Infection by Pseudocercospora musae leads to an early reprogramming of the Musa paradisiaca defense transcriptome

Abstract

Deep sequencing technologies such as RNA sequencing can help unravel mechanisms governing defense or resistance responses in plant-pathogen interactions. Several studies have been carried out to investigate the transcriptomic changes in Musa germplasm against Yellow Sigatoka disease, but the defense response of Musa paradisiaca has not been investigated so far. We carried out transcriptome sequencing of M. paradisiaca var. Kachkal infected with the pathogen Pseudocercospora musae and found that a vast set of genes were upregulated while many genes were downregulated in the resistant cultivar as a result of infection. After transcriptome assembly and differential gene expression analysis, 429 upregulated and 156 downregulated genes were filtered out (considering fold change ± 2, p < 0.01). Functional annotation of the differentially expressed genes (DEGs) enriched the upregulated genes into 49 gene ontology (GO) classes of biological processes (BP), 20 classes of molecular function (MF) and 9 classes of cellular component (CC). Similarly, the downregulated genes were classified into 35 GO classes of BP, 28 classes of MF and 6 classes of CC. The KEGG enrichment analysis revealed that the upregulated genes were most highly represented in 'metabolic' and 'biosynthesis of secondary metabolites' pathways. Additionally, 'plant hormone signal transduction', 'plant-pathogen interaction' and 'phenylpropanoid biosynthesis' pathways were also significantly enriched indicating their involvement in resistance responses against the pathogen. The RNA-seq analysis also depicts that a range of important defense-related genes are modulated as a result of infection, all of which are responsible for either mediating or activating resistance responses in the host. We studied and validated the expression profiles of ten important defense-related genes potentially involved in conferring resistance to the pathogen through qRT-PCR. Almost all the selected defense-related genes were found to be highly and significantly upregulated within 24 h post inoculation (hpi) and for some genes, the expression remained consistently high till the later time point of 72 hpi. These results, thus, indicate that the infection by P. musae leads to a rapid reprogramming of the defense transcriptome of the resistant banana cultivar. The defense-related genes identified to be modulated in response to infection are important not only for pathogen recognition and perception but also for activation and persistence of defense in the host.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-022-03245-9.

Keywords: Differentially expressed genes; Host–pathogen interaction; Musa paradisiaca; Sigatoka; Transcriptome.

Fig. 1

Heat map of differentially expressed genes (DEGs) in M. paradisiaca upon P. musae infection

Fig. 2

Graphical representation of the top 20 GO classes, under which the genes upregulated during the M. paradisiaca–P. musae interaction were enriched

Fig. 3

Graphical representation of the top 20 GO classes, under which the genes downregulated during the M. paradisiaca–P. musae interaction were enriched

Fig. 4

Venn diagram depicting GO distribution showing numbers of overlapping genes (upregulated and downregulated genes) among the classes of biological process, molecular function and cellular component

Fig. 5

Visualization of DEGs involved in the plant–pathogen interaction pathway in M. paradisiaca upon P. musae infection at 48 hpi. White box or no color fill means no DEG was assigned to that ontology term and red represents upregulation

Fig. 6

Visualization of DEGs involved in the plant hormone signal transduction pathway in M. paradisiaca upon P. musae infection at 48 hpi White box or no color fill means no DEG was assigned to that ontology term and red represents upregulation

Fig. 7

qRT-PCR-based differential expression analysis of selected defense-related genes upregulated in M. paradisiaca in response to infection by P. musae: (i) PR1 (ii) PR4, (iii) PR-like, (iv) GLP (v) OMT, (vi) Ras-LRR, (vii) LRR-STK, (viii) UGP, (ix) ERF, (x) WRKY, across 24, 48 and 72 hpi using (xi) Tubulin (as internal control) (Y axis –RQ obtained from RT-PCR analysis of the genes; X axis samples at different conditions viz. control and infected leaf tissue at 24 hpi, 48 hpi and 72 hpi)