Dataset Information

Comparative analysis of the transcriptomes of the calyx abscission zone of sweet orange insights into the huanglongbing-associated fruit abscission.

ABSTRACT: Citrus greening disease or huanglongbing (HLB) is associated with excessive pre-harvest fruit drop. To understand the mechanisms of the HLB-associated fruit abscission, transcriptomes were analyzed by RNA sequencing of calyx abscission zones (AZ-C) of dropped "Hamlin" oranges from HLB-diseased trees upon shaking the trees (Dd), retained oranges on diseased trees (Rd), dropped oranges from healthy shaken trees (Dh), and retained oranges on healthy trees (Rh). Cluster analysis of transcripts indicated that Dd had the largest distances from all other groups. Comparisons of transcriptomes revealed 1047, 1599, 813, and 764 differentially expressed genes (DEGs) between Dd/Rd, Dd/Dh, Dh/Rh, and Rd/Rh. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses indicated hormone signaling, defense response, and secondary metabolism were involved in HLB-associated fruit abscission. Ethylene (ET) and jasmonic acid (JA) synthesis/signaling-related genes were upregulated in Dd, while other phytohormone-related genes were generally downregulated. In addition, genes related to JA/ET-activated defense response were upregulated in Dd as well. Consistent with the phytohormone gene expression data, increased levels (p?

SUBMITTER: Zhao W

PROVIDER: S-EPMC6544638 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Comparative analysis of the transcriptomes of the calyx abscission zone of sweet orange insights into the huanglongbing-associated fruit abscission.

Zhao Wei W Baldwin Elizabeth A EA Bai Jinhe J Plotto Anne A Irey Mike M

Horticulture research 20190601

Citrus greening disease or huanglongbing (HLB) is associated with excessive pre-harvest fruit drop. To understand the mechanisms of the HLB-associated fruit abscission, transcriptomes were analyzed by RNA sequencing of calyx abscission zones (AZ-C) of dropped "Hamlin" oranges from HLB-diseased trees upon shaking the trees (Dd), retained oranges on diseased trees (Rd), dropped oranges from healthy shaken trees (Dh), and retained oranges on healthy trees (Rh). Cluster analysis of transcripts indic ...[more]

PMID: 31231529

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Project description:Citrus greening or huanglongbing (HLB) disease is caused by Candidatus liberibacter asiaticus (CLas) and associated with an increase in pre-harvest fruit drop, for which the molecular mechanisms remain unknown. In order to understand the molecular basis of the HLB-associated fruit abscission, by means of RNA-Sequencing analysis (RNA-Seq), transcriptomes in citrus calyx abscission zones were analyzed and compared among fruit dropped (D) or retained (R) from healthy (h) or HLB-diseased (d) trees upon shaking the trees. Cluster analysis based on the transcript reads indicates that dropped fruit from HLB-diseased trees (Dd) have largest distances from all other groups. Differentially expressed genes (DEGs) were identified between Dd and Rd, Dh and Rh, Rd and Rh, Dd and Dh. Wilcoxon test of the whole dataset of DEGs revealed that consistently up-regulated genes in Dd versus Rd and Dd versus Dh are in the functional categories of “secondary metabolism, lipid metabolism and hormone-ethylene and –jasmonate”; while those down-regulated genes didn’t show clear pattern of regulation. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses indicated that the significant biological processes or pathways involved in HLB-related fruit abscission were those related to defense response, secondary metabolism and hormone signaling. Among them, “response to chitin” was the most significant (p= 9.95E-13) biological process, and “jasmonic acid biosynthesis” was the most significant (p= 4.6E-5) pathway. Genes related to synthesis and signaling of ethylene (ET) and jasmonate (JA) were consistently up-regulated, while abscisic acid, auxin, brassinosteroid, cytokinin, and gibberellin were generally down-regulated in Dd; but not in Dh. Consistent with the transcriptomic data, fruit ethylene production was detected in two third of the Dd fruit, but none of Rd, Dh or Rh fruit. And, in agreement with the hormone expression profiles, substantial numbers of downstream JA/ET-responsive defense related genes were up-regulated in Dd, but not in Dh. Thirty representative DEGs covering categories of hormone, secondary metabolism, and JA/ET responsive defense responses were verified by qRT-PCR. The results indicate that HLB-associated pre-harvest fruit abscission is mediated by JA/ET signaling, which has been known to be triggered by infection of necrotrophic pathogens.

Project description:To evaluate the transcriptome response of roots towards Hoagland solution of two-year-old healthy (C) and HLB-affected (T) sweet orange (Citrus sinensis L.) cultivar Midsweet grafted on Kuharskei Carrizo rootstock at three different time points; D1 (at the start of the experiment), D2 (After 3 days of Hoagland solution), D3 (After nine days of Hoagland solution), were performed using RNA sequencing analysis. A total of 9, 19, and 2324 DEGs were expressed in HLB-affected and healthy trees feeder roots on D1, D2, and D3, respectively. Due to a small number of DEGs in HLB-affected and healthy trees roots on D1 and D2, enrichment analysis could not be performed. At D3, Gene Ontology (GO) enrichment analysis was performed using upregulated and downregulated DEGs in HLB-affected roots compared to healthy roots. For the upregulated DEGs in HLB-affected roots, the most enriched biological GO categories were related to transport, cellular amino acid metabolic process, oxoacid metabolic process, organic acid metabolic processes, phenylpropanoid biosynthesis process, response to carbohydrate stimulus, ethylene and the jasmonic acid-mediated signaling pathway, and regulation of plant hormone. The biological GO categories based on the number of DEGs associated with downregulated DEGs were the developmental process, phosphate metabolic process, protein modification process, defense response, growth, cell cycle, cell death, and ABA-mediated signaling pathway. The results of this study strongly suggest; although, the reduced biomass limits the nutrient uptake capacity in the plants as a whole, so in order to compensate for reduced root to shoot ratio the existing root undergo anatomical and transcriptomic changes to improve nutrient uptake efficiency to meet the nutrient demand of shoot systems. It is likely that higher inputs of energy in nutrient uptake possibly results in reducing the root longevity of HLB-affected trees. Good nutrition management practices are critical for the survival of HLB-affected trees as the availability and uptake of nutrients allow HLB-affected trees in response to abiotic and biotic stress.

Project description:BackgroundThe objective of this study was to characterize molecular mechanism of calyx persistence in Korla fragrant pear by transcriptome and small RNA sequencing. Abscission zone tissues of flowers at three stages (the first, fifth and ninth days of the late bloom stage), with 50 mg/L GA3 (calyx persistence treatment, C_1, C_5, C_9) or 500 mg/L PP333 (calyx abscission treatment, T_1, T_5, T_9), were collected and simultaneously conducted transcriptome and small RNA sequencing.ResultsThrough association analysis of transcriptome and small RNA sequencing, mRNA-miRNA network was conducted. Compared calyx persistence groups with calyx abscission groups during the same stage, 145, 56 and 150 mRNA-miRNA pairs were obtained in C_1 vs T_1, C_5 vs T_5 and C_9 vs T_9, respectively; When C_1 compared with C_5 and C_9, 90 and 506 mRNA-miRNA pairs were screened respectively, and 255 mRNA-miRNA pairs were obtained from the comparison between C_5 and C_9; When T_1 compared with the T_5 and T_9, respectively, 206 and 796 mRNA-miRNA pairs were obtained, and 383 mRNA-miRNA pairs were obtained from the comparison between T_5 and T_9. These mRNAs in miRNA-mRNA pairs were significantly enriched into the terpenoid backbone biosynthesis, photosynthesis - antenna proteins, porphyrin and chlorophyll metabolism, carotenoid biosynthesis, zeatin biosynthesis and plant hormone signal transduction. In addition, we obtained some key genes from miRNA-mRNA pairs that may be associated with calyx abscission, including protein phosphatase 2C (psi-miR394a-HAB1), receptor-like protein kinase (psi-miR396a-5p-HERK1), cellulose synthase-like protein D3 (psi-miR827-CSLD3), beta-galactosidase (psi-miR858b-β-galactosidase), SPL-psi-miR156j/157d, abscisic acid 8'-hydroxylase 1 (psi-miR396a-5p-CYP707A1) and auxin response factor (psi-miR160a-3p-ARF6, psi-miR167d-ARF18, psi-miR167a-5p-ARF25), etc. CONCLUSION: By integrated analysis mRNA and miRNA, our study gives a better understanding of the important genes and regulation pathway related to calyx abscission in Korla fragrant pear. We have also established the network of miRNA-mRNA pairs to learn about precise regulation of miRNA on calyx abscission.

Dataset Information

Comparative analysis of the transcriptomes of the calyx abscission zone of sweet orange insights into the huanglongbing-associated fruit abscission.

Publications

Comparative analysis of the transcriptomes of the calyx abscission zone of sweet orange insights into the huanglongbing-associated fruit abscission.

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