Deep sequencing reveals divergent expression patterns within the small RNA transcriptomes of cultured and vegetative tissues of sugarcane
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ABSTRACT:
ORGANISM(S): Saccharum sp.
PROVIDER: GSE53304 | GEO | 2013/12/13
SECONDARY ACCESSION(S): PRJNA231629
REPOSITORIES: GEO
Similar Datasets
Project description:We report the deep sequencing of small RNA populations derived from apex, internode 3, internode 6, internode 16, leaf +3, calli and suspesion cells from sugarcane cultivar Q117 Each vegetative tissue was sampled from three independent field grown plants, pooled and sequenced using the GAIIx platform. Calli and suspension cell cultures were sequenced using the HiSeq 2000 platform.
2013-12-13 | E-GEOD-53304 | biostudies-arrayexpress
Project description:Sugarcane accumulates high concentrations of sucrose in the mature stalk, with numerous physiological processes in maturing stalk tissue both directly and indirectly involved. A considerable portion of carbohydrate metabolism is also devoted to cell wall synthesis and fibre production. Previously, we have identified differentially expressed transcripts correlated with sucrose accumulation and fibre production in various internodes of the sugarcane stalk. In this study, we have examined tissue-specific expression patterns to further explore gene pathways responsible for sucrose accumulation and fibre synthesis. We performed large-scale expression profiling of storage parenchyma, vascular bundles and rind dissected from a maturing stalk internode from field-grown commercial sugarcane harvested at 11 months of age. We identified 10 cellulose synthase subunit genes in sugarcane and examined significant differences in the expression of their corresponding transcripts and those of several sugar transporters between the different tissues. These were further correlated with differential expression patterns for transcripts of specific COBRA-like proteins and other proteins with acknowledged roles in cell wall metabolism. We found that the sugar transporters ShPST2a, ShPST2b and ShSUT4 were significantly up-regulated in storage parenchyma while ShSUT1 was up-regulated in vascular bundles. Two co-ordinately expressed groups of cell wall related transcripts were also identified. One group which is associated with primary cell wall synthesis (ShCesA1, ShCesA7, ShCesA9 and Shbk2l3) was up-regulated in parenchyma. The other group which is associated with secondary cell wall synthesis (ShCesA10, ShCesA11, ShCesA12 and Shbk-2) was up-regulated in rind. We also report an unexpected paucity in differential expression of cell wall-related genes in vascular bundles. Our results indicate that there is spatial separation for elevated expression of these important targets in both sucrose accumulation and cell wall synthesis, allowing for increased clarity in our understanding of sucrose transport and fibre synthesis in sugarcane.
2015-10-13 | GSE67897 | GEO
Project description:Sugarcane is an important crop in tropical regions of the world, producing a very large biomass and accumulating large amounts of sucrose in the stem. In this study, we present the first report of transcript profiling using the GeneChip Sugarcane Genome Array. We have identified transcripts that are differentially expressed in the sugarcane stem during development by expression profiling using the array and total RNA derived from three disparate stem tissues (meristem, internodes 1-3; internode 8; internode 20) from four replicates of the sugarcane variety Q117 grown in the field. We have identified 119 transcripts that were highly differentially expressed with stem development and have characterised members of the cellulose synthase (CesA) and cellulose synthase-like (Csl) gene families which displayed coordinated expression during stem development. In addition, we determined that many other transcripts involved in cell wall metabolism and lignification were also co-expressed with members of the CesA and Csl gene families, offering additional insights into the dynamics of primary and secondary cell wall synthesis in the developing sugarcane stem. Keywords: stem development profile
2006-11-19 | GSE5021 | GEO
Project description:Transcriptional profiling of sugarcane leaf+1 and upper internode harvested at one and five days after chemical (ethephon and AVG) application (DAA) compared to control (mock) samples. Co-hybridization of chemical-treated samples with control samples as reference (one or five DAA chemical treated-samples against one DAA control sample; and five DAA chemical treated-sample against five DAA control sample) was performed to monitor gene expression changes in a two-color Agilent custom microarray, using a dye-swap design. Our goal was to determine the effect of ethylene on global gene expression of sugarcane plants at the maturation stage.
2016-10-31 | GSE85489 | GEO
Project description:The project is aimed at analysing the comparitive proteomics of red rot resistant cultivar (BO91) and red rot susceptible cultivar (COJ64) of sugarcane. The differentially abundant proteins shall be used to identify the corresponding genes.
2023-03-23 | PXD033375 | Pride
Project description:Sugarcane is an economically important crop contributing to the world’s sugar and ethanol production with 80% and 40%, respectively. In recent years, the growing demands for sugar and ethanol production has prompted the necessity to increase sugarcane productivity through conventional breeding programs. However, sugarcane breeders have encountered several difficulties to raise productivity, mainly due to its complex genetics. Sugarcane has a polyploidy genome, with many varieties being aneuploidy. Today, the majority of the planted sugarcane cultivars are complex hybrids derived mainly from crosses between Saccharum officinarum and S. spontaneum. Therefore, proteomics can provide some insight into deciphering gene regulation and changes in carbon metabolism and sucrose accumulation in the culms at different stages of plant development. The aim of this work was to compare the quantitative changes of proteins in sugarcane culms, during plant growth and sucrose accumulation. Total proteins were isolated from both, juvenile and maturing internodes at three stages of plant development. Label free shotgun proteomics was used for protein profiling and quantification. The internodes 5 (I5) and 9 (I9) of 4, 7 and 10 month-old-plants (4M, 7M and 10M, respectively) were harvested and used for proteomic analyses. To mimic field conditions of sucrose accumulation during sugarcane maturation, we stopped watering 10M plants for 10 days. An average of 1130 proteins, unique and differentially expressed across all ages were identified and quantified. Proteins were categorized within 27 functional groups, related to biological process. The patterns of expression for some categories, such as cellular amino acids, metabolic processes, secondary metabolic processes and translation were down-regulated in the immature internode (I5-10M), while up-regulated in the mature I9-10M. We observed an increase in the abundance of several enzymes of the glycolytic pathway and isoforms of alcohol dehydrogenase (ADH) and pyruvate decarboxylase (PDC), in the juvenile stages of development of I9. These changes in enzymes contents indicates that at the early stages of internode development, hypoxia is increasing the glycolytic and ethanolic fermentation pathways, in order to supply ATP for plant growth and NAD+ for mitochondrial respiration, which might be impaired by the low oxygen availability inside the culm.
2021-09-09 | PXD027410 | Pride
Project description:Using nylon filter arrays, we analyzed the expression profile of 1536 expressed sequence tags (ESTs) of sugarcane (Saccharum sp.) exposed to the phytormone methyl jasmonate (MeJA) for 0-12 h. 26 ESTs were differentially expressed, including novel genes and also genes that had not previously been reported as being MeJA-inducible. Data are for two independent experiments. Keywords = sugarcane Keywords = methyl jasmonate Keywords = nylon arrays
2010-10-08 | E-GEOD-1546 | biostudies-arrayexpress
Project description:Using nylon filter arrays, we analyzed the expression profile of 1536 expressed sequence tags (ESTs) of sugarcane (Saccharum sp.) exposed to the phytormone methyl jasmonate (MeJA) for 0-12 h. 26 ESTs were differentially expressed, including novel genes and also genes that had not previously been reported as being MeJA-inducible. Data are for two independent experiments. Keywords = sugarcane Keywords = methyl jasmonate Keywords = nylon arrays Keywords: time-course
2004-07-23 | GSE1546 | GEO
Project description:Salt stress is one of the most common stresses in agricultural regions worldwide. In particular, sugarcane is affected by these conditions and there are still no cultivars that show high productivity allied with a tolerance to salt stress. Proteomic analysis is an important tool for elucidating important pathways involved in the response to various abiotic stresses at the biochemical and molecular levels. Thus, the aim of this study was to analyse the proteomic effects of salt stress in the micropropagated shoots of two sugarcane cultivars (CB38-22 and RB855536) using a label-free proteomic approach. Cultivar RB855536 is more tolerant to salt stress than is CB38-22.
2017-04-26 | PXD006075 | Pride
Project description:Sugarcane is a very efficient crop to produce ethanol. In recent years, extensive efforts have been made in order to increase sugarcane yields. To reach this goal, molecular biology tools have been used comprehensively, identifying genes, pathways and genetic polymorphisms. However, some important molecular components, like microRNAs, have not been deeply investigated. MicroRNAs are an important class of endogenous small, noncoding RNAs that regulate gene expression at the post-transcription level and play fundamental roles in diverse aspects of animal and plant biology. Plant genomes harbor numerous miRNA genes that regulate many protein-coding genes to influence key processes ranging from development, metabolism, and responses to abiotic and biotic stresses. There is wide range of pests and diseases that affect sugarcane, yet the mechanisms that regulate pathogen interactions with sugarcane have not been thoroughly investigated. To gain knowledge on the physiological responses to pathogens mediated by microRNAs in sugarcane, we screened the transcriptoma of sugarcane plants infected with Acidovorax avenae subsp avenae, the causal agent of red stripe disease in sugarcane, and detected several microRNAs modulated in the presence of the pathogen. Furthermore, we validated with qPCR a number of microRNA expression patterns observed by bioinformatics analysis. In addition, we observed high expression levels of several star microRNAs, in numbers larger than the mature microRNAs in some cases. Interestingly, sof-miR408 was consistently down-regulated in the presence of several pathogens, but not in the presence beneficial microbes. This result indicates that the sugarcane senses pathogenic or beneficial microorganisms differentially and triggers specific epigenetic regulatory mechanisms accordingly
2012-11-30 | GSE42628 | GEO