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Discovery of novel and conserved microRNAs in Spirodela polyrhiza by deep sequencing

ABSTRACT: MicroRNAs (miRNAs) are a class of small, endogenous non-coding RNAs, which play key roles in a variety of developmental and physiological processes by regulating gene expressions at post-transcriptional or translational levels. The objective of our work was to explore conserved and novel miRNAs in Spirodela at the whole-genome level, and further characterize their potential roles in gene regulation.

ORGANISM(S): Spirodela polyrhiza

PROVIDER: GSE55208 | GEO | 2014/02/21

SECONDARY ACCESSION(S): PRJNA238917

REPOSITORIES: GEO

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Discovery of novel and conserved microRNAs in Spirodela polyrhiza by deep sequencing

Project description:MicroRNAs (miRNAs) are a class of small, endogenous non-coding RNAs, which play key roles in a variety of developmental and physiological processes by regulating gene expressions at post-transcriptional or translational levels. The objective of our work was to explore conserved and novel miRNAs in Spirodela at the whole-genome level, and further characterize their potential roles in gene regulation. 1 sample

2014-02-21 | E-GEOD-55208 | biostudies-arrayexpress

Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata)

Project description:MicroRNAs (miRNAs) play a critical role in post-transcriptional gene regulation. miRNAs have been shown to control many genes involved in various biological and metabolic processes. Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants. In this research, we used Solexa sequencing to discover new microRNAs in trifoliate orange (Citrus trifoliata) an important rootstock of citrus. A total of 13,106,753 reads representing 4,876,395 distinct sequences were obtained from a short RNA library generated from small RNA extracted from C. trifoliata flower and fruit tissues, Based on sequence similarity and hairpin structure prediction, we found that 178,102 reads representing 89 sequences from 42 highly conserved miRNA families, have perfect matches to known miRNAs. We also identified 10 novel miRNA candidates, whose precursors were all potentially generated from citrus ESTs. And of them five miRNA* sequences were also sequenced. These sequences had not been described in other plant species and accumulation of these 10 novel miRNAs were confirmed by qRT-PCR analysis. Potential target genes were predicted for most conserved and novel miRNAs. Moreover, four target genes included one encoding IRX12 copper ion binding/ oxidoreductase and three genes encoding NB-LRR disease resistance protein have been experimentally verified by detection of the miRNA-mediated mRNA cleavage in C. trifoliata.

2010-08-18 | GSE22089 | GEO

Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata)

2010-08-17 | E-GEOD-22089 | biostudies-arrayexpress

Spirodela polyrhiza

Project description:Spirodela polyrhiza overview

| PRJNA46627 | ENA

Spirodela polyrhiza root and frond phosphate starvation RNA-Seq

Project description:Spirodela polyrhiza (9509) was grown under replete conditions for 10d, subject to media without phosphate or control for 24h, and then sequenced.

2023-03-05 | GSE226143 | GEO

A Spirodela polyrhiza genome and proteome reveal conserved chromosomal structure and translation favoring energy production

Project description:Duckweeds are a monophyletic group of rapidly reproducing aquatic monocots in the Lemnaceae family. Spirodela polyrhiza, the Greater Duckweed, has the largest body plan yet the smallest genome size in the family (1C = 150 Mb). Given their clonal, exponentially fast reproduction, a key question is whether genome structure is conserved across the species in the absence of meiotic recombination. We generated a highly contiguous, chromosome-scale assembly of Spirodela polyrhiza line Sp7498 using Oxford Nanopore plus Hi-C scaffolding (Sp7498_HiC) that is highly syntenic with a related line (Sp9509). Both the Sp7498_HiC and Sp9509 genome assemblies reveal large chromosomal misorientations in a recent PacBio assembly of Sp7498, highlighting the necessity of orthogonal long-range scaffolding techniques like Hi-C and BioNano optical mapping. Proteome analysis of Sp7498 verified the expression of nearly 2,250 proteins and revealed a high level of proteins involved in photosynthesis and carbohydrate metabolism among other functions. In addition, a strong increase in chloroplast proteins was observed that correlated to chloroplast density. This Sp7498_HiC genome was generated cheaply and quickly with a single Oxford Nanopore MinION flow cell and one Hi-C library in a classroom setting. Combining these data with a mass spectrometry-generated proteome, demonstrates that duckweed is a model for genomics- and proteomics-based education.

2022-10-26 | PXD017093 | Pride

Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata).

Project description: Not available

| S-EPMC2996959 | biostudies-literature

Spirodela polyrhiza strain:7498

Project description:Spirodela polyrhiza mitochondrial genome

| PRJNA67853 | ENA

Spirodela polyrhiza

Project description:Spirodela polyrhiza clone 9509 sequenced with Oxford Nanopore

| PRJEB27612 | ENA

A comprehensive survey of degradation and 3′ end modification of plant microRNAs by deep sequencing

Project description:The degradation and 3′ end modification of plant microRNAs (miRNAs) play crucial roles in regulating miRNA function and stability. However, the process and mechanism of miRNA degradation and 3′ end modification has, to date, been poorly characterized. Here, we report that analysis of the two small RNA libraries constructed from two hickory floral differentiation stages by deep sequencing obtained a large number of truncated miRNAs and miRNAs with 3′ end modifications. The presence of so many truncated miRNAs suggests that plant miRNAs may be degraded through the 5′ to 3′ and 3′ to 5′ ends simultaneously, but the probability of miRNAs being truncated from the 3′ end was higher than from the 5′ end. Single- or double-nucleotide 3′ additions to miRNAs has been observed in many families. In this study, the 3′ addition of adenine to miRNA was the most common, accounting for more than 50% of all miRNA 3′ end modification in both small RNA libraries, followed by uridine addition. This suggests that the 3′ end modification of miRNAs shows a bias towards adenine and uridine in plants. Furthermore, we observed that both truncated miRNA and isomiR expressions associated with mature miRNAs. Our study provides more information regarding the degradation and 3′ end modification of miRNAs in plants. Examination of 2 different female flower buds

2014-07-02 | E-GEOD-48584 | biostudies-arrayexpress

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