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ABSTRACT: maize small RNA, transcriptome and degradome sequencing

PROVIDER: PRJNA438075 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6829170_1.fastq.gz	Fastqsanger.gz
	SRR6829170_2.fastq.gz	Fastqsanger.gz
	SRR6829171_1.fastq.gz	Fastqsanger.gz
	SRR6829171_2.fastq.gz	Fastqsanger.gz
	SRR6829172.fastq.gz	Fastqsanger.gz

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Whole-transcriptome RNA sequencing and degradome sequencing were performed on maize inbred lines Chang7-2 (resistant to SCMV) and Mo17 (susceptible to SCMV).

Project description:The maize inbred lines Chang7-2 (resistant to SCMV) and Mo17 (susceptible to SCMV) were inoculated with SCMV (SC, SM) and phosphate buffer (MC, MM), respectively to subjected to whole-transcriptome RNA sequencing and degradome sequencing.

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Genome-Wide Identification of microRNAs and Their Targets in Cold-Stored Potato Tubers by Deep Sequencing and Degradome Analysis

Project description:Two small RNA libraries and 2 degradome libraries were constructed from potato tubers stored at room temperature or exposed to cold stress for deep sequencing. Through small RNA sequencing, 53 known miRNAs and 59 novel miRNAs were identified. Seventy genes were identified as miRNA targets by degradome sequencing. Small RNA sequencing and degradome sequencing of control and cold treated Solanum tuberosum tubers

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2015-12-24 | GSE43237 | GEO

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Identification of miRNAs and their target genes associated with improved corn seed vigor induced by gibberellin (GA3) through small RNAs and degradome sequencing

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:Small RNA and degradome sequencing

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An improved method of constructing degradome library suitable for Illumina high-throughput sequencing platform

Project description:Post-transcriptional gene regulation is a critical layer of overall gene expression programs and microRNAs (miRNAs) play an indispensable role in this process by guiding cleavage on the messenger RNA targets. The miRNA-guided cleavage on the mRNA targets can be confirmed by analyzing the sequenced degradome or PARE or GMUCT libraries. However, high-throughput sequencing of PARE or degradome libraries is not as straightforward as sequencing small RNA libraries. Moreover, the currently used degradome or PARE methods utilize Mme1 restriction site and the resulting fragments are only 20-nt long, which often poses difficulty in distinguishing between the family members of the same gene family. In this modified degradome protocol, EcoP15I recognition site is introduced to the 3' end of the 5’RNA adaptor of TruSeq small RNA library, the double strand DNA adaptor sequence is modified to suit with the ends generated by the EcoP15I. These modifications allow amplification of the degradome library by primer pairs used for small RNA library preparation. Therefore, degradome library generated using this protocol can be sequenced as easily as small RNA library, and the resulting tag length is ~27-nt, which is longer than previous methods (20-nt). The protocol allows sequencing small RNA and degradome libraries simultaneously.

2019-12-17 | GSE138545 | GEO

Integrated Four Comparative-Omics Reveals the Mechanism of the Terpenoid Biosynthesis in Two Different Overwintering Cryptomeria fortunei Phenotypes

Project description:Chinese cedar (Cryptomeria fortunei) is a tree species with important ornamental, medicinal, and economic value. Terpenoids extracted from the essential oil of C. fortunei 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 C. fortunei 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 C. fortunei 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 C. fortunei 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

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