Criteria for Annotation of Plant MicroRNAs

By Blake C. Meyers, Michael J. Axtell, B. Bartel, David P. Bartel, David C. Baulcombe, J. Bowman, Xiaofeng Cao, James C. Carrington, Xuemei Chen, Pamela J. Green and 11 more. The Plant Cell Online, 2008

1,197 citations recorded by the source corpus.

Subfields: Plant Science

View Paper: https://www.semanticscholar.org/paper/62c4feda673bc935229a239268f77a3afa9122cd

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Citations in the corpus

Uncovering Small RNA-Mediated Responses to Phosphate Deficiency in Arabidopsis by Deep Sequencing1[W][OA] (2009, background): “5C), the primary criterion of miRNA definition (Meyers et al., 2008).”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, positive): “To identify previously undiscovered miRNAs, a standard computation pipeline was applied based on the recently published criteria for plant microRNAs (Meyers et al., 2008).”
PsRobot: a web-based plant small RNA meta-analysis toolbox (2012, background): “This has made the predictions for plant miRNA targets relatively straightforward, yielding limited numbers of targets per miRNA rather than hundreds of ones in animals (9,13).”
miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments (2012, background): “These different properties has resulted that the miRNA analysis pipelines, such as novel miRNA prediction and target prediction, are quite different between plants and animals [9-11].”
Identification and validation of conserved microRNAs along with their differential expression in roots of Vigna unguiculata grown under salt stress (2010, background): “The potential pre-miRNAs should meet all of the following criteria (Zhang et al. 2006c; Meyers et al. 2008) as described previously: (a) predicted mature miRNAs have 0–3 nt mismatches compared with the query sequences; (b) the secondary structure of the candidate sequences should have the stem-loop…”
Origin, biogenesis, and activity of plant microRNAs. (2009, positive): “, 2003), only one remains strongly reliable in plants: that miRNAs are precisely excised as discrete species from the stem of an imperfect stem-loop precursor, whereas siRNAs occur as populations produced from perfect or near-perfect RNA duplexes (Meyers et al., 2008).”
miRBase: integrating microRNA annotation and deep-sequencing data (2010, background): “Updated annotation criteria were recently suggested to distinguish microRNAs from other classes of short RNAs in plants (9).”
Evolution and Functional Diversification of MIRNA Genes (2011, background): “Many roads to maturity: MicroRNA biogenesis pathways and their regulation. Nat. Cell Biol. 11: 228–234. Wright, S.I., Lauga, B., and Charlesworth, D. (2002). Rates and patterns of molecular evolution in inbred and outbred Arabidopsis.”
ShortStack: comprehensive annotation and quantification of small RNA genes. (2013, methodology): “Importantly, annotation as a MIRNA locus by ShortStack requires a strict set of structural and expression-based criteria, following the recommendations of Meyers et al. (2008).”
RNA-based antiviral immunity (2010, background): “Therefore, these virus-derived small RNAs are distinct from miRNAs, which are excised from one stem of a stem–loop precursor as a single, discrete specie”