Characterization of the stress associated microRNAs in Glycine max by deep sequencing

Li, Haiyan; Dong, Yanjun; Yin, Hai-Long; Wang, Nan; Yang, Jing; Liu, Xiuming; Wang, Yanfang; Wu, Jinyu; Li, Xiaokun

doi:10.1186/1471-2229-11-170

Cited by 154 publications

(103 citation statements)

References 47 publications

(56 reference statements)

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“…Various environmental stresses, in plants, cause overexpress or underexpress miRNAs, thus resulting in novel miRNAs which might be involved in the adaptive response against various stresses (Navarro et al, 2006;Sunkar and Zhu, 2007). It has been reported that stress responsive miRNAs were ubiquitously found in plants including Arabidopsis, Polulus, soybean, or other plants (Gao et al, 2011;Li et al, 2011;Khraiwesh et al, 2012). The stresses include nutrient deficiency (Fuji et al, 2005), cold (Zhou et al, 2008), salinity (Liu et al, 2008), drought (Zhou et al, 2010), mechanical shock (Lu et al, 2005), and bacterial infection (Navaro et al, 2006).…”

Section: Role Of Non-coding Rnas In Abiotic Stress Of Plantmentioning

confidence: 99%

“…In addition to these biological functions, some small RNAs also play roles in various stress responses in plant as well as in animal. These responses include oxidative, nutrient deficiency, dehydration, drought, soil salinity, extreme temperature, or mechanical stress (Gao et al, 2011;Li et al, 2011;Khraiwesh et al, 2012). Plants appear to respond to environmental stresses through regulation of their genes including small non-coding RNAs as well as coding RNAs.…”

Section: Introductionmentioning

confidence: 99%

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Non-coding RNAs Associated with Biotic and Abiotic Stresses in Plants

Kang¹,

Yoon²,

Lee³

et al. 2012

Journal of Applied Biological Chemistry

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Many of biochemical or physiological processes can be regulated by non-coding RNAs as well as coding RNAs in plants, animals and microbes. Recently, many small RNAs including microRNAs (miRNAs) and endogenous small interference RNAs (siRNAs) and long non-coding RNAs have been discovered from ubiquitous organisms including plants. Biotic and abiotic stresses are main causal agents of crop losses all over the world. Much efforts have been performed for understanding the complex mechanism of stress responses. Up to date, many of these researches have been related with the identification and investigation of stress-related proteins, showing limitation to resolve the complex mechanism. Recently, noncoding RNAs as well as coding genes have been gradually interested because of its potential roles in plant stress responses as well as other biophysical aspects. In this review, various potential roles of non-coding RNAs, especially miRNAs and siRNAs, are reviewed in relation with plant biotic and abiotic stresses.

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Section: Role Of Non-coding Rnas In Abiotic Stress Of Plantmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Non-coding RNAs Associated with Biotic and Abiotic Stresses in Plants

Kang¹,

Yoon²,

Lee³

et al. 2012

Journal of Applied Biological Chemistry

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“…Soybean was the first legume species with a published high-quality draft genome sequence (Schmutz et al, 2010). Because miRNAs play an important regulatory role in a wide variety of developmental and metabolic processes in plants, more and more soybean miRNAs have been identified (Zhang et al, 2008;Chen et al, 2009;Wang et al, 2009;Guo et al, 2011;Kulcheski et al, 2011;Li et al, 2011;Song et al, 2011;Wong et al, 2011;Zeng et al, 2012;Hu et al, 2013), but the features of the upstream sequences of these miRNAs have not been comprehensively analyzed. Core promoters and cis-acting elements of 82 soybean miRNAs from the miRBase database were analyzed by bioinformatics methods (Liu et al, 2010), but this analysis involved a relatively small number of miRNA genes.…”

Section: Introductionmentioning

confidence: 99%

Analysis of promoters of microRNAs from a Glycine max degradome library

Han

Zheng

et al. 2014

J. Zhejiang Univ. Sci. B

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Abstract:Objective: MicroRNAs (miRNAs) are genome-encoded, small non-coding RNAs that play important functions in development, biotic and abiotic stress responses, and other processes. Our aim was to explore the regulation of miRNA expression. Methods: We used bioinformatics methods to predict the core promoters of 440 miRNAs identified from a soybean (Glycine max) degradome library and to analyze cis-acting elements for 369 miRNAs. Results: The prediction results showed that 83.86% of the 440 miRNAs contained promoters in their upstream sequences, and 8.64% (38 loci) in their downstream sequences. The distributions of two core promoter elements, TATA-boxes and transcription start sites (TSSs), were similar. The cis-acting elements were examined to provide clues to the function and regulation of spatiotemporal expression of the miRNAs. Analyses of miRNA cis-elements and targets indicated a potential auxin response factor (ARF)-and gibberellin response factor (GARF)-mediated negative feedback loop for miRNA expression. Conclusions: The features of miRNAs from a Glycine max degradome library obtained here provide insights into the transcription regulation and functions of miRNAs in soybean.

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“…The first plant miRNAs were identified in Arabidopsis thaliana (Park et al, 2002); currently the latest miRBase release (v21, June 2014) contains 46231 mature microRNAs. Earlier microRNAs were identified using bioinformatics analysis or Sanger sequencing; currently high-throughput sequencing platforms are showing significant promise for small RNA discovery and genome-wide transcriptome analysis at single-base pair resolution (Li et al, 2011). High-throughput sequencing was used to identify miRNAs in many plant species, such as rice (Sunkar et al, 2008), alfalfa , grape (Pantaleo et al, 2010), tomato , orange (Song et al, 2010), soybean (Song et al, 2011), peanut (Zhao et al, 2010), poplar (Klevebring et al, 2009), and black gram (Paul et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Identification of microRNAs and their targets in Finger millet by high throughput sequencing

Usha

Jyothi

Sharadamma

et al. 2015

Gene

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a b s t r a c t a r t i c l e i n f oMicroRNAs are short non-coding RNAs which play an important role in regulating gene expression by mRNA cleavage or by translational repression. The majority of identified miRNAs were evolutionarily conserved; however, others expressed in a species-specific manner. Finger millet is an important cereal crop; nonetheless, no practical information is available on microRNAs to date. In this study, we have identified 95 conserved microRNAs belonging to 39 families and 3 novel microRNAs by high throughput sequencing. For the identified conserved and novel miRNAs a total of 507 targets were predicted. 11 miRNAs were validated and tissue specificity was determined by stem loop RT-qPCR, Northern blot. GO analyses revealed targets of miRNA were involved in wide range of regulatory functions. This study implies large number of known and novel miRNAs found in Finger millet which may play important role in growth and development.

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Characterization of the stress associated microRNAs in Glycine max by deep sequencing

Cited by 154 publications

References 47 publications

Non-coding RNAs Associated with Biotic and Abiotic Stresses in Plants

Non-coding RNAs Associated with Biotic and Abiotic Stresses in Plants

Analysis of promoters of microRNAs from a Glycine max degradome library

Identification of microRNAs and their targets in Finger millet by high throughput sequencing

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