Genome-Wide Identification of Phytophthora sojae-Associated microRNAs and Network in a Resistant and a Susceptible Soybean Germplasm

Guo, Na; Tahir, Ammara; Cui, Xiaoxia; Xu, Jianyu; Sun, Jixiang; Zhang, Nannan; Sun, Ruidong; Deng, Sushuang; Han, Xiaobin; Zhao, Jinming

doi:10.3390/agronomy12122922

Cited by 3 publications

(1 citation statement)

References 55 publications

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“…In Solanum lycopersicum , 207 known miRNAs and 67 novel miRNAs were identified in tomato response to P. infestans , of which 70 miRNAs were manifested to change significantly when inoculated with the pathogen [ 10 ]. In Glycine max , 528 known and 555 novel miRNAs were identified in the soybean response to P. sojae , of which 74 known and 75 novel miRNAs were differentially expressed in the resistant line Nannong10-1; and 55 known and 43 novel miRNAs were differentially expressed in the susceptible line 06-070583 [ 11 ]. In Capsicum annuum , 79 known miRNAs and 477 novel miRNAs were identified in pepper’s response against P. capsici infection [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

Integrative Transcriptome Analysis of mRNA and miRNA in Pepper’s Response to Phytophthora capsici Infection

Li,

Wang,

Guo

et al. 2024

Biology

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Phytophthora blight of pepper is a notorious disease caused by the oomycete pathogen Phytophthora capsici, which poses a great threat to global pepper production. MicroRNA (miRNA) is a class of non-coding small RNAs that regulate gene expressions by altering the translation efficiency or stability of targeted mRNAs, which play important roles in the regulation of a plant’s response to pathogens. Herein, time-series mRNA-seq libraries and small RNA-seq libraries were constructed using pepper roots from the resistant line CM334 and the susceptible line EC01 inoculated with P. capsici at 0, 6, 24, and 48 h post-inoculation, respectively. For mRNA-seq analysis, a total of 2159 and 2971 differentially expressed genes (DEGs) were identified in CM334 and EC01, respectively. For miRNA-seq analysis, 491 pepper miRNAs were identified, including 330 known miRNAs and 161 novel miRNAs. Among them, 69 and 88 differentially expressed miRNAs (DEMs) were identified in CM334 and EC01, respectively. Examination of DEMs and their targets revealed 22 regulatory networks, predominantly featuring up-regulated miRNAs corresponding to down-regulated target genes. Notably, these DEM-DEG regulatory networks exhibited significant overlap between CM334 and EC01, suggesting that they might contribute to pepper’s basal defense against P. capsici. Furthermore, five selected DEMs (miR166, miR1171, miR395, miR530 and miRN2) and their target genes underwent qRT-PCR validation, confirming a consistent negative correlation in the expression patterns of miRNAs and their targets. This comprehensive analysis provides novel insights into the regulatory networks of miRNAs and their targets, offering valuable contributions to our understanding of pepper’s defense mechanisms against P. capsici.

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Section: Introductionmentioning

confidence: 99%

Integrative Transcriptome Analysis of mRNA and miRNA in Pepper’s Response to Phytophthora capsici Infection

Li,

Wang,

Guo

et al. 2024

Biology

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Identification of self- and pathogen-targeted miRNAs from resistant and susceptible Theobroma cacao variety to black pod disease

Septiani,

Pramesti,

Ningsih

et al. 2024

Sci Rep

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Cacao (Theobroma cacao) is a highly valuable crop with growing demand in the global market. However, cacao farmers often face challenges posed by black pod disease caused by Phytophthora spp., with P. palmivora being the most dominant. Regulations of various gene expressions influence plant resistance to pathogens. One mechanism involves targeting the 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 defence 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. Extracted miRNA from resistant and susceptible varieties of T. Cacao was sequenced, identified, and matched to host and pathogen mRNA. In total, 54 known miRNAs from 40 miRNA families and 67 novel miRNAs were identified. Seventeen miRNAs were differentially expressed in susceptible variety compared to resistant one, with 9 miRNAs upregulated and 8 miRNAs downregulated. In T. cacao transcripts, the upregulated miRNAs were predicted to target several genes, including defence genes. The suppression of these defense genes can lead to a reduction in plant resistance against pathogen infection. In P. palmivora transcripts, the upregulated miRNAs were predicted to target several genes, including P. palmivora effector genes. In the future, limiting expression of miRNAs that target T. cacao’s defence genes and applying miRNAs that target P. palmivora effector genes hold promise for enhancing cacao plant resistance against P. palmivora infection.

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Identification of self- and pathogen-targeted miRNAs from resistant and susceptible Theobroma cacao variety to black pod disease

Septiani,

Pramesti,

Ningsih

et al. 2023

Preprint

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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 total, 54 known miRNAs from 40 miRNA families and 67 Novel miRNAs were identified. 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. 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.

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Genome-Wide Identification of Phytophthora sojae-Associated microRNAs and Network in a Resistant and a Susceptible Soybean Germplasm

Cited by 3 publications

References 55 publications

Integrative Transcriptome Analysis of mRNA and miRNA in Pepper’s Response to Phytophthora capsici Infection

Integrative Transcriptome Analysis of mRNA and miRNA in Pepper’s Response to Phytophthora capsici Infection

Identification of self- and pathogen-targeted miRNAs from resistant and susceptible Theobroma cacao variety to black pod disease

Identification of self- and pathogen-targeted miRNAs from resistant and susceptible Theobroma cacao variety to black pod disease

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