Zea mays
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ABSTRACT:
PROVIDER: PRJNA320257 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and IFC （incompletely fused carpels） Maize Ovary Transcriptomes
| PRJNA308601 | ENA
Project description:To identify miRNAs involved in carpels fusion development in maize, four independent small RNA libraries and two degradome libraries from WT and IFC ovaries were constructed at the carpels fusion deficiency just being observed. A total of 162 known miRNAs distributed in 33 faimilies were identified, of which 20 known miRNAs were differentially expressed. In addition, 19 novel miRNAs were shown difference in expression levels between IFC and WT ovaries. By degradome analysis, totals of 113 and 78 target genes were predicted for known and novel miRNAs, respectively. 24 (60%) target genes of the differentially expressed known miRNAs coded for transcription factors, among which target genes encoding auxin response factors (ARF), TB1-CYC-PCFs (TCP), APETALA2 (AP2), growth regulating factor (GRF), MYB, NAC and NF-YA were classified as Class I. These target genes showed opposite expression patterns with their corresponding miRNAs according to quantitative real-time PCR results. The results suggested that the incomplete carpels fusion may partly due to the differential expression of these miRNAs and their target genes
2017-06-13 | GSE80998 | GEO
Project description:To identify tomato miRNAs involved in chilling response, two small RNA libraries and two degradome libraries from chilling-treated(4M-BM-0C/4M-BM-0C for 1hM-oM-<M-^L4h, 8h, 12h, 24h and 48h) and non-chilling-treated (25M-BM-0C/20M-BM-0C for 1hM-oM-<M-^L4h, 8h, 12h, 24h and 48h)leaves of LA1777M-bM-^@M-^Y (S. habrochaites) seedlings were constructed. A total of 4342604 and 7231609 clean reads were obtained by high-throughput sequencing of the two libraries, respectively. 161 conserved miRNAs and 236 novel miRNAs were identified in the two librayies. Of these miRNAs, 192 were upregulated, whereas 205 were downregulated in response to chilling stress. Among these, 23 miRNAs and 26 miRNAs were significantly upregulated and downregulated in response to chilling stress, respectively.Through degradome sequencing,62 target genes were cleaved by 42 conserved miRNAs, while nine target genes were cleaved by nine novel miRNAs. Target gene functional analysis revealed that most target genes played positive role in the chilling response, primarily by regulating the expression of anti-stress proteins, antioxidant enzymes and genes involved in cell wall formation. tomato miRNA-seq and Degradome-seq after chilling
2015-03-03 | E-GEOD-57335 | biostudies-arrayexpress
Project description:Background: High seed vigor is crucial for agricultural production owing to its potential in high quality and yield of crops. A better understanding of the underlying mechanisms is highly necessary. Results: To better understand the involvement and regulatory mechanism of miRNAs correlated with maize seed vigor, small RNAs and degradome sequencing of two inbred lines Yu537A and Yu82 were performed. A total of 791 mature miRNAs were obtained with different expressions, among of which 505 miRNAs were newly identified and the rest miRNAs were more or less reported before by comparing the miRNAs with the sequences in miRbase database. Analysis of miRNA families showed maize seeds contain fewer miRNA families and larger miRNA families compared with animals, indicating that functions of miRNAs in maize seeds were more synergistic than animals. Degradome sequencing was used to identify the targets of miRNAs and the results showed a total of 6196 targets were obtained. Function analysis of differentially expressed miRNAs and targets showed Glycan degradation and galactose metabolism were closely correlated with improved corn seed vigor. Conclusions: These findings provide valuable information to understand the involvement of miRNAs with corn seed vigor and these putative genes will be valuable resources for improving the seed vigor in future corn breeding.
2022-09-08 | GSE196738 | GEO
Project description:Chinese cedar (<i>Cryptomeria fortunei</i>) is a tree species with important ornamental, medicinal, and economic value. Terpenoids extracted from the essential oil of <i>C. fortunei</i> needles have been considered valuable ingredients in the pharmaceutical and cosmetic industries. However, the possible gene regulation mechanisms that limit terpenoid biosynthesis in this genus are poorly understood. Here, we adopted integrated metabolome analysis, transcriptome, small-RNA (sRNA), and degradome sequencing to analyze the differences in terpenoid regulatory mechanisms in two different overwintering <i>C. fortunei</i> phenotypes (wild-type and an evergreen mutant). A total of 1447/6219 differentially synthesized metabolites (DSMs)/unigenes (DEGs) were detected through metabolome/transcriptome analyses, and these DSMs/DEGs were significantly enriched in flavonoid and diterpenoid biosynthesis pathways. In <i>C. fortunei</i> needles, 587 microRNAs (miRNAs), including 67 differentially expressed miRNAs (DERs), were detected. Among them, 8346 targets of 571 miRNAs were predicted using degradome data, and a 72-miRNA-target regulatory network involved in the metabolism of terpenoids and polyketides was constructed. Forty-one targets were further confirmed to be involved in terpenoid backbone and diterpenoid biosynthesis, and target analyses revealed that two miRNAs (i.e., aly-miR168a-5p and aof-miR396a) may be related to the different phenotypes and to differential regulation of diterpenoid biosynthesis. Overall, these results reveal that <i>C. fortunei</i> plants with the evergreen mutation maintain high terpenoid levels in winter through miRNA-target regulation, which provides a valuable resource for essential oil-related bioengineering research.
2022-08-12 | MTBLS3183 | MetaboLights
Project description:We investigate the miRNA expression profiles with the attempt to identify deregulated molecules useful as NEN biomarkers. SmallRNA-Seq was performed allowing the identification of miRNAs commonly expressed in all samples. Three sera from the same samples were also sequenced.
2022-06-30 | E-MTAB-11598 | biostudies-arrayexpress
Project description:Genome-wide target genes of ZmAN3 were identified through ChIP-seq on the growth zone of the maize leaf, encompassing the division, transition and expansion zone. For ChIP-seq, ZmAN3 was fused to the GSyellow TAP tag and expressed from the ubiquitin promoter (pUBIL). The pUBIL:ZmAN3-GSyellow construct was transformed into the maize inbred line B104. ChIP was performed using anti-GFP antibody (abcam290).
2018-08-07 | E-MTAB-6527 | biostudies-arrayexpress
Project description:The small RNAs and their targets were characterized in Amborella genome by deep sequencing the small RNA populations of leaf tissue and opened-female flower tissue. The small RNA targets were also validated from degradome populations of leaf tissue and opened-female flower tissue. We generated integrative maps of small RNA profiles (sRNA-seq) and degradome (PARE-seq) profiles to characterize the miRNAs and their targets from Amborella.
2013-07-01 | E-GEOD-41811 | biostudies-arrayexpress