues were prepared from seven trees that failed to take up water and from one healthy tree. These RNA extracts were used for transcriptomic analyses using paired end RNA-Seq from an Illumina 2500 system. The expression of transcripts annotated as polyprotein of citrus endogenous pararetrovirus were estimated by both RT-qPCR and RNA-Seq

Methods

Results

Discussion

Conclusion