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Characterizing microRNAs and their targets in differnt organs of Camellia sinensis [miRNA-seq]

ABSTRACT: MicroRNAs (miRNAs) are a type of small non-coding RNAs, which play important roles in plant growth, development and stress responses. Tea (Camellia sinensis) prepared from tea tree is the oldest and most popular nonalcoholic beverages in the world, and has large economic, medicinal and cultural significance. Nevertheless, there are a few studies on the miRNAs and their functions in Camellia sinensis. We sequenced 9 small RNA libraries and 9 RNA-Seq libraries from roots, leaves and flowers tissues. Through comprehensive computational analyses of 9 small RNA profiles, we identified 200 conserved miRNAs of which 138 have not been reported, and 56 novel miRNAs with 33 have not been reported. Nearly, two thousands genes have significantly different expression levels in tissues. In order to identify targets of miRNAs, we sequenced two degradome profiles from leaves and roots, respectively. Totally, more than 3,000 putative targets of conserved miRNAs were identified in both degradome profiles by using the SeqTar algorithm. These results clearly enhanced our understanding about small RNA guided gene regulations in Camellia sinensis.

ORGANISM(S): Camellia sinensis

PROVIDER: GSE138149 | GEO | 2020/12/31

REPOSITORIES: GEO

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Characterizing microRNAs and their targets in differnt organs of Camellia sinensis [degradome]

Project description:MicroRNAs (miRNAs) are a type of small non-coding RNAs, which play important roles in plant growth, development and stress responses. Tea (Camellia sinensis) prepared from tea tree is the oldest and most popular nonalcoholic beverages in the world, and has large economic, medicinal and cultural significance. Nevertheless, there are a few studies on the miRNAs and their functions in Camellia sinensis. We sequenced 9 small RNA libraries and 9 RNA-Seq libraries from roots, leaves and flowers tissues. Through comprehensive computational analyses of 9 small RNA profiles, we identified 200 conserved miRNAs of which 138 have not been reported, and 56 novel miRNAs with 33 have not been reported. Nearly, two thousands genes have significantly different expression levels in tissues. In order to identify targets of miRNAs, we sequenced two degradome profiles from leaves and roots, respectively. Totally, more than 3,000 putative targets of conserved miRNAs were identified in both degradome profiles by using the SeqTar algorithm. These results clearly enhanced our understanding about small RNA guided gene regulations in Camellia sinensis.

2020-12-31 | GSE138150 | GEO

Characterizing microRNAs and their targets in differnt organs of Camellia sinensis [RNA-seq]

2020-12-31 | GSE138148 | GEO

Identification of regulatory networks of microRNAs and their targets in immunity to Colletotrichum gloeosporioides in tea plant (Camellia sinensis L.)

Project description:Anthracnose disease is caused by Colletotrichum gloeosporioides, and is common in leaves of the tea plant Camellia sinensis. MicroRNAs (miRNAs) have been known as key modulators of gene expression in defense responses; however, the role of miRNAs in tea plant during defensive responses to C. gloeosporioides remains unexplored. Six miRNA sequencing data sets and two degradome data sets were generated from C. gloeosporioides-inoculated and control tea leaves. A total of 485 conserved and 761 novel miRNAs were identified. Of those, 239 known and 369 novel miRNAs exhibited significantly differential expression under C. gloeosporioides stress. 1134 and 596 mRNAs were identified as targets of 389 and 299 novel and conserved miRNAs by degradome analysis, respectively. The expression levels of twelve miRNAs and their targets were validated by quantitative real-time PCR. The predicted targets of five interesting miRNAs were further validated through 5'RLM-RACE. Furthermore, Gene Ontology and metabolism pathway analysis revealed that most of the target genes were involved in translation, carbohydrate metabolism and signal transduction pathways. This study enriches the resources of defense-responsive miRNAs and their targets in C. sinensis, and thus, provides novel insights into the miRNA-mediated regulatory mechanisms underlying immunity responses to biotic stress in tea plant.

2019-04-10 | GSE119728 | GEO

Impact of exogenous caffeine on regulatory networks of microRNAs in response to Colletotrichum gloeosporioides in tea plant.

Project description:Anthracnose, caused by Colletotrichum gloeosporioides is one of the most serious diseases of tea plant [Camellia sinensis (L.) O. Kuntze]. MicroRNAs are key modulators of gene expression in defense responses and plant immunity; although, foliar application of exogenous caffeine in anthracnose disease control management has proven to be effective, miRNA-mediated regulatory mechanisms underlying caffeine-induced plant defense response to C. gloeosporioides remain unexplored in tea plant. Using high-throughput-sequencing, 24 miRNA sequencing data sets and 8 degradome data sets were generated from the susceptible cultivar Longjing43 (LJ43) and the resistant cultivar Zhongcha108 (ZC108) leaves treated with CK (Water), C. gloeosporioides-inoculation (CgI), exogenous caffeine (CN) and CgI + CN. Using sRNA sequencing, 424 conserved miRNAs and 417 novel miRNAs were identified; of these, 146 and 130 miRNAs were differentially expressed under CgI + CN treatment in the LJ43 and ZC108, respectively. Degradome sequencing identified 599 targets predicted to be cleaved by 210 conserved and 70 novel miRNAs. Majority of the annotated targets were found to involve in regulation of transcription factors, oxidation-reduction and metabolic process for plant growth and development as well as stress responses in tea plant against C. gloeosporioides stress. The expression pattern of eight miRNAs and their targets were validated by qRT-PCR, and correlation analysis of csn-miR164a_R+1_1ss21AG/NAC-17 and csn-miR396b-5p/GRF-1 showed highly significant negative R-value at 7th dpi under CgI + CN in the LJ43. This study provides important insights into the novel approach of exogenous caffeine-induced miRNAs dynamically exerts its fungicidal activity through regulating JA/ET signaling pathway, thereby accurately switch on LJ43 susceptibility nature to resistance activity against C. gloeosporioides infection.

2021-12-29 | GSE146713 | GEO

Genome-Wide Identification and Comprehensive Analysis of Conserved MicroRNAs and Phased small Interfering RNAs in Watermelon [degradome]

Project description:MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, flowers, and fruits, and one published small RNA profile of mixed tissues. To identify the targets of miRNAs and phasiRNAs, we generated a degradome profile for watermelon leaf which is analyzed with the SeqTar algorithm. We identified 97 conserved pre-miRNAs, of which 58 have not been reported previously and 348 conserved mature miRNAs without precursors. We also found 9 novel pre-miRNAs encoding 18 mature miRNAs. One hundred and one 21 nucleotide (nt) PHAS loci, and two hundred and forty one 24 nt PHAS loci were also identified. We identified 120 conserved targets of the conserved miRNAs and TAS3-derived tasiRNAs by analyzing a degradome profile of watermelon leaf. The presented results provide a comprehensive view of small regulatory RNAs and their targets in watermelon.

2018-05-23 | GSE102029 | GEO

Genome-Wide Identification and Comprehensive Analysis of Conserved MicroRNAs and Phased small Interfering RNAs in Watermelon [miRNA-Seq]

2018-05-23 | GSE102028 | GEO

Identification and characterization of cold responsive microRNAs in tea plant (Camellia sinensis) based on high-throughput sequencing and their targets using degradome analysis [microarray]

Project description:Solexa sequencing technology was used to perform high throughput sequencing of the small RNA library from the cold treatment of tea leaves. Subsequently, aligning these sequencing date with plant known miRNAs, we characterized 112 C. sinensis conserved miRNAs. In addition, 215 potential candidate miRNAs were found; among them, 131 candidates with star sequence were chosen as novel miRNAs. There are both congruously and differently regulated miRNAs, and line-specific miRNAs were identified by microarray-based hybridization in response to cold stress. The miRNA chip included 3228 miRNA probes corresponding to miRNA transcripts listed in Sanger miRBase release 19.0 and 283 novel miRNAs probes founding in tea plant. In the study presented here, two tea plant cultivars, ‘Yingshuang’ (YS, a cold-tolerant tea plant cultivar) and ‘Baiye 1’ (BY, a cold-sensitive tea plant cultivar), were kept at 4°C for 4,12, 24 h, respectively, and 28°C for as control. These samples were used to acquire expression profiles of a total of 3,511 unique genes, leading to the successful construction of supervised

2015-05-14 | E-GEOD-53632 | biostudies-arrayexpress

Identification and characterization of cold responsive microRNAs in tea plant (Camellia sinensis) based on high-throughput sequencing and their targets using degradome analysis [microarray]

2015-05-14 | GSE53632 | GEO

Identification of wild soybean miRNAs and their target genes responsive to aluminum stress

Project description:In this study, two small RNA libraries and two degradome libraries were constructed from roots of Al-treated and Al-free Glycine soja seedlings. For miRNA, a total of 7,287,655 and 7,035,914 clean reads in Al-treated and Al-free small RNAs libraries were generated, and 105 known miRNAs ,51 p3/p5 strands of known miRNA and 80 novel miRNAs were identified. Among them, expression of 34 miRNAs was responsive to Al stress. Through degradome sequencing, 82 and 11 genes were identified as tagerts of known and novel miRNAs obtained from this study, respectively. Gene Ontology (GO) annotations of target transcripts indicated that 52 out of 66 targets cleaved by conserved miRNA families may play role in regulation of transcription. sample 1: Examination of small RNA in Al-free wild soybean roots; sampple 2: Examination of small RNA in Al-treated wild soybena roots; sample 3: identification of miRNA targets in Al-free wild soybean roots; sample 4: identification of miRNA targerts in Al-treated wild soybean roots

2012-05-25 | E-GEOD-38065 | biostudies-arrayexpress

Nitrosoproteomic Analysis Deciphers the S-Nitrosylome in Carbon Metabolism of Tea Leaves

Project description:Cysteine S-nitrosylation is a reversible protein post-translational modification and critically regulates the activity, localization and stability of proteins. Tea (Camellia sinensis (L.)) is one of the most thoroughly studied evergreen crop due to its broad non-alcoholic beverage and huge economic impact in the world. However, to date, little is known about the S-nitrosylome in this plant. Here, we performed a global analysis of cysteine S-nitrosylation in tea leaves. In total, 228 cysteine S-nitrosylation sites were identified in 191 proteins, representing the first extensive data on the S-nitrosylome in tea plants. These S-nitrosylated proteins were located in multiple subcellular compartments, especially in the chloroplast and cytoplasm. The analysis of functional enrichment and PPI network revealed that the S-nitrosylated proteins were mainly involved in carbon metabolism, especially in Calvin cycle and TCA cycle. These results suggested that S-nitrosylated proteins in tea leaves might play critical regulatory roles in the carbon metabolism. Overall, this study not only globally analyzed the functional annotation of cysteine S-nitrosylation in tea leaves, but also preliminarily provided the valuable information for further investigating the functions of cysteine S-nitrosylation in tea plants.

2020-05-26 | PXD012443 | Pride

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