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Degradome sequencing

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Integrated small RNA and Degradome sequencing provide insights into salt tolerance in sesame (Sesamum indicum L.)

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To better investigate the regulatory functions of miRNAs, their target genes were identified using degradome sequencing, and the summary of sequencing data is shown in Table S3.. Degradome cleavage site and alignment range of target genes are also listed in Table S4. In addition, degradome analysis showed that 210 genes were the tar- gets of 85 differentially expressed miRNAs in sesame (Table S5).

A dynamic degradome landscape on miRNAs and their predicted targets in sugarcane caused by Sporisorium scitamineum stress

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Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing

PmiRDiscVali: An integrated pipeline for plant microRNA discovery and validation

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Result summary of the case study on the miRNA prediction in Dendrobium officinale . degradome-seq: Degradome sequencing. RNA-seq: RNA sequencing. The high-throughput sequencing data sets used for the case study were retrieved from NCBI SRA (https://www.ncbi.nlm.nih.gov/sra. miRBase: annotating high confidence microRNAs using deep sequencing data. Tracking microRNA processing signals by Degradome sequencing data analysis.

Genome-wide characterization of the SPL gene family involved in the age development of Jatropha curcas

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Target plots of the targets cleaved by the miR156 family through degradome sequencing. The T-plots show the distribution of the degradome tags along the full-length of the target mRNA se- quence (bottom). JCY and GTY participated in the sequence analysis and data interpretation. played no role in the design of the study or collection, analysis and interpretation of data.. The datasets used and analyzed during the current study are available in the manuscript and its additional files..

Analysis of microRNAs, phased small interfering RNAs and their potential targets in Rosa rugosa Thunb.

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The obtained small RNA sequencing profiles were deposited to the NCBI GEO database under the accession number GSE110490 (https://www.ncbi.nlm.nih.. The obtained degradome sequencing profile was deposited to the NCBI GEO database under the accession number GSE110494 (https://www.ncbi.nlm.nih.gov/geo/query/acc.. The full contents of the supplement are available at https://bmcgenomics.. Genome-Wide Analysis of the.

Construction and analysis of degradomedependent microRNA regulatory networks in soybean

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Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing.

Identification of microRNAs in response to aluminum stress in the roots of Tibetan wild barley and cultivated barley

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XZ29 and Golden Promise were used for small RNA and degradome sequencing. Al stress. Length variation at both 3’ and 5’ ends and two mismatches inside of the sequence were allowed in the alignment. miRNAs responsive to Al stress should meet the rules as showed below. To validate the small RNA sequencing data, four ran- domly selected target genes from miRNAs responsive to Al stress were used to perform qRT-PCR analysis. The difference in root elongation of three genotypes under Al stress.

Genotype- and tissue-specific miRNA profiles and their targets in three alfalfa (Medicago sativa L) genotypes

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Although the alfalfa is one of the important legumes ag- ronomically, the genome sequencing and annotations are not available so far. Degradome sequencing was used in this study to identify the cleaved mRNA fragments cor- responding to the miRNA recognition sites in all three alfalfa genotypes. Approximately 30 million degradome reads were obtained from the transcripts of each of the alfalfa genotypes (Table 4) and these reads were analysed using SeqTar program.

Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon

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As miRNAs are critical in generation of phasiRNAs, we identified miRNA triggers for these PHAS loci on both strands by using the degradome sequencing profile and the SeqTar algorithm. We found that the MIR169r-5p may trigger the generations of 21 phasiRNAs at three PHAS loci (Fig. Except miR390 with 21 nt, most miRNA triggers of 21 nt PHAS loci are 22 nt, such as miR482/miR miR828.

Phased secondary small interfering RNAs in Panax notoginseng

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Because miRNAs are critical in processing pathways of phasiRNAs, we identified miRNA triggers for these PHAS loci on both strands by using the degradome sequencing. 4 Identified targets of 21 nt phasiRNAs in P. The arrows in the upper panels correspond to the positions pointed by the arrows of the same colors in the lower panels.

Environmental RNAi pathways in the twospotted spider mite

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Genome-wide identification of the Pha- seolus vulgaris sRNAome using small RNA and degradome sequencing. doi:https://doi.org/10.1186/. et al. Nat Commun doi:https://doi.org/10.1038/s . https://doi.org/10.1186/gb . https://doi.org/10.1038/nrm2479.. https://doi.org/10.1111/j..

Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development

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Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing. Regulation of the alkaloid biosynthesis by miRNA in opium poppy. Molecular evolution and diversification of the Argonaute family of proteins in plants. Genome sequence of the palaeopolyploid soybean

Small RNA and degradome deep sequencing reveal respective roles of coldrelated microRNAs across Chinese wild grapevine and cultivated grapevine

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Here, sRNA and degradome deep sequencing were performed to detect and analyze cold-related miR- NAs and their target genes in Chinese wild grapevine.. For example, orthologous pairs include Chinese wild grape miR172a with culti- vated grape Vvi-172a. Chinese wild grape miR159a with cultivated grape Vvi-159a. and Chinese wild grape miR160b with cultivated grape Vvi-miR160b..

Identification and integrated analysis of glyphosate stress-responsive microRNAs, lncRNAs, and mRNAs in rice using genomewide high-throughput sequencing

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Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis Degradome.. Differential expression of RNA-Seq data at the gene level – the DESeq package

High-throughput deep sequencing reveals the important role that microRNAs play in the salt response in sweet potato (Ipomoea batatas L.)

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We also predicted the targets of miRNAs and further investigated their network by GO and KEGG analyses using sweet potato transcriptome and degradome data. The transcriptome sequencing of sweet potato (Xu32) was performed by Illumina high-throughput sequencing.. Identification of known miRNAs in sweet potato.

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

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In this study, we used a tripartite approach (sRNA-Seq, mRNA-Seq, and degradome-seq) to describe the set of small RNAs differentially expressed in barley roots and shoots under low-Pi stress. Integrated deep- sequencing data were used to describe organ-specific ad- aptations to low-Pi through either activation or repres- sion of different classes of 18–25 nt small RNAs..

MicroRNA-guided regulation of heat stress response in wheat

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Identification of cleaved miRNA targets through sequencing of the degradome. Sequencing of the 24 degradome libraries yielded a total of 404 M reads. Prediction of heat stress associated regulatory networks Degradome validated miRNA targets queried to STRING DB predominantly associated with redox homeostasis, antioxidant activity and ubiquitination (Fig.

Banana sRNAome and degradome identify microRNAs functioning in differential responses to temperature stress

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The cleavage site detected in the degradome is indicated in blue and yellow letters.

TarDB: An online database for plant miRNA targets and miRNA-triggered phased siRNAs

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Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome.. https://doi.org/10.1016/j.cub . https://doi.org/10.1038/nbt1417.. https://doi.org . https://doi.org/10.1104/pp . https://doi.org/10.1038/nplants.2017.77.. https://doi.org/10.1093/molbev/msw154.

Integrated transcriptome, small RNA, and degradome analysis reveals the complex network regulating starch biosynthesis in maize

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FC, fold-change of the expression of the miRNAs/target genes in Ji419 relative to that in Mo17 at 15 DAP based on the sequencing data.. Black bars represent expression of miRNAs. grey bars represent expression of target genes. 4 Differential expression of miRNAs and their target genes in the endosperm of maize inbred lines Mo17 and Ji419 at 25 DAP. FC, fold-change of the expression of the miRNAs/target genes in Ji419 relative to that in Mo17 at 25 DAP based on the sequencing data..