Integrated Transcriptomics and Metabolomics Analyses Provide Insights Into the Response of Chongyi Wild Mandarin to Candidatus Liberibacter Asiaticus Infection

Abstract

Candidatus Liberibacter asiaticus (CLas) is the causative agent of Huanglongbing (HLB), which has caused great economic losses to the citrus industry. The molecular mechanism of the host response to CLas in wild citrus germplasm has been reported less. Eighteen weeks after inoculation via grafting, all the CLas-inoculated Chongyi wild mandarin (Citrus reticulata) were positive and showed severe anatomical aberrations, suggesting its susceptibility to HLB. Transcriptomics and metabolomics analyses of leaves, barks, and roots from mock-inoculated (control) and CLas-inoculated seedlings were performed. Comparative transcriptomics identified 3,628, 3,770, and 1,716 differentially expressed genes (DEGs) between CLas-infected and healthy tissues in the leaves, barks, and roots, respectively. The CLas-infected tissues had higher transcripts per kilobase per million values and more genes that reached their maximal expression, suggesting that HLB might cause an overall increase in transcript accumulation. However, HLB-triggered transcriptional alteration showed tissue specificity. In the CLas-infected leaves, many DEGs encoding immune receptors were downregulated. In the CLas-infected barks, nearly all the DEGs involved in signaling and plant-pathogen interaction were upregulated. In the CLas-infected roots, DEGs encoding enzymes or transporters involved in carotenoid biosynthesis and nitrogen metabolism were downregulated. Metabolomics identified 71, 62, and 50 differentially accumulated metabolites (DAMs) in the CLas-infected leaves, barks and roots, respectively. By associating DEGs with DAMs, nitrogen metabolism was the only pathway shared by the three infected tissues and was depressed in the CLas-infected roots. In addition, 26 genes were determined as putative markers of CLas infection, and a hypothesized model for the HLB susceptibility mechanism in Chongyi was proposed. Our study may shed light on investigating the molecular mechanism of the host response to CLas infection in wild citrus germplasm.

Nontargeted metabolomics-based multiple machine learning modeling boosts early accurate detection for citrus Huanglongbing

“…Overall, most of the metabolites in the pathway of carbon fixation in photosynthetic organisms were downregulated, and those distributed in other pathways were upregulated (see Figure 2 and Supplementary Data S3 ). This result is quite consistent with the previous reports [ 19 , 39 – 45 ].…”

“…As shown in Figure 4a , six metabolites located on the pathway of carbon fixation in photosynthetic organisms, including pyruvate, L-alanine, L-aspartate, L-phenylalanine, phenylpyruvate and sedoheptulose were detected to be significantly downregulated in the infected group compared to the healthy group. Peng et al [ 39 ] reported that the leaves of “Chongyi” wild mandarin ( Citrus reticulata ) showed downregulation of transcripts and metabolites relevant to carbon fixation after 18 weeks of graft-inoculation with Ca Las-infected buds by the integrated transcriptomics and metabolomics analyses. Wei et al [ 40 ] also reported that the number of differentially expressed genes (DEGs) related to photosynthesis detected in “Valencia” orange ( C. sinensis ) at one and five days of post- Ca Las-infected psyllid infection was greatly less than that of healthy psyllid infection.…”

Metabolomic Analysis Revealed Distinct Physiological Responses of Leaves and Roots to Huanglongbing in a Citrus Rootstock

“…Sugars not only provide energy for plants’ growth and defense responses, but also act as signals in modulating plants’ adaptation to internal and external stimuli, including invading pathogens. Several of the previous investigations have revealed that the level of different types of sugars were altered in the HLB-infected tissues, such as leaves, barks, roots, and fruits, but the trend varied depending on the variety, tissues, and disease progression [ 17 , 22 , 30 , 42 , 43 , 44 ]. Generally, the sugar contents were decreased after infection.…”

“…Generally, the sugar contents were decreased after infection. Peng et al [ 22 ] explored the metabolomic changes of the Chongyi wild mandarin in the positive- or mock-inoculated plants. The sucrose levels were increased in both the infected leaves and barks, but did not change in the roots.…”

“…Besides these visible alterations, extensive systemic physiological and molecular changes were also reported as being uncovered through transcriptomic, proteomic, or metabolomic approaches. In particular, the gene expression and proteomic profile comparison between HLB-tolerant and sensitive varieties revealed several candidate targets of CLas, and have inferred the possible pathways that the host plant utilizes to fight the bacteria invasion [ 11 , 12 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 ]. The components involved in the defense system, cell wall integrity, energy production, and catabolism were among the most disturbed pathways.…”