Bioinformatic identification and expression analysis of new microRNAs from Medicago truncatula

Zhou, Zhao; Huang, Shudong; Yang, Zhi Min

doi:10.1016/j.bbrc.2008.07.083

Cited by 166 publications

(129 citation statements)

References 41 publications

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“…Therefore, one should expect that these miRNAs should be functional. This approach was successfully used for the identification of new miRNAs in plants (Zhang et al 2005;Yao et al 2007;Dryanova et al 2008;Sunkar and Jagadeeswaran 2008;Zhou et al 2008;Unver and Budak 2009). miRNA sequences of main monocot species with the greatest number of registered miRNAs were used in blast analysis.…”

Section: Discussionmentioning

confidence: 99%

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Bioinformatic identification and expression analysis of new microRNAs from wheat (Triticum aestivum L.)

2017

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As an essential regulatory component in plants, microRNAs (miRNAs) have been intensively studied over the past decade. Although hundreds of miRNAs have been identified and analyzed in many important crops and model plants, very little is known about the function of common wheat (Triticum aestivum L.) miRNAs. In this study, we performed computational prediction of novel wheat miRNAs based on BLAST searches of the expressed sequence tag database. The expression profiles of all miRNAs were performed for both vegetative and reproductive tissues to identify developmentally regulated miRNAs. A total of 19 new miRNAs belonging to 12 MIR families were identified using stringent criteria for miRNA annotation. For all of the miRNAs, the secondary structures of their precursor sequences were predicted. Two pairs of distinct miRNAs were found to be located on the same precursor. The predicted miRNAs were experimentally verified by a stemloop qRT-PCR-based assay. The expression profiles were performed in both vegetative and reproductive tissues to find the potential correlations between the developmental phase and miRNA activity. Thirteen out of 19 miRNAs were upregulated at certain phases of plant development, and three of them (miR319, miR395, and miR171) showed the greatest expression in young spikes during microsporogenesis. Our results provide useful information for future studies of miRNA-mediated regulation of flower and grain development in wheat.

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Section: Discussionmentioning

confidence: 99%

“…The putative miRNA sequences are then validated based on criteria proposed for miRNA annotation. Although only conserved miRNAs can be found by blast searches, the vast amount of plant miRNAs have been identified by this strategy (Yao et al 2007;Dryanova et al 2008;Sunkar and Jagadeeswaran 2008;Zhou et al 2008).…”

Section: Electronic Supplementary Materialsmentioning

confidence: 99%

Bioinformatic identification and expression analysis of new microRNAs from wheat (Triticum aestivum L.)

2017

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“…Identification of miRNAs using EST analysis has two significant advantages (1) There is no specialized software required and it can be used to identify miRNAs in any species if they are previously registered EST sequences; (2) Since EST are derived from transcribed sequences, EST analysis also provided direct evidence for miRNA expression. In view of these advantages, EST analysis had been used to identify conserved miRNAs in Brassica napus (Xie et al, 2007), Medicago truncatula (Zhou et al, 2008), Lycopersicon esculentum (Yin et al, 2008), Glycine max (Zhang et al, 2008), citrus (Song et al, 2010), Nicotiana tabacum , Panicum virgatum , Solanum tuberosum (Xie et al, 2011), Malus domestica , strawberry (Dong et al, 2012), etc.…”

Section: Introductionmentioning

confidence: 99%

Identification of miRNAs and their targets in tea (Camellia sinensis)

Zhu

Luo

2013

J. Zhejiang Univ. Sci. B

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MicroRNAs (miRNAs) are endogenous small RNAs playing a crucial role in plant growth and development, as well as stress responses. Among them, some are highly evolutionally conserved in the plant kingdom, this provide a powerful strategy for identifying miRNAs in a new species. Tea (Camellia sinensis) is one of the most important commercial beverage crops in the world, but only a limited number of miRNAs have been identified. In the present study, a total of 14 new C. sinensis miRNAs were identified by expressed sequence tag (EST) analysis from 47 452 available C. sinensis ESTs. These miRNAs potentially target 51 mRNAs, which can act as transcription factors, and participate in stress response, transmembrane transport, and signal transduction. Analysis of gene ontology (GO), based on these targets, suggested that 37 biological processes were involved, such as oxidation-reduction process, stress response, and transport. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis inferred that the identified miRNAs took part in 13 metabolic networks. Our study will help further understanding of the essential roles of miRNAs in C. sinensis growth and development, and stress response.

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“…Majority of miRNAs are conserved across the species making it possible to identify putative miRNAs in other species using comparative genomics (Ding et al 2013 ). Recently, it has been reported that miRNAs act as crucial regulators of multiple physiological processes, including plant development, signal transduction, and adaption to heavy metal stresses (Sunkar et al 2006 ;Zhou et al 2008Zhou et al , 2012Huang et al 2009 ;Mendoza-Soto et al 2012 ;Hartwig 1995, Jagadeesan et al 2010. Some of the studies on cadmium stress regulatory microRNAs in O. sativa (Huang et al 2009, Ding et al 2011, B. napus (Zhou et al 2012 ), and M. truncatula (Zhou et al 2008 ) and the putative stress-related functions were annotated (Table 11.4 ).…”

Section: Functional Genomics Of Heavy Metal Tolerance In Plants: Apprmentioning

confidence: 99%

Analysis of Signaling Pathways During Heavy Metal Toxicity: A Functional Genomics Perspective

Rout

Panigrahi

2015

Elucidation of Abiotic Stress Signaling in Plants

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Abiotic stresses have major limiting factors for plant growth and crop productivity. Plants have different mechanisms to maintain the physiological concentrations of essential metal ions and to minimize exposure to non-essential heavy metals. Some mechanisms are ubiquitous because they are also required for general metal homeostasis, and they minimize the damage caused by high concentrations of heavy metals in plants by detoxifi cation, thereby conferring tolerance to heavy metal stress. Metals in the cell are addressed using a range of storage and detoxifi cation strategies, including metal transport, chelating, traffi cking, and sequestration into the vacuole. A large number of genes encoding MAPK pathway components have a major role in cell proliferation and hormone action as well as in stress signaling. Germin-like protein genes were developed by various stresses including metal stress. Functional genomics (integrating genome sequencing, transcriptomics, proteomics, metabolomics, ionomics, and phenomics) allows large-scale gene function analysis with high-throughput technology and incorporates interaction of gene products at cellular and organism level.

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Bioinformatic identification and expression analysis of new microRNAs from Medicago truncatula

Cited by 166 publications

References 41 publications

Bioinformatic identification and expression analysis of new microRNAs from wheat (Triticum aestivum L.)

Bioinformatic identification and expression analysis of new microRNAs from wheat (Triticum aestivum L.)

Identification of miRNAs and their targets in tea (Camellia sinensis)

Analysis of Signaling Pathways During Heavy Metal Toxicity: A Functional Genomics Perspective

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