Ontology highlight
ABSTRACT:
PROVIDER: PRJNA731301 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14597889_1.fastq.gz | Fastqsanger.gz | |||
| SRR14597889_2.fastq.gz | Fastqsanger.gz | |||
| SRR14597890_1.fastq.gz | Fastqsanger.gz | |||
| SRR14597890_2.fastq.gz | Fastqsanger.gz |
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Project description:Bulked segregant analysis (BSA) is an efficient method to rapidly and efficiently map genes responsible for mutant phenotypes. This procedure, however, requires access to quantitative genetic markers that are polymorphic in the mapping population. We have developed a modification of BSA (BSR-Seq) that makes use of RNA-Seq reads to efficiently map genes even in populations for which no polymorphic markers have been previously identified. Because of the digital nature of next-generation sequencing (NGS) data, it is possible to conduct de novo SNP discovery and quantitatively genotype BSA samples using the same RNA-Seq data. In addition, analysis of the RNA-Seq data provides information on the effects of the mutant on global patterns of gene expression at no extra cost. In combination these results greatly simplify gene cloning experiments. To demonstrate the utility of this strategy BSR-Seq was used to clone the glossy3 (gl3) gene of maize. Mutants of the glossy loci exhibit altered accumulation of epicuticular waxes on juvenile leaves. We previously generated a large collection of glossy mutants using the Mu transposon system. By subjected a reference allele to BSR-Seq, we were able to map the gl3 locus to a ~2.3Mb interval that is consistent with the results of prior mapping experiments. The single gene located in the 2.3Mb mapping interval that contained a Mu insertion and whose expression was down-regulated in the mutant pool was subsequently demonstrated to be the gl3 gene via the analysis of multiple independently Mu transposon induced mutant alleles. The gl3 gene encodes a putative myb transcription factor, which directly or indirectly affects the expression of a number of genes involved in the biosynthesis of very-long-chain fatty acids.
2012-12-03 | E-MTAB-4234 | biostudies-arrayexpress
Project description:Circular RNA (circRNA) is a covalently-closed single-stranded RNA molecule that plays an important role in transcriptional regulation of gene expression in a variety of species. Light intensity is a pivotal environmental factor affecting plant growth and development. However, little is known regarding photoresponsive plant circRNAs. Here, we aimed to investigate the expression and function of circRNAs in lettuce leaves in response to different light intensity treatments. We performed RNA sequencing (RNA-Seq) on leaves of lettuce (Lactuca sativa) to determine circRNA expression profiles and reverse-transcription polymerase chain reaction (PCR) to validate the candidate circRNA molecules. We then combined bioinformatics approach to explore the function of the parental genes of circRNA, including network, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway analysis. We identified 1650 circRNAs in lettuce, of which 1508 (86.40%) were derived from exons. Using real-time PCR, we characterized 10 validated differentially expressed circRNAs and their parental genes, all of which showed expression patterns consistent with RNA-Seq data. Interestingly, the expression of circRNA was, in some cases, inversely correlated with the expression of the parental gene. Furthermore, analysis of the circRNA–microRNA–mRNA network suggests that circRNAs may be involved in plant hormone signaling and chlorophyll metabolism during photoreactivity. These findings provide an essential reference basis for studying circRNAs’ biological mechanisms in light-treated plants.
2020-04-14 | GSE148578 | GEO
Project description:To characterize plant growth in net zero energy greenhouse models with semi-transparent organic solar cell (OSC) filter roofs, RNA was extracted from red oak leaf lettuce leaves grown under 3 OPV filters (FTAZ:IT-M, PTB7-Th:IEICO-4F, FTAZ:PCBM) an clear and shaded glass controls. 2 light intensity experiments were used. PPPFD Controlled (PC) treatments had a constant light intensity and different light spectra created by the filters. Height Controlled (HC) treatments varied in both light intensity and spectra, according to the light transmission of each filter. When light intensity was controlled, plants grown under FTAZ:IT-M had a DEG profile distinct from plants grown under the other 2 filters. Key genes were up or down-regulated that indicate changes in anthocyanin accumulation, nitrogen metabolism and pest defense.
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Project description:Verotoxigenic Escherichia coli (VTEC) are a leading cause of food-borne illness. Fruit and vegetables are recognised as an important source of the pathogen and can account for ~ 25 % of food-borne VTEC outbreaks, globally. The ability of VTEC to colonise leaves and roots of leafy vegetables, spinach (Spinacia oleracea) and lettuce (Lactuca sativa), was compared. The highest levels of colonisation occurred in the roots and rhizosphere, whereas colonisation of the leaves was lower and significantly different between the species. Colonisation of the leaves of prickly lettuce (L. serriola), a wild relative of domesticated lettuce, was especially poor. Differential VTEC gene expression in spinach extracts was markedly different for three tissue types, with little overlap. Comparison of expression in the same tissue type, cell wall polysaccharides, for lettuce and spinach also showed substantial differences, again with virtually no overlap. The transcriptional response was largely dependent on temperatures that are relevant to plant growth, not warm-blooded animals. The data show that VTEC adaptation to plant hosts and subsequent colonisation potential is underpinned by wholescale changes in gene expression that are specific to both plant tissue type and to the species.
2016-08-01 | E-MTAB-3249 | biostudies-arrayexpress
Project description:Verotoxigenic Escherichia coli (VTEC) are a leading cause of food-borne illness. Fruit and vegetables are recognised as an important source of the pathogen and can account for ~ 25 % of food-borne VTEC outbreaks, globally. The ability of VTEC to colonise leaves and roots of leafy vegetables, spinach (Spinacia oleracea) and lettuce (Lactuca sativa), was compared. The highest levels of colonisation occurred in the roots and rhizosphere, whereas colonisation of the leaves was lower and significantly different between the species. Colonisation of the leaves of prickly lettuce (L. serriola), a wild relative of domesticated lettuce, was especially poor. Differential VTEC gene expression in spinach extracts was markedly different for three tissue types, with little overlap. Comparison of expression in the same tissue type, cell wall polysaccharides, for lettuce and spinach also showed substantial differences, again with virtually no overlap. The transcriptional response was largely dependent on temperatures that are relevant to plant growth, not warm-blooded animals. The data show that VTEC adaptation to plant hosts and subsequent colonisation potential is underpinned by wholescale changes in gene expression that are specific to both plant tissue type and to the species.
2016-08-01 | E-MTAB-4120 | biostudies-arrayexpress
Project description:Chitin soil amendment is known to improve soil quality, plant growth and plant stress resilience, but the underlying mechanisms are not well understood. In this study, we monitored chitin’s effect on lettuce physiology every two weeks through an eight-week growth period, analyzed the early transcriptional reprogramming and related metabolomic changes of lettuce, in response to crab chitin treatment in peat-based potting soil. In commercial growth conditions, chitin amendment still promoted lettuce growth, increased chlorophyll content, the number of leaves and crop head weight from week six. The flavonoid content in lettuce leaves was altered as well, showing an increase at week two but a decrease from week six. Transcriptomic analysis showed that over 300 genes in lettuce root were significant differentially expressed after chitin soil treatment. Gene Ontology-term (GO) enrichment analysis revealed statistical overrepresentation of GO terms linked to photosynthesis, pigment metabolic process and phenylpropanoid metabolic process. Further analysis of the differentially expressed genes (DEGs) showed that the flavonoid pathway is mostly upregulated whereas the bifurcation of upstream phenylpropanoid pathway towards lignin biosynthesis is mostly downregulated. Metabolomic analysis revealed the upregulation of salicylic acid, chlorogenic acid, ferulic acid, and p-coumaric acid in chitin treated lettuce seedlings. These phenolic compounds mainly influence the phenylpropanoid biosynthesis pathway and may play important roles in plant defense reactions. Our results suggest that chitin soil amendments might activate induced resistance by priming lettuce plants and promote lettuce growth via transcriptional changes.
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Project description:Leaf size and flatness directly affect photosynthesis and are closely related to agricultural yield. The final leaf size and shape are coordinately determined by cell proliferation, differentiation, and expansion during leaf development. Lettuce (Lactuca sativa L.) is one of the most important leafy vegetables worldwide, and lettuce leaves vary in shape and size. However, the molecular mechanisms of leaf development in lettuce are largely unknown. In this study, we showed that the lettuce APETALA2 (LsAP2) gene regulates leaf morphology. LsAP2 encodes a transcriptional repressor that contains the conserved EAR motif, which mediates interactions with the TOPLESS/TOPLESS-RELATED (TPL/TPR) corepressors. Overexpression of LsAP2 led to small and crinkly leaves, and many bulges were seen on the surface of the leaf blade. LsAP2 physically interacted with the CINCINNATA (CIN)-like TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors and inhibited their transcriptional activation activity. RNA sequencing analysis showed that LsAP2 affected the expression of auxin- and polarity-related genes. In addition, LsAP2 directly repressed the abaxial identity gene KANADI2 (LsKAN2). Together, these results indicate that LsAP2 regulates leaf morphology by inhibiting CIN-like TCP transcription factors and repressing LsKAN2, and our work provides insights into the regulatory mechanisms of leaf development in lettuce.
2021-03-29 | GSE168886 | GEO
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.
2012-03-28 | E-GEOD-36885 | biostudies-arrayexpress