Illumina®truseq® vs Nebnext® Small Rna Library Preparation Kit for Mirna Profiling in Persicaria Minor: Which Better?

Samad, Abdul Fatah A.; Ali, Nazaruddin Muhammad; Ismail, Ismanizan

doi:10.11113/jt.v77.6720

Cited by 2 publications

(3 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The integrity of the RNA was assessed by running a 1% agarose gel and Bioanalyzer analysis (Agilent 2100 Bioanalyzer, USA). A small RNA library was constructed using the NEBNext Small RNA Library preparation kit as reported by a previous study [22]. Then, the libraries were sent to Universiti Malaya, Malaysia for sequencing using an Illumina HiSeq 2500™ in Rapid Run mode.…”

Section: Methodsmentioning

confidence: 99%

“…Next generation sequencing (NGS), a more recent approach, has also been introduced for miRNA study, and this method has been found to be more advanced and efficient. This approach can detect low copy number miRNAs at levels of one transcript per million [21, 22]. To date, a total of 38,589 miRNAs from animals, plants, and viruses have been discovered and deposited in public miRNA databases [23].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Regulation of terpenoid biosynthesis by miRNA in Persicaria minor induced by Fusarium oxysporum

et al. 2019

Self Cite

View full text Add to dashboard Cite

Background Persicaria minor (kesum) is an herbaceous plant with a high level of secondary metabolite compounds, particularly terpenoids. These terpenoid compounds have well-established roles in the pharmaceutical and food industries. Although the terpenoids of P. minor have been studied thoroughly, the involvement of microRNA (miRNA) in terpenoid regulation remains poorly understood and needs to be explored. In this study, P. minor plants were inoculated with the pathogenic fungus Fusarium oxysporum for terpenoid induction. Result SPME GC-MS analysis showed the highest terpenoid accumulation on the 6th day post-inoculation (dpi) compared to the other treatment time points (0 dpi, 3 dpi, and 9 dpi). Among the increased terpenoid compounds, α-cedrene, valencene and β-bisabolene were prominent. P. minor inoculated for 6 days was selected for miRNA library construction using next generation sequencing. Differential gene expression analysis showed that 58 miRNAs belonging to 30 families had significantly altered regulation. Among these 58 differentially expressed genes (DEGs), 33 miRNAs were upregulated, whereas 25 miRNAs were downregulated. Two putative novel pre-miRNAs were identified and validated through reverse transcriptase PCR. Prediction of target transcripts potentially involved in the mevalonate pathway (MVA) was carried out by psRobot software, resulting in four miRNAs: pmi-miR530, pmi-miR6173, pmi-miR6300 and a novel miRNA, pmi-Nov_13. In addition, two miRNAs, miR396a and miR398f/g, were predicted to have their target transcripts in the non-mevalonate pathway (MEP). In addition, a novel miRNA, pmi-Nov_12, was identified to have a target gene involved in green leaf volatile (GLV) biosynthesis. RT-qPCR analysis showed that pmi-miR6173, pmi-miR6300 and pmi-nov_13 were downregulated, while miR396a and miR398f/g were upregulated. Pmi-miR530 showed upregulation at 9 dpi, and dynamic expression was observed for pmi-nov_12. Pmi-6300 and pmi-miR396a cleavage sites were detected through degradome sequence analysis. Furthermore, the relationship between miRNA metabolites and mRNA metabolites was validated using correlation analysis. Conclusion Our findings suggest that six studied miRNAs post-transcriptionally regulate terpenoid biosynthesis in P. minor . This regulatory behaviour of miRNAs has potential as a genetic tool to regulate terpenoid biosynthesis in P. minor . Electronic supplementary material The online version of this article (10.1186/s12864-019-5954-0) contains supplementary material, which is available to authorized users.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Regulation of terpenoid biosynthesis by miRNA in Persicaria minor induced by Fusarium oxysporum

et al. 2019

Self Cite

View full text Add to dashboard Cite

show abstract

“…DNA libraries for sequencing were prepared with three kinds of preparation kits; TruSeq Small RNA Library Prep Kit (TruSeq, Illumina, Inc.) [19], NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEBNext, New England BioLabs Inc.) and SMARTer1 micro-RNA-Seq Kit (SMARTer, Takara Bio USA, Inc.) [20][21][22]. In general, manufacturer's protocols were used except for the final size selection step.…”

Section: Sequencingmentioning

confidence: 99%

Expression analysis of box C/D snoRNAs with SNPs between C57BL/6 and MSM/Ms strains in male mouse

et al. 2023

View full text Add to dashboard Cite

MSM/Ms mouse derived from the Japanese wild mouse has unique characteristics compared to the widely used C57BL/6 mouse. To examine the usefulness of the MSM/Ms mouse for the comparative genomic analysis, expression of small RNAs were analyzed by the large-scale sequence analysis for two strains of mouse, C57BL/6 and MSM/Ms. As a trial, expression of box C/D snoRNAs, which are the most abundant small RNAs in the cell, were analyzed. By the comparison of the read number for each fragment, 11 snoRNAs with single nucleotide polymorphisms (SNPs) were detected. One of the snoRNAs, SNORD53, shows the expression only for MSM/Ms and this snoRNA has a mutation in the box sequence in C57BL/6. Thus, it was demonstrated that the proposed experimental system using SNPs can give new insight for the gene expression regulation.

show abstract

Illumina®truseq® vs Nebnext® Small Rna Library Preparation Kit for Mirna Profiling in Persicaria Minor: Which Better?

Cited by 2 publications

References 15 publications

Regulation of terpenoid biosynthesis by miRNA in Persicaria minor induced by Fusarium oxysporum

Regulation of terpenoid biosynthesis by miRNA in Persicaria minor induced by Fusarium oxysporum

Expression analysis of box C/D snoRNAs with SNPs between C57BL/6 and MSM/Ms strains in male mouse

Contact Info

Product

Resources

About