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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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Gap distribution among the scaffolds and unigenes found in ‘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 2: Gap distribution among the scaffolds and unigenes found in ‘Brazilian’ (susceptible wild-type) and cv ‘Nongke No 1’ (resistant mutant) following inoculation with Fusarium oxysporum f. sp. cubense tropical race 4.

Mentions: Approximately 51.4 million and 51.9 million 90-bp clean paired end (PE) reads (Accession No. SRA049253.1) were generated for ‘Brazilan’ and ‘Nongke No 1’, respectively (Table1). After the reads were assembled into contigs, scaffolds and clusters successively, they were analyzed for unigenes, of which more than 90,000 were present in ‘Brazilan’ and more than 100,000 in ‘Nongke No 1’ (Table2). After the unigenes were merged for DGE analysis, 88,161 non-redundant unigenes that partially overlapped were removed (Accession No for B. JV310321-378292; Accession No for NK. JV378293- 451650). During de novo assembly, small gaps within the scaffolds containing the least number of unknown nucleotides (Ns) were filled in, permitting more than half of the gaps to be filled. The gap distribution for unigenes is shown in Figure2.


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)

Gap distribution among the scaffolds and unigenes found in ‘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 2: Gap distribution among the scaffolds and unigenes found in ‘Brazilian’ (susceptible wild-type) and cv ‘Nongke No 1’ (resistant mutant) following inoculation with Fusarium oxysporum f. sp. cubense tropical race 4.
Mentions: Approximately 51.4 million and 51.9 million 90-bp clean paired end (PE) reads (Accession No. SRA049253.1) were generated for ‘Brazilan’ and ‘Nongke No 1’, respectively (Table1). After the reads were assembled into contigs, scaffolds and clusters successively, they were analyzed for unigenes, of which more than 90,000 were present in ‘Brazilan’ and more than 100,000 in ‘Nongke No 1’ (Table2). After the unigenes were merged for DGE analysis, 88,161 non-redundant unigenes that partially overlapped were removed (Accession No for B. JV310321-378292; Accession No for NK. JV378293- 451650). During de novo assembly, small gaps within the scaffolds containing the least number of unknown nucleotides (Ns) were filled in, permitting more than half of the gaps to be filled. The gap distribution for unigenes is shown in Figure2.

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