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Transcriptome profiling of resistant and susceptible Cavendish banana roots following inoculation with Fusarium oxysporum f. sp. cubense tropical race 4.

Li CY, Deng GM, Yang J, Viljoen A, Jin Y, Kuang RB, Zuo CW, Lv ZC, Yang QS, Sheng O, Wei YR, Hu CH, Dong T, Yi GJ - BMC Genomics (2012)

Bottom Line: Expression patterns of genes involved in pathogen-associated molecular pattern (PAMP) recognition, activation of effector-triggered immunity (ETI), ion influx, and biosynthesis of hormones as well as pathogenesis-related (PR) genes, transcription factors, signaling/regulatory genes, cell wall modification genes and genes with other functions were analyzed and compared.This study generated a substantial amount of banana transcript sequences and compared the defense responses against Foc TR4 between resistant and susceptible Cavendish bananas.The results contribute to the identification of candidate genes related to plant resistance in a non-model organism, banana, and help to improve the current understanding of host-pathogen interactions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.

ABSTRACT

Background: Fusarium wilt, caused by the fungal pathogen Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), is considered the most lethal disease of Cavendish bananas in the world. The disease can be managed in the field by planting resistant Cavendish plants generated by somaclonal variation. However, little information is available on the genetic basis of plant resistance to Foc TR4. To a better understand the defense response of resistant banana plants to the Fusarium wilt pathogen, the transcriptome profiles in roots of resistant and susceptible Cavendish banana challenged with Foc TR4 were compared.

Results: RNA-seq analysis generated more than 103 million 90-bp clean pair end (PE) reads, which were assembled into 88,161 unigenes (mean size = 554 bp). Based on sequence similarity searches, 61,706 (69.99%) genes were identified, among which 21,273 and 50,410 unigenes were assigned to gene ontology (GO) categories and clusters of orthologous groups (COG), respectively. Searches in the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) mapped 33,243 (37.71%) unigenes to 119 KEGG pathways. A total of 5,008 genes were assigned to plant-pathogen interactions, including disease defense and signal transduction. Digital gene expression (DGE) analysis revealed large differences in the transcriptome profiles of the Foc TR4-resistant somaclonal variant and its susceptible wild-type. Expression patterns of genes involved in pathogen-associated molecular pattern (PAMP) recognition, activation of effector-triggered immunity (ETI), ion influx, and biosynthesis of hormones as well as pathogenesis-related (PR) genes, transcription factors, signaling/regulatory genes, cell wall modification genes and genes with other functions were analyzed and compared. The results indicated that basal defense mechanisms are involved in the recognition of PAMPs, and that high levels of defense-related transcripts may contribute to Foc TR4 resistance in banana.

Conclusions: This study generated a substantial amount of banana transcript sequences and compared the defense responses against Foc TR4 between resistant and susceptible Cavendish bananas. The results contribute to the identification of candidate genes related to plant resistance in a non-model organism, banana, and help to improve the current understanding of host-pathogen interactions.

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Transcriptomic comparison of the unigenes CEBiP (left) and the Elicitor-responsive protein (right) between ‘Brazilian’ (susceptible wild-type) and cv ‘Nongke No 1’ (resistant mutant) following inoculation with Fusarium oxysporum f. sp. cubense tropical race 4.
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Figure 5: Transcriptomic comparison of the unigenes CEBiP (left) and the Elicitor-responsive protein (right) between ‘Brazilian’ (susceptible wild-type) and cv ‘Nongke No 1’ (resistant mutant) following inoculation with Fusarium oxysporum f. sp. cubense tropical race 4.

Mentions: To analyze the global transcriptional changes in banana infected with Foc TR4, the method described by Audic et al.[5] was applied to identify differentially expressed genes from the normalized DGE data by pairwise comparisons between the wild-type (‘Brazilian’) and mutant banana (‘Nongke No 1’) at different time points after infection. To characterize the functional consequences of gene expression changes associated with infection with Foc in the resistant mutant, pathway analysis of differentially expressed genes was performed, based on the KEGG database using the two-side Fisher’s exact test. Nine metabolic pathways that are related to immunity were selected for further analysis. The selected pathways included Perception of PAMPs by Pattern Recognition Receptors (PRRs), Effector-triggered immunity (ETI), Ion fluxes, Transcription factors (TFs), Oxidative burst, Pathogenesis-related proteins (PRs), Programmed cell death (PCD), Plant hormones and Cell wall modification (Figure4). Fifty-two types of differentially expressed genes with known or implicated functions were identified (Additional file2: Table S2). All differentially expressed unigenes are involved in the recognition of PAMPs, and the high accumulated levels of defense-related transcripts may contribute to Foc TR4 resistance in banana (Additional file2: Table S2; Additional file3: Table S3). Transcriptomic comparison of two differentially expressed unigenes between’Brazilian’ and ‘Nongke No 1’ is shown in Figure5. Based on the above results, a schematic illustration of plant defense in Cavendish banana against Foc TR4 was constructed (Figure6).


Transcriptome profiling of resistant and susceptible Cavendish banana roots following inoculation with Fusarium oxysporum f. sp. cubense tropical race 4.

Li CY, Deng GM, Yang J, Viljoen A, Jin Y, Kuang RB, Zuo CW, Lv ZC, Yang QS, Sheng O, Wei YR, Hu CH, Dong T, Yi GJ - BMC Genomics (2012)

Transcriptomic comparison of the unigenes CEBiP (left) and the Elicitor-responsive protein (right) between ‘Brazilian’ (susceptible wild-type) and cv ‘Nongke No 1’ (resistant mutant) following inoculation with Fusarium oxysporum f. sp. cubense tropical race 4.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3473311&req=5

Figure 5: Transcriptomic comparison of the unigenes CEBiP (left) and the Elicitor-responsive protein (right) between ‘Brazilian’ (susceptible wild-type) and cv ‘Nongke No 1’ (resistant mutant) following inoculation with Fusarium oxysporum f. sp. cubense tropical race 4.
Mentions: To analyze the global transcriptional changes in banana infected with Foc TR4, the method described by Audic et al.[5] was applied to identify differentially expressed genes from the normalized DGE data by pairwise comparisons between the wild-type (‘Brazilian’) and mutant banana (‘Nongke No 1’) at different time points after infection. To characterize the functional consequences of gene expression changes associated with infection with Foc in the resistant mutant, pathway analysis of differentially expressed genes was performed, based on the KEGG database using the two-side Fisher’s exact test. Nine metabolic pathways that are related to immunity were selected for further analysis. The selected pathways included Perception of PAMPs by Pattern Recognition Receptors (PRRs), Effector-triggered immunity (ETI), Ion fluxes, Transcription factors (TFs), Oxidative burst, Pathogenesis-related proteins (PRs), Programmed cell death (PCD), Plant hormones and Cell wall modification (Figure4). Fifty-two types of differentially expressed genes with known or implicated functions were identified (Additional file2: Table S2). All differentially expressed unigenes are involved in the recognition of PAMPs, and the high accumulated levels of defense-related transcripts may contribute to Foc TR4 resistance in banana (Additional file2: Table S2; Additional file3: Table S3). Transcriptomic comparison of two differentially expressed unigenes between’Brazilian’ and ‘Nongke No 1’ is shown in Figure5. Based on the above results, a schematic illustration of plant defense in Cavendish banana against Foc TR4 was constructed (Figure6).

Bottom Line: Expression patterns of genes involved in pathogen-associated molecular pattern (PAMP) recognition, activation of effector-triggered immunity (ETI), ion influx, and biosynthesis of hormones as well as pathogenesis-related (PR) genes, transcription factors, signaling/regulatory genes, cell wall modification genes and genes with other functions were analyzed and compared.This study generated a substantial amount of banana transcript sequences and compared the defense responses against Foc TR4 between resistant and susceptible Cavendish bananas.The results contribute to the identification of candidate genes related to plant resistance in a non-model organism, banana, and help to improve the current understanding of host-pathogen interactions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.

ABSTRACT

Background: Fusarium wilt, caused by the fungal pathogen Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), is considered the most lethal disease of Cavendish bananas in the world. The disease can be managed in the field by planting resistant Cavendish plants generated by somaclonal variation. However, little information is available on the genetic basis of plant resistance to Foc TR4. To a better understand the defense response of resistant banana plants to the Fusarium wilt pathogen, the transcriptome profiles in roots of resistant and susceptible Cavendish banana challenged with Foc TR4 were compared.

Results: RNA-seq analysis generated more than 103 million 90-bp clean pair end (PE) reads, which were assembled into 88,161 unigenes (mean size = 554 bp). Based on sequence similarity searches, 61,706 (69.99%) genes were identified, among which 21,273 and 50,410 unigenes were assigned to gene ontology (GO) categories and clusters of orthologous groups (COG), respectively. Searches in the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) mapped 33,243 (37.71%) unigenes to 119 KEGG pathways. A total of 5,008 genes were assigned to plant-pathogen interactions, including disease defense and signal transduction. Digital gene expression (DGE) analysis revealed large differences in the transcriptome profiles of the Foc TR4-resistant somaclonal variant and its susceptible wild-type. Expression patterns of genes involved in pathogen-associated molecular pattern (PAMP) recognition, activation of effector-triggered immunity (ETI), ion influx, and biosynthesis of hormones as well as pathogenesis-related (PR) genes, transcription factors, signaling/regulatory genes, cell wall modification genes and genes with other functions were analyzed and compared. The results indicated that basal defense mechanisms are involved in the recognition of PAMPs, and that high levels of defense-related transcripts may contribute to Foc TR4 resistance in banana.

Conclusions: This study generated a substantial amount of banana transcript sequences and compared the defense responses against Foc TR4 between resistant and susceptible Cavendish bananas. The results contribute to the identification of candidate genes related to plant resistance in a non-model organism, banana, and help to improve the current understanding of host-pathogen interactions.

Show MeSH