In silico identification and characterization of conserved plant microRNAs in barley

Wu, Xiaoming; Hornyik, Csaba; Bayer, Micha; Marshall, David; Waugh, Robbie; Zhang, Runxuan

doi:10.2478/s11535-014-0308-z

Cited by 3 publications

(5 citation statements)

References 52 publications

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“…(2017) reported in silico miRNA identification approach as an accurate, precise, less expensive, fast and reliable method [ 37 , 53 ]. The principle employed for the computational analysis include correct hairpins secondary structure, high degree evolutionary conservation between the closely related species and value of minimum folding energy [ 2 , 5 , 7 , 9 , 10 ]. We believe that the methodology opted here is sensitive enough to predict the miRNA homologs as performed by [ 5 ].…”

Section: Discussionmentioning

confidence: 99%

“…MicroRNA (miRNAs) are a class of non-coding short RNAs [ 1 , 2 ] that regulate the gene expression by post-transcriptional gene silencing by catalyzing the cleavage or by translational repression of target messenger RNA (mRNA) [ 3 , 4 ]. They play important regulatory roles in both animals [ 5 , 6 ] and plants [ 4 , 7 ] as well as found in viruses [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

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In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattle

et al. 2018

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The modern cattle was domesticated from aurochs, sharing its physiological traits into two subspecies Bos taurus and Bos indicus. MicroRNAs (miRNAs) are a class of non-coding short RNAs of ~22nt which have a key role in the regulation of many cellular and physiological processes in the animal. The current study was aimed to predict and annotate the potential mutations in indicine miRNAs throughout the genome using de novo and homology-based in silico approaches. Genome-wide mapping was performed in available indicine assembly by the homology-based approach and 768 miRNAs were recovered out of 808 reported taurine miRNAs belonging to 521 unique mature miRNA families. While 42 precursors were dropped due to lack of secondary miRNA structure, increasing stringency or decreasing similarity between the two genomes’ miRNA. Increasing tendency of miRNAs incidence was observed on chr5, chr7, chr8, chr12 and chr21 with 19 polycistronic miRNA within 1-kilobase distance throughout the indicine genome. Notably, 12 miRNAs showed copy number variation. Eighteen miRNAs showed a mutation in their mature sequences in which eight were found in their seed region. Whilst in de novo based approach, 12 novel potential miRNAs on Y chromosome in indicine cattle along with a new miRNA (bind-miR-1264) on chrX were found. The final data set is annotated and explains the impending target genes that are responsible for enhanced immunity, heat tolerance and disease tolerance regulation in indicine. The study conforms to better understanding and perceptive approach towards indicine genome.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattle

et al. 2018

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“…The differential response of miR408 in reported studies could also be due to the different developmental stages of testes plant, stress intensity, growth conditions and methods employed to monitor miRNAs activity (Zhang, 2015). Two other types of nutrition-sensitive markers, hvu-miR399 and hvu-miR827 belong to the most conserved miRNA families in barley genome (Wu et al, 2014), which points to their importance in plants genome. They play an important role in regulatory mechanisms related to nutrient homeostasis (Hsieh et al, 2009;Schreiber et al, 2011;Wu et al, 2014;Melnikova et al, 2015;Melnikova et al, 2016).…”

Section: Resultsmentioning

confidence: 92%

“…Two other types of nutrition-sensitive markers, hvu-miR399 and hvu-miR827 belong to the most conserved miRNA families in barley genome (Wu et al, 2014), which points to their importance in plants genome. They play an important role in regulatory mechanisms related to nutrient homeostasis (Hsieh et al, 2009;Schreiber et al, 2011;Wu et al, 2014;Melnikova et al, 2015;Melnikova et al, 2016). We assumed that as a consequence of water deprivation the plants will suffer of nutrition deficiency.…”

Section: Resultsmentioning

confidence: 99%

MicroRNA-based markers as a tool to monitor the barley (Hordeum vulgare L.) response to soil compaction

Ražná

Rataj

Macák

et al. 2020

Acta fytotechn zootechn

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Plants are often exposed to adverse environmental conditions that can significantly interfere with their genomic response. Soil compaction induced by heavy field machinery represents a major problem for crop production mainly due to restricted root growth and penetration into soil and therefore reduced water and nutrient uptake by the plants. Tested hypotheses were to declare whether the plant‘s genome responds to soil compaction and whether the microRNA-based markers are suitable to determine this response. A long term field scale experiment was established in 2009 where different levels of soil compaction are researched from the soil and crop point of view. The analyzed barley (Hordeum vulgare L.) plants were collected during the growing season in 2019. The effect of soil compaction was analysed by four different DNA-based markers corresponding to miRNA sequences of dehydratation stress-responsive barley miRNAs (hvu-miR156, and hvu-miR408) and nutrition-sensitive markers (hvu-miR399 and hvu-miR827), within the leaf, stem and root tissues of barley plants. Our preliminary data support hypotheses that plant genome response was tissue-specific due to significant induction of the biomarkers to dehydratation and nutrition stress. The most affected part of the plant by dehydration, were roots and lack of nutrient supply was most pronounced on leaves.

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“…Mature plant miRNAs are 19–25-nucleotide-long ribonucleic acids that can have either intergenic (miRNA gene is localized between two protein-coding sequences of the DNA) or intragenic origin [ 26 ], where miRNAs are cleaved from the mRNA sequences during the splicing (also called intron-derived miRNAs [ 27 ]). Specifically, in barley, more than 75% of miRNAs are transcribed from intergenic loci [ 28 ]. The biogenesis of miRNAs is ensured by the DNA-dependent RNA polymerase II which is responsible for the biosynthesis itself [ 2 ].…”

Section: Plant Mirnas—biogenesis and Regulatory Potentialmentioning

confidence: 99%

What Do We Know about Barley miRNAs?

Volná

Bartas

Pečínka

et al. 2022

IJMS

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Plant miRNAs are powerful regulators of gene expression at the post-transcriptional level, which was repeatedly proved in several model plant species. miRNAs are considered to be key regulators of many developmental, homeostatic, and immune processes in plants. However, our understanding of plant miRNAs is still limited, despite the fact that an increasing number of studies have appeared. This systematic review aims to summarize our current knowledge about miRNAs in spring barley (Hordeum vulgare), which is an important agronomical crop worldwide and serves as a common monocot model for studying abiotic stress responses as well. This can help us to understand the connection between plant miRNAs and (not only) abiotic stresses in general. In the end, some future perspectives and open questions are summarized.

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In silico identification and characterization of conserved plant microRNAs in barley

Abstract: Abstract

Cited by 3 publications

References 52 publications

In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattle

In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattle

MicroRNA-based markers as a tool to monitor the barley (Hordeum vulgare L.) response to soil compaction

What Do We Know about Barley miRNAs?

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