Small noncoding RNAs in tomato pollen
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ABSTRACT:
PROVIDER: PRJEB10390 | ENA |
REPOSITORIES: ENA
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Project description:We used tomato pollen in order to identify pollen stage-specific small non-coding RNAs (sncRNAs) and their target mRNAs. We further deployed elevated temperatures to discern stress responsive sncRNAs. For this purpose high throughput sncRNA-sequencing was performed for three-replicated sncRNAs libraries derived from tomato tetrad, post-meiotic, and mature pollen under control and heat stress conditions.
2015-08-20 | E-MTAB-3830 | biostudies-arrayexpress
Project description:Sets of small RNAs from strains of Botrytis cinerea isolated from tomato or grapevine were compared to determine whether some small RNAs were specific to a population. The small RNAs were mapped to the retrotransposons identified in Sl3, Vv3 or B05.10 genomes.
2022-03-09 | GSE181592 | GEO
Project description:Tomato pollen production and viability is highly vulnerable to higher temperature. Hot summers with temperature reaching above 32°C can disrupt production of viable pollens and fruit set, resulting in yield loss. In recent years, temperature above 35-38oC has become a norm during mid-summer with potential adverse impacts on the production of tomatoes and many other crop species. Pollens are developed through the microsporogenesis and micro-gametogenesis stages. The most heat sensitive period is from the meiotic process of the microsporocytes, at the young microspore stage (uninucleate stage of microspore) to during late pollen development (pollen mitosis). This project studied the heat-induced proteomes in microsporocyte, also called pollen mother cells (PMC). Homogenous PMC samples were collected from cross-sectioned frozen fresh anther tissues of tomato ‘Maxifort’ using laser capture microdissection (LCM). Tandem mass tag (TMT) proteomics analysis was conducted to identify proteomics changes related to heat tolerance during pollen development.
2022-04-07 | PXD018915 | Pride
Project description:Background: Partial pollen and embryo sac sterilities are the two main reasons for low fertility in autotetraploid rice. Our previous study revealed that small RNAs changes may associate with pollen fertility in autotetraploid rice. However, knowledge on comparative analysis between the development of pollen and embryo sac by small RNAs in autotetraploid rice is still unknown. In the present study, WE-CLSM (whole-mount eosin B-staining confocal laser scanning microscopy) and high-throughput sequencing technology was employed to examine the cytological variations and to analyze small RNAs changes during pollen and embryo sac development in autotetraploid rice compared with its diploid counterpart. Results: A total of 321 and 368 differentially expressed miRNAs (DEM) were detected during development of pollen and embryo sac in autotetraploid rice, respectively. Gene Ontology enrichment analysis on the targets of miRNAs-enriched during the development of pollen and embryo sac in autotetraploid rice revealed 30 prominent functional gene classes, such as cell differentiation and signal transduction during embryo sac development. However, only 7 prominent functional gene classes, such as flower development and transcription factor activity, were detected during pollen development. The expression levels of 39 DEM, which revealed interaction with meiosis-related genes, showed opposite expression levels in pollen and embryo sac development. Of these DEM, osa-miR1436_L+3_1ss5CT and osa-miR167h-3p were associated with the female meiosis, while osa-miR159a.1 and osa-MIR159a-p5 were related with the male meiosis. 21nt-phasiRNAs were detected both during pollen and embryo sac development, while 24nt-phasiRNAs were found only in pollen development, which displayed down-regulation in autotetraploid compared to diploid rice and their spatial-temporal expression patterns were similar to osa-miR2275d. 24nt TEs-siRNAs were found to be up-regulated in embryo sac but down-regulated in pollen development. Conclusion: The above results not only provide the small RNAs changes during four landmark stages of pollen and embryo sac development in autotetraploid rice but also have identified specifically expressed miRNAs, especially meiosis-related miRNAs, pollen-24nt-phasiRNAs and TEs-siRNAs in autotetraploid rice. Together, these findings provide a foundation for understanding the effect of polyploidy on small RNAs expression patterns during pollen and embryo sac development that may lead to different abnormalities in autotetraploid rice.
2017-03-09 | GSE90479 | GEO
Project description:There are multiple types of small RNAs that may affect rice pollen’s development. To investigate the small RNA populations’ change during rice pollen development, 13-40 nt RNA were extracted from uninucleate microspores (UNM) and bicellular pollen (BCP) for high throughput sequencing. Together with our laboratory’s previous published rice tricellular pollen (TCP) small RNA sequencing data (GSM722128), sharp increase of tRNA fragments (tRFs) in BCP stage and a slightly decreased tRFs in TCP were found. Among which, new lengths of tRFs were also discovered. Our work accomplished the knowledge about tRFs in rice pollen development.
2017-09-01 | GSE101998 | GEO
Project description:High throughput sequencing was used to investigate the production of small RNAs from cultivated tomato cultivar M82 and its wild relative Solanum pennellii. In order to understand the pattern of inheritance of the samll RNAs, interspecific hybrids (F1 and F2) along with series of introgressed lines comprising precise short genomic regions from S. pennellii in M82 background were used. Examination of small RNA production in several tomato lines.
2012-05-29 | E-GEOD-23562 | biostudies-arrayexpress
Project description:To assay siRNA movement in the pollen grain, we took advantage of the known behavior of 22nt siRNAs to target transcripts for cleavage and initiate secondary siRNA biogenesis. Previous research has demonstrated that when targeted by a 22nt microRNA, a transcript containing a truncated non-fluorescent ~400 bp version of GFP (trGFP) will produce GFP secondary siRNAs that can target a second copy of a functional full-length GFP mRNA in trans. Therefore, we created a ~400 bp non-fluorescent version of trGFP with a 5’ 22nt microRNA target site driven by the vegetative cell-specific KRP6 promoter and transformed this construct into a line homozygous for the sperm-specific functional full-length GFP driven by the MGH3 promoter. If cleaved by a 22nt microRNA, the vegetative cell-driven trGFP will be cleaved into secondary siRNAs, and if the RNA components of this system are mobile and transferred into the sperm cells, the sperm-specific fluorescence of GFP will be reduced. We used two versions of the microRNA target site, which included a mock target site that is not targeted by small RNAs, the target site of microRNA173 (which is a 22nt known to induce the production of secondary siRNAs). We demonstrate that when the 22nt microRNA173 target site is used in the vegetative cell transcript, a corresponding decrease in sperm cell fluorescence is observed. In the mock small RNA target site this reduction in fluorescence was not observed. To ensure the transitive silencing sperm cell transcripts is occurring via secondary small RNAs, we transferred this trGFP experiment into a dcl2/dcl4 mutant background that is defective in TE 21-22nt siRNA silencing. In dcl2/dcl4 double mutants with the trGFP system, we find that the GFP fluorescence of the mock target site transgene does not change, while the repression found in wild-type pollen with the 22nt microRNA173 target site is alleviated. The data for microRNA173 is particularly important, as DCL2 and DCL4 are not necessary for microRNA173 production, and therefore this demonstrates that specifically secondary siRNAs acting downstream of microRNA action are required to silence the sperm cell GFP. We further analyzed the production of sRNAs derived from GFP in pollen grains of transgenic lines expressing the 22nt miR173 or 22nt mock target sites inserted on the 5’ region of the trGFP transgene in both wt and dcl2/dcl4 backgrounds.
2016-03-24 | GSE68154 | GEO
Project description:RNAs of Pollen from Columbia and WS were compared Keywords: ecotype comparison
2006-09-22 | GSE5885 | GEO
Project description:RNAs of Pollen from Columbia and WS were compared Keywords: ecotype comparison
2007-01-31 | GSE6910 | GEO
Project description:The mutagenic activity of transposable elements (TEs) is suppressed by epigenetic silencing and small interfering RNAs (siRNAs), especially in gametes that would transmit transposed elements to the next generation. In pollen from the model plant Arabidopsis, we show that TEs are unexpectedly reactivated and transpose, but only in the pollen vegetative nucleus, which accompanies the sperm cells but does not provide DNA to the fertilized zygote. TE expression coincides with down-regulation of the heterochromatin remodeler DECREASE IN DNA METHYLATION 1 and of most TE siRNAs. However, 21 nucleotide siRNA from Athila retrotransposons is generated in pollen and accumulates in sperm, indicating that siRNA from TEs activated in the vegetative nucleus can target silencing in gametes. We propose a conserved role for reprogramming in germline companion cells, such as nurse cells in insects and vegetative nuclei in plants, to reveal intact TEs in the genome and regulate their activity in gametes. Mature pollen was collected from Columbia reference strain plants by vacuum filtration (Johnson-Brousseau and McCormick, 2004). DNA and RNA were isolated from a ddm1-2 plant in the Columbia reference background. Small RNAs of 19–28 nt were size selected by denaturing 15% PAGE, and cloned as in Brennecke et al. (2007). Additional details regarding the cloning of small RNAs are found in the Supplemental Data. The small RNA libraries were sequenced on Illumina 1G sequencer. The total number of sequences perfectly matching the Arabidopsis genome were as follows: WT inflorescence, 4,158,848 (2,286,133 unique); WT pollen, 1,034,665 (437,984 unique); ddm1 inflorescence, 4,098,772 (1,637,771 unique); and WT sperm, 760,651 (429,972 unique).
2014-09-04 | E-GEOD-61028 | biostudies-arrayexpress