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Series GSE244955 Query DataSets for GSE244955
Status Public on Feb 14, 2024
Title Identification of self- and pathogen-targeted miRNAs from resistant and susceptible Theobroma cacao variety to black pod disease
Organism Theobroma cacao
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Cacao (Theobroma cacao) is a highly valuable crop with growing demands in the global market. However, cacao farmers often face challenges posed by black pod disease caused by Phytophthora spp. with P. palmivora as the most dominant. Regulations of various gene expression influence plant resistance to pathogens. One mechanism involves targeting mRNA of virulence genes in the invading pathogens, suppressing their infection. However, resistance also could be suppressed by plant-derived miRNAs that target their own defense genes. The objective of this study is to identify differentially expressed miRNAs in black pod resistant and susceptible Cacao varieties and to predict their targets in T. cacao and P. palmivora transcripts. In our research, 54 known miRNAs from 40 miRNA families and 67 Novel miRNAs were identified. As much as 17 miRNAs were differentially expressed in susceptible variety compared to resistant one, with 9 miRNAs were upregulated and 8 miRNAs downregulated. In T. cacao transcripts, the upregulated miRNAs were predicted to target several genes, including defense genes. The suppression of these defense genes can lead to a reduction in plant resistance against pathogen infection. While in P. palmivora transcripts, the upregulated miRNAs were predicted to target several genes, including P. palmivora effector genes and other important metabolism activities genes. In the future, limiting expression of miRNAs that target T. cacao's defense genes and applying miRNAs that target P. palmivora effector genes hold promise for enhancing cacao plant resistance against P. palmivora infection.
 
Overall design Identifying cacao pod miRNAs in resistant (TS858) and susceptible (Sulawesi 1) varieties with 2 replicates respectively.
Performed miRNA quantification using Rsubread and differentially expressed miRNA analysis using DeSeq2.
 
Contributor(s) Septiani P, Meitha K, Pramesti Y, Ningsih DU, Pancaningtyas S
Citation(s) 38332251
Submission date Oct 10, 2023
Last update date Feb 15, 2024
Contact name Popi Septiani
Organization name Institut Teknologi Bandung
Department School of Life Sciences and Technology
Street address Jl. Ganesha no. 10
City Bandung
State/province West Java
ZIP/Postal code 40116
Country Indonesia
 
Platforms (1)
GPL33828 Illumina NovaSeq 6000 (Theobroma cacao)
Samples (4)
GSM7832522 Pod, resistance, replicate 1
GSM7832523 Pod, resistance, replicate 2
GSM7832524 Pod, susceptible replicate 1
Relations
BioProject PRJNA1026493

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Supplementary file Size Download File type/resource
GSE244955_RAW.tar 10.0 Kb (http)(custom) TAR (of TXT)
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Raw data are available in SRA

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