RNA-seq of coding RNA from 4-day old wheat root samples with or without colonisation by bacterium Azospirillum brasilense
ABSTRACT: Plant growth promoting bacteria (PGPB) might be an alternative to increase nitrogenous use efficiency (NUE) in important crops such wheat. Azospirillum brasilense is one of the most promising PGPB and wheat roots colonized by Azospirillum brasilense is a good model to investigate the molecular basis of plant-PGPB interaction including improvement in plant-NUE promoted by PGPB. An RNA-seq transcriptional analysis of Triticum aestivum roots was carried out in two independent samples (biological replicates) of each treatment (PGPB-colonized or non-inoculated), yielding a total of 4 sequencing libraries, which were designated CWR1 and CWR2 libraries (colonized roots) and N-IWR1 and N-IWR2 (non-inoculated roots).
INSTRUMENT(S): AB SOLiD System 3.0, AB SOLiD 4 System
Project description:Colonization of barley roots with the basidiomycete fungus Piriformospora indica enhances resistance against the leaf pathogen Blumeria graminis f.sp. hordei (Bgh). To identify genes involved in this mycorrhiza-induced systemic resistance, we used the Affymetrix Barley1 22K gene chip for leaf transcriptome analysis of P. indica-colonized and non-colonized barley plants 12, 24 and 96 hours post inoculation (hpi) with a compatible Bgh strain.
Project description:Leafy green vegetables, such as lettuce, have been increasingly implicated in outbreaks of foodborne illnesses due to contamination by Escherichia coli O157:H7. While E. coli can survive in soils, colonize plants, and survive on produce, very little is known about the interaction of E. coli with the roots of growing lettuce plants. In these studies, a combination of microarray analyses and surface enhanced Raman spectroscopy (SERS) were used to gain a comprehensive understanding of bacterial genes involved in the colonization and growth of E. coli O157:H7 on lettuce roots and compared to E. coli K12 using a hydroponic system (HS) which we have reported in the previous studies. Using microarray, after three days of interaction with lettuce roots, 94 and 109 genes of E. coli O157:H7 were significantly up-regulated and down-regulated at least 1.5 fold, respectively. Only 8 genes were also found in the E. coli K12 up-regulated genes. No genes were found in the down-regulated genes clusters between those two strains. For E. coli O157:H7, forty out of the 94 up-regulated genes (43%) were involved in protein synthesis and were highly repressed compared to 40 out of 193 (23%) E. coli K12 up-regulated genes associated with protein synthesis. The wildtype of E.coli O157:H7 colonized two log CFU per root less compared to E. coli K12. Genes involved in biofilm modulation (bhsA and ybiM) were significantly up-regulated in E. coli O157:H7 and curli production (crl and csgA) were found important for E. coli K12 to attach to lettuce roots in the previous studies. BhsA mutant of E. coli O157:H7 was impaired in the colonization of lettuce roots. The SERS spectra of E. coli K12 and O157 controls (cells without interacting with roots) were very similar. The spectra of E. coli K12 and O157 exposed to the hydroponic system (HS) showed some differences in the nucleic acid, protein, and lipid regions compared with controls. The spectra of E. coli K12 HS cells exhibited significant differences compared to spectra from E. coli O157 HS cells in the RNA and protein regions. The overall band intensity of amide regions declined for E. coli O157 HS cells, while it increased for E. coli K12 HS cells. The intensity of the RNA bands of E. coli K12 HS cells were also found much higher than those of E. coli O157 HS cells. These findings were in agreement to our Microarray data. Our microarray and SERS data showed that E. coli K12 and O157:H7 behavior dramatically differently in colonizing on lettuce roots. Compared to K12, E. coli O157:H7 colonized less efficiently on lettuce roots. Escherichia coli O157:H7 strains were grown in the lettuce rhizosphere for three days. Transcriptional profiling of E. coli was compared between cells grown with and without rhizosphere . Three biological replicates of each treatment were prepared, and six microarray slides were used.
Project description:Arbuscular mycorrhizal symbiosis is a predominant relationship between plant and arbuscular mycorrhizal fungi. To idendify arbuscular mycorrhiza responsive miRNAs, small RNA libraries were constructed in tomato roots colonized with Rhizophagus irregularis and without Rhizophagus irregularis. We identify miRNAs in tomato roots and provide a new profile of tomato miRNAs. And we found that some miRNAs were responsive to arbuscular mycorrhiza by comparing miRNAs in treatment with that in control. Examination of arbuscular mycorrhiza responsive miRNAs in tomato through high-throughput small RNA sequencing of roots with Rhizophagus irregularis and that without Rhizophagus irregularis
Project description:Contrary to the relative wealth of information regarding pathogen defense responses in aboveground plant parts, little is known about the mechanistic basis and regulation of plant immunity in root tissues. Aiming to further our fundamental understanding of root immune responses, we have investigated the interaction between rice and one of its major root pathogens, the oomycete Pythium graminicola. The specificic objectives of this study were twofold: i) to disentangle the molecular and genetic basis of the rice-Pythium interaction by comparing the transcriptome of rice roots at different times after inoculation with a highly virulent Pythium strains, and ii) to offer fundamental insights into the genetic architecture and regulation of rice disease resistance pathways operative in root tissue and to identify the molecular players controlling the possible nodes of convergence between these resistance conduits Comparison between P. graminicola- and mock-infected rice roots. Two treatments (infected and non-infected) x three timepoints (1, 2 and 4 days post inoculation) x three biological replicates
Project description:cortical cell of non-mycorrhizal roots (cor), arbuscule-containing cells (arb) and non-arbuscule-containing cells (nac) of M. truncatula roots colonized with Glomus intraradices were collected by laser capture microdissection (LCM) and used for RNA extraction and Medicago microarray hybridisation
Project description:Inoculation of Medicago truncatula roots with zoospores of the oomycetic pathogen Aphanomyces euteiches leads to rapid upregulation of a gene encoding a sesquiterpene synthase followed by release of sesquiterpenes that may have a defense function against A. euteiches.
Project description:Potential components of the barrier to radial oxygen loss (ROL) are suberin and/or lignin, which accumulate at the cell wall in the cells of peripheral cell layers of the root. Chemical composition of the apoplastic barrier in rice roots was characterized and it was suggested that ROL can be restricted by the formation of a suberized exodermis and/or lignified sclerenchyma in the outer part of the root. To characterize reorganization of primary carbon metabolism in rice roots during the ROL barrier formation, we obtained the profiles of polar metabolites and the profiles of fatty acids of different zones of rice roots from plants growing in stagnant (anaerobic) and in well aerated medium. Biochemical data are combined with the results of microarray analysis. Nine days after germination, the seedlings were transferred to well aerated nutrient solution or stagnant deoxygenated nutrient solution. Stagnant solution contained 0.1% (w/v) dissolved agar and was deoxygenated (dissolved oxygen, <0.5 mg l–1) prior to use by flushing with N2 gas. After 14 d (23 d old), adventitious roots, 100-150 mm long, were harvested from rice plants grown either in aerated or stagnant conditions and RNA was extracted from 10 mm segments from the regions 0-10 mm, 10-20 mm and 20-30 mm from the root apex have been cut with sterile razor blade and collected and processed separately. Total RNAs were labeled with a Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. Aliquots of Cy5-labeled and Cy3-labeled cRNA (825 ng each) were used for hybridization in a rice 44K oligo-DNA microarray.