Dataset Information

Transcriptomic Profiling of Populus Roots Challenged with Fusarium Reveals Differential Responsive Patterns of Invertase and Invertase Inhibitor-Like Families within Carbohydrate Metabolism.

ABSTRACT: Fusarium solani (Fs) is one of the notorious necrotrophic fungal pathogens that cause root rot and vascular wilt, accounting for the severe loss of Populus production worldwide. The plant-pathogen interactions have a strong molecular basis. As yet, the genomic information and transcriptomic profiling on the attempted infection of Fs remain unavailable in a woody model species, Populus trichocarpa. We used a full RNA-seq transcriptome to investigate the molecular interactions in the roots with a time-course infection at 0, 24, 48, and 72 h post-inoculation (hpi) of Fs. Concomitantly, the invertase and invertase inhibitor-like gene families were further analyzed, followed by the experimental evaluation of their expression patterns using quantitative PCR (qPCR) and enzyme assay. The magnitude profiles of the differentially expressed genes (DEGs) were observed at 72 hpi inoculation. Approximately 839 genes evidenced a reception and transduction of pathogen signals, a large transcriptional reprogramming, induction of hormone signaling, activation of pathogenesis-related genes, and secondary and carbohydrate metabolism changes. Among these, a total of 63 critical genes that consistently appear during the entire interactions of plant-pathogen had substantially altered transcript abundance and potentially constituted suitable candidates as resistant genes in genetic engineering. These data provide essential clues in the developing new strategies of broadening resistance to Fs through transcriptional or translational modifications of the critical responsive genes within various analyzed categories (e.g., carbohydrate metabolism) in Populus.

SUBMITTER: Su T

PROVIDER: S-EPMC7911864 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:BACKGROUND:Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long ncRNAs (lncRNAs) and circular RNAs (circRNAs), accomplish remarkable variety of biological functions. However, the composition of ncRNAs and their interactions with coding RNAs in modulating and controlling of cellular process in plants is largely unknown. Using a diverse group of high-throughput sequencing strategies, the mRNA, miRNA, lncRNA and circRNA compositions of tobacco (Nicotiana tabacum) roots determined and their alteration and potential biological functions in response to topping treatment analyzed. RESULTS:A total of 688 miRNAs, 7423 non-redundant lncRNAs and 12,414 circRNAs were identified, among which, some selected differentially expressed RNAs were verified by quantitative real-time PCR. Using the differentially expressed RNAs, a co-expression network was established that included all four types of RNAs. The number of circRNAs identified were higher than that of miRNAs and lncRNAs, but only two circRNAs were present in the co-expression network. LncRNAs appear to be the most active ncRNAs based on their numbers presented in the co-expression network, but none of them seems to be an eTM (endogenous Target Mimicry) of miRNAs. Integrated with analyses of sequence interaction, several mRNA-circRNA-miRNA interaction networks with a potential role in the regulation of nicotine biosynthesis were uncovered, including a QS-circQS-miR6024 interaction network. In this network miR6024 was significantly down-regulated, while the expression levels of its two targets, circQS and its host gene QS, were sharply increased following the topping treatment. CONCLUSIONS:These results illustrated the transcriptomic profiles of tobacco roots, the organ responsible for nicotine biosynthesis. mRNAs always play the most important roles, while ncRNAs are also expressed extensively for topping treatment response, especially circRNAs are the most activated in the ncRNA pool. These studies also provided insights on the coordinated regulation module of coding and non-coding RNAs in a single plant biological sample. The findings reported here indicate that ncRNAs appear to form interaction complex for the regulation of stress response forming regulation networks with transcripts involved in nicotine biosynthesis in tobacco.

Project description:Banana wilt disease, caused by the fungal pathogen Fusarium oxysporum f. sp. cubense 4 (Foc4), is regarded as one of the most devastating diseases worldwide. Cavendish cultivar 'Yueyoukang 1' was shown to have significantly lower disease severity and incidence compared with susceptible cultivar 'Brazilian' in greenhouse and field trials. De novo sequencing technology was previously performed to investigate defense mechanism in middle resistant 'Nongke No 1' banana, but not in highly resistant cultivar 'Yueyoukang 1'. To gain more insights into the resistance mechanism in banana against Foc4, Illumina Solexa sequencing technology was utilized to perform transcriptome sequencing of 'Yueyoukang 1' and 'Brazilian' and characterize gene expression profile changes in the both two cultivars at days 0.5, 1, 3, 5 and 10 after infection with Foc4. The results showed that more massive transcriptional reprogramming occurs due to Foc4 treatment in 'Yueyoukang 1' than 'Brazilian', especially at the first three time points, which suggested that 'Yueyoukang 1' had much faster defense response against Foc4 infection than 'Brazilian'. Expression patterns of genes involved in 'Plant-pathogen interaction' and 'Plant hormone signal transduction' pathways were analyzed and compared between the two cultivars. Defense genes associated with CEBiP, BAK1, NB-LRR proteins, PR proteins, transcription factor and cell wall lignification were expressed stronger in 'Yueyoukang 1' than 'Brazilian', indicating that these genes play important roles in banana against Foc4 infection. However, genes related to hypersensitive reaction (HR) and senescence were up-regulated in 'Brazilian' but down-regulated in 'Yueyoukang 1', which suggested that HR and senescence may contribute to Foc4 infection. In addition, the resistance mechanism in highly resistant 'Yueyoukang 1' was found to differ from that in middle resistant 'Nongke No 1' banana. These results explain the resistance in the highly resistant cultivar and provide more insights in understanding the compatible and incompatible interactions between banana and Foc4.

Project description:The integral role of microbial communities in plant growth and health is now widely recognized, and, increasingly, the constituents of the microbiome are being defined. While phylogenetic surveys have revealed the taxa present in a microbiome and show that this composition can depend on, and respond to, environmental perturbations, the challenge shifts to determining why particular microbes are selected and how they collectively function in concert with their host. In this study, we targeted the isolation of representative bacterial strains from environmental samples of Populus roots using a direct plating approach and compared them to amplicon-based sequencing analysis of root samples. The resulting culture collection contains 3,211 unique isolates representing 10 classes, 18 orders, 45 families, and 120 genera from 6 phyla, based on 16S rRNA gene sequence analysis. The collection accounts for ∼50% of the natural community of plant-associated bacteria as determined by phylogenetic analysis. Additionally, a representative set of 553 had their genomes sequenced to facilitate functional analyses. The top sequence variants in the amplicon data, identified as Pseudomonas, had multiple representatives within the culture collection. We then explore a simplified microbiome, comprised of 10 strains representing abundant taxa from environmental samples, and tested for their ability to reproducibly colonize Populus root tissue. The 10-member simplified community was able to reproducibly colonize on Populus roots after 21 days, with some taxa found in surface-sterilized aboveground tissue. This study presents a comprehensive collection of bacteria isolated from Populus for use in exploring microbial function and community inoculation experiments to understand basic concepts of plant and environmental selection. IMPORTANCE Microbial communities play an integral role in the health and survival of their plant hosts. Many studies have identified key members in these communities and led to the use of synthetic communities for elucidating their function; however, these studies are limited by the available cultured bacterial representatives. Here, we present a bacterial culture collection comprising 3,211 isolates that is representative of the root community of Populus. We then demonstrate the ability to examine underlying microbe-microbe interactions using a synthetic community approach. This culture collection will allow for the greater exploration of the microbial community function through targeted experimentation and manipulation.

Dataset Information

Transcriptomic Profiling of Populus Roots Challenged with Fusarium Reveals Differential Responsive Patterns of Invertase and Invertase Inhibitor-Like Families within Carbohydrate Metabolism.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets