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Series GSE70423 Query DataSets for GSE70423
Status Public on Jul 01, 2015
Title High-throughput sequencing of Moringa oleifera microRNAs: a bioinformatics and functional approach for cross-kingdom regulation
Organism Moringa oleifera
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary MicroRNAs (miRNAs) are endogenous, noncoding, smallRNAs that regulate gene expression at the post-transcriptional level during plant development, growth and seed germination. Among all medicinal plants, Moringa oleifera is one of the most useful trees for which, despite its diffusion, no information about its miRNAs and their respective target genes is available. In this research, we report results obtained from a high-throughput sequencing analysis performed with the Illumina platform. A total of 31,290,964 raw reads were produced from M. oleifera seed smallRNA library. First, we found 99 conserved miRNAs and 43 novel ones that we partially validated by qRT- PCR. Second, by comparing their expression abundances with those of other common plants, we identified 20 conserved M. oleifera miRNAs. For both these results an in silico analysis allowed us to predict some of their targets which in turn allowed us to link them to a wide range of physiological processes. Based on qRT-PCR expression analyses, we reported the expression profile of some selected conserved miRNAs in different M. oleifera tissues (roots, stems and leafs). We compared the most conserved miRNAs found in Moringa with those of other edible plants, such as Olea europaea and Brassica rapa. Furthermore, by taking advantage of a recently developed web- application based on an algorithm that compares plants and mammalian miRNAs, we identify a few possible plant miRNAs with functional homologies with mammalian ones. We used the 20 most abundant M. oleifera miRNAs to conduct a preliminary analysis to investigate potential cross-kingdom gene regulation. To our knowledge, this is the first report of M. oleifera miRNAs that uses high-throughput sequencing analysis. Our analysis increases the amount of information about plant miRNAs currently available and it can help us understanding the molecular mechanism of this medical plant.
 
Overall design microRNA profile of M. oleifera seed, germinated on paper soaked in sterile water.
 
Contributor(s) Pirro S, Galgani A
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Submission date Jun 30, 2015
Last update date May 15, 2019
Contact name Stefano Pirro'
E-mail(s) stefano.pirro@uniroma2.it
Phone +390672594237
Organization name University of Rome "Tor Vergata"
Department Biology
Street address Via della Ricerca Scientifica
City Rome
ZIP/Postal code 00133
Country Italy
 
Platforms (1)
GPL20643 Illumina HiSeq 2500 (Moringa oleifera)
Samples (1)
GSM1730487 m_oleifera_seed_s1
Relations
BioProject PRJNA288608
SRA SRP060001

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE70423_RAW.tar 16.2 Mb (http)(custom) TAR (of CSV, FASTA, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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