Computational identification of microRNAs and their targets in Gossypium hirsutum expressed sequence tags

Qiu, Cheng; Xie, Fu Liang; Zhu, Yiyong; Guo, Kai; Nie, Li; Yang, Zhi Min

doi:10.1016/j.gene.2007.01.034

Cited by 125 publications

(91 citation statements)

References 61 publications

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“…A maximum of 19 miRNAs and minimum of 1 miRNA were detected in a single family, and the length of matured ranged from 18 to 22 nt long (Table 2 and Fig. 1), consistent with the findings in B. napus and cotton (Qiu et al, 2007). The majority of miRNAs were 21 nt long (54.84%) followed by, 20 (21.51%), 19 (10.22%) 18 (9.14%), and 22 (2.69%) (Fig.…”

Section: Resultssupporting

confidence: 88%

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

Dhandapani

Ramchiary

Pavlidis

et al. 2011

Molecules and Cells

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MicroRNAs (miRNAs) are recently discovered, noncoding, small regulatory RNA molecules that negatively regulate gene expression. Although many miRNAs are identified and validated in many plant species, they remain largely unknown in Brassica rapa (AA 2n =, 20). B. rapa is an important Brassica crop with wide genetic and morphological diversity resulting in several subspecies that are largely grown for vegetables, oilseeds, and fodder crop production. In this study, we identified 186 miRNAs belonging to 55 families in B. rapa by using comparative genomics. The lengths of identified mature and pre-miRNAs ranged from 18 to 22 and 66 to 305 nucleotides, respectively. Comparison of 4 nucleotides revealed that uracil is the predominant base in the first position of B. rapa miRNA, suggesting that it plays an important role in miRNA-mediated gene regulation. Overall, adenine and guanine were predominant in mature miRNAs, while adenine and uracil were predominant in pre-miRNA sequences. One DNA sequence producing both sense and antisense mature miRNAs belonging to the BrMiR 399 family, which differs by 1 nucleotide at the, 20 th position, was identified. In silico analyses, using previously established methods, predicted 66 miRNA target mRNAs for 33 miRNA families. The majority of the target genes were transcription factors that regulate plant growth and development, followed by a few target genes that are involved in fatty acid metabolism, glycolysis, biotic and abiotic stresses, and other cellular processes. Northern blot and qRT-PCR analyses of RNA samples prepared from different B. rapa tissues for 17 miRNA families revealed that miRNAs are differentially expressed both quantitatively and qualitatively in different tissues of B. rapa.

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Section: Resultssupporting

confidence: 88%

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

Dhandapani

Ramchiary

Pavlidis

et al. 2011

Molecules and Cells

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“…The formation of the secondary structure stem-loop was obtained using Mfold (Table 2), a broadly used algorithm for computational prediction of miRNAs in plants (Zhang et al, 2005;Qiu et al, 2007;Subramanian et al, 2008;Wang et al, 2009;Kulcheski et al, 2011) based mainly on minimum estimates of ΔG (Zuker, 2003). The free energy of pre-miRNAs is generally lower than in that in other noncoding RNAs (ncRNAs) (Bonnet et al, 2004); therefore, an important parameter in predicting new miRNAs is the quantification of the stability of secondary structures (Mathews and Turner, 2006).…”

Section: Resultsmentioning

confidence: 99%

“…Despite the current knowledge of miRNAs involved in the regulation of nodulation, activity during the initial stages (e.g., the regulation of homeostasis and auxin signaling process) and nodule maturation (e.g., the nitrogen fixation process) (Subramanian et al, 2008;Wang et al, In silico identification of miRNAs 2009; Li et al, 2010), their functions are still not fully understood. Computational strategies have proven to be successful, highly effective, and important in identifying new miRNAs, as shown by the studies of Qiu et al (2007), Xie et al (2007), and Lu and Yang (2010), among others, where new miRNAs and target genes were identified by in silico analysis based on expressed sequence tags of Gossypium hirsutum, Brassica napus, and Vigna unguiculata, respectively. Our study performed an in silico analysis of miRNAs and their target genes present in a subtractive library of soybean roots inoculated with the Bradyrhizobium japonicum strain CPAC 15 obtained in a previous study (Barros de Carvalho et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Prediction of potential novel microRNAs in soybean when in symbiosis

Barros-Carvalho¹,

Paschoal²,

Marcelino-Guimarães³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. MicroRNAs (miRNAs) are small molecules, noncoding proteins that are involved in many biological processes, especially in plants; among these processes is nodulation in the legume. Biological nitrogen fixation is a key process, with critical importance to the soybean crop. This study aimed to identify the potential of novel miRNAs to act during the root nodulation process. We utilized a set of transcripts that were differentially expressed in soybean roots 10 days after inoculation with Bradyrhizobium japonicum, which were obtained in a previous study, and performed a set of computational analyses that led us to select new miRNAs potentially involved in nodulation. Among these analyses, the set of transcripts were submitted to an in silico annotation of noncoding RNAs, including a search of similarity against miRNA public databases, ab initio tools for miRNA identification, structural search against miRNA families, prediction of the secondary structure of miRNA precursors, and prediction of the sequences of mature miRNAs. Subsequently, we applied filter procedures based on miRNA selections described in the literature (e.g., free energy value). In the next step, a manual curation inspection of the annotation was performed and the top candidates were selected and used for prediction of potential target genes, which were later checked manually in the database of the soybean genome. This prediction led us to the identification of 9 potential new miRNAs; among these, 4 were conserved in other plants. Moreover, we predicted their target genes might play important roles in the regulation of nodulation.

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“…miRNAs have also been identified in other plant species, such as Nicotiana tabacum (Billoud et al 2005), Zea mays (Dezulian et al 2005), Sorghum bicolor (Bedell et al 2005), Populus Tuskan et al 2006), Gossypium hirsutum (Qiu et al 2007), Brassica napus ) and Vitis vinifera (Velasco et al 2007). Furthermore, miRNAs were predicted to play important roles in mosses Physcomitrella (Arazi et al 2005), and unicellular green alga C. reinhardtii (Zhao et al 2007).…”

Section: Mirnas and Plant Defensementioning

confidence: 99%

Roles of microRNA in plant defense and virus offense interaction

Gan

Chi

et al. 2008

Plant Cell Rep

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MicroRNAs (miRNA) that are around 22 nucleotides long non-protein-coding RNAs, play key regulatory roles in plants. Recent research findings show that miRNAs are involved in plant defense and viral offense systems. Advances in understanding the mechanism of miRNA biogenesis and evolution are useful for elucidating the complicated roles they play in viral infection networks. In this paper a brief summary of evolution of plant antivirus defense is given and the function of miRNAs involved in plant-virus competition is highlighted. It is believed that miRNAs have several advantages over homology-dependent and siRNA-mediated gene silencing when they are applied biotechnologically to promote plant anti-virus defense. miRNA-mediated anti-virus pathway is an ancient mechanism with a promising future. However, using miRNAs as a powerful anti-virus tool will be better realized only if miRNA genomics and functions in plant viral infection are fully understood.

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Computational identification of microRNAs and their targets in Gossypium hirsutum expressed sequence tags

Cited by 125 publications

References 61 publications

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

Prediction of potential novel microRNAs in soybean when in symbiosis

Roles of microRNA in plant defense and virus offense interaction

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