Integrating transcriptome and microRNA analysis identifies genes and microRNAs for AHO-induced systemic acquired resistance in N. tabacum

Chen, Yongdui; Dong, Jiahong; Bennetzen, Jeffrey L.; Zhong, Mingyu; Yang, Jun; Zhang, Jie; Li, Shun‐Lin; Hao, Xiao‐Jiang; Zhang, Zhiqing Philippe; Wang, Xuewen

doi:10.1038/s41598-017-12249-y

Cited by 27 publications

(31 citation statements)

References 84 publications

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“…The 24-nt miRNAs are the major class of miRNAs, which is similar to previous observation in tomato and N. tabacum [ 1 , 24 ]. This indicates that different species might have undergone similar evolution to expand genes coding for 24-nt miRNAs.…”

Section: Discussionsupporting

confidence: 87%

Identification of Arbuscular Mycorrhiza Fungi Responsive microRNAs and Their Regulatory Network in Maize

Zhu

Liu

et al. 2018

IJMS

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Maize can form symbiotic relationships with arbuscular mycorrhiza (AM) fungus to increase productivity and resistance, but the miRNAs in maize responsible for this process have not been discovered. In this study, 155 known and 28 novel miRNAs were identified by performing high-throughput sequencing of sRNA in maize roots colonized by AM fungi. Similar to the profiles in other AM-capable plants, a large proportion of identified maize miRNAs were 24 nt in length. Fourteen and two miRNAs were significantly down- and up-regulated in response to AM fungus Glomus intraradices inoculation, respectively, suggesting potential roles of these miRNAs in AM symbiosis. Interestingly, 12 of 14 significantly down-regulated known maize miRNAs belong to the miR399 family, which was previously reported to be involved in the interaction between Medicago truncatula and AM fungi. This result indicated that the miR399 family should regulate AM symbiosis conservatively across different plant lineages. Pathway and network analyses showed that the differentially expressed miRNAs might regulate lipid metabolism and phosphate starvation response in maize during the symbiosis process via their target genes. Several members of the miR399 family and the miR397 family should be involved in controlling the fatty acid metabolism and promoting lipid delivering from plants to AM fungi. To the best of our knowledge, this is the first report on miRNAs mediating fatty acids from plant to AM fungi. This study provides insight into the regulatory roles of miRNAs in the symbiosis between plants and AM fungi.

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Section: Discussionsupporting

confidence: 87%

Identification of Arbuscular Mycorrhiza Fungi Responsive microRNAs and Their Regulatory Network in Maize

Zhu

Liu

et al. 2018

IJMS

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“…In total, three RNA preps were obtained from three independent green-house experimental replicates for each time point for each variety under each condition. mRNA was isolated from total RNAs using polyT beads and used to construct an RNA-Seq library following previous procedures (Chen et al, 2017). Approximately 6 G bp RNA-Seq reads of paired-end 150 bp were generated from each sample with an Illumina X Ten platform.…”

Section: Rna-seq Data Generation Abundance Analysis and Annotationmentioning

confidence: 99%

Analysis of Dynamic Global Transcriptional Atlas Reveals Common Regulatory Networks of Hormones and Photosynthesis Across Nicotiana Varieties in Response to Long-Term Drought

Wang

Zhang

et al. 2020

Front. Plant Sci.

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Land plants evolve drought acclimation. Existing knowledge of gene regulation mainly comes from short-term drought treatment. However, common regulatory mechanism shared by multiple varieties under long-term drought is little explored. Here we investigated changes in physiology, hormones and transcriptomes in leaves of Nicotiana varieties K326 and Basma Xanthi with/without drought treatment at time courses spanning 1 month. Analyses of deep RNA-Seq data and further full-length Iso-Seq data revealed an atlas of dynamic changes of transcripts, spliced isoforms, gene expression, associated Gene Ontology, and metabolism pathways. Fewer differentially expressed genes (DEGs) were induced by drought in high tolerance variety than susceptible variety. Comparison among seven hormone signal pathways identified that genes in both abscisic acid and auxin signaling pathways were highly induced although specific genes were depended on the variety. Common hormone regulatory network analysis revealed that genes encoding clade A protein phosphatase 2C gene (PP2C) in abscisic acid pathway was the pivotal hub. Expressional regulation in photosynthesis was also common and variety specific. We conclude that long-term drought inducing gene regulatory networks of hormones and photosynthesis are variety dependent, and PP2C is the center of the common hormone regulatory network. Thus, this study improves our understanding of gene regulatory network in drought response.

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“…As a group of small, noncoding RNAs, siRNAs regulate post-transcriptional gene expression and participate in diverse biological processes, including resistance against stress [81][82][83][84]. In screening and study of a class of miRNAs related to Phytophthora sojae resistance in three soybean cultivars [85], the expression of miR393 in soybean significantly increases in response to P. sojae infection [86].…”

Section: Discussionmentioning

confidence: 99%

Host-Induced Gene Silencing of an Adenylate Kinase Gene Involved in Fungal Energy Metabolism Improves Plant Resistance to Verticillium dahliae

et al. 2020

Biomolecules

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Verticillium wilt, caused by the ascomycete fungus Verticillium dahliae (Vd), is a devastating disease of numerous plant species. However, the pathogenicity/virulence-related genes in this fungus, which may be potential targets for improving plant resistance, remain poorly elucidated. For the study of these genes in Vd, we used a well-established host-induced gene silencing (HIGS) approach and identified 16 candidate genes, including a putative adenylate kinase gene (VdAK). Transiently VdAK-silenced plants developed milder wilt symptoms than control plants did. VdAK-knockout mutants were more sensitive to abiotic stresses and had reduced germination and virulence on host plants. Transgenic Nicotiana benthamiana and Arabidopsis thaliana plants that overexpressed VdAK dsRNAs had improved Vd resistance than the wild-type. RT-qPCR results showed that VdAK was also crucial for energy metabolism. Importantly, in an analysis of total small RNAs from Vd strains isolated from the transgenic plants, a small interfering RNA (siRNA) targeting VdAK was identified in transgenic N. benthamiana. Our results demonstrate that HIGS is a promising strategy for efficiently screening pathogenicity/virulence-related genes of Vd and that VdAK is a potential target to control this fungus.

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Integrating transcriptome and microRNA analysis identifies genes and microRNAs for AHO-induced systemic acquired resistance in N. tabacum

Cited by 27 publications

References 84 publications

Identification of Arbuscular Mycorrhiza Fungi Responsive microRNAs and Their Regulatory Network in Maize

Identification of Arbuscular Mycorrhiza Fungi Responsive microRNAs and Their Regulatory Network in Maize

Analysis of Dynamic Global Transcriptional Atlas Reveals Common Regulatory Networks of Hormones and Photosynthesis Across Nicotiana Varieties in Response to Long-Term Drought

Host-Induced Gene Silencing of an Adenylate Kinase Gene Involved in Fungal Energy Metabolism Improves Plant Resistance to Verticillium dahliae

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