MirCure: a tool for quality control, filter and curation of microRNAs of animals and plants

Molecular evolution and functional modification of plant miRNAs with CRISPR

Gene editing using clustered regularly interspaced short palindromic repeat/CRISPR-associated proteins (CRISPR/Cas) has revolutionized biotechnology and provides genetic tools for medicine and life sciences. However, the application of this technology to miRNAs, with the function as negative gene regulators, has not been extensively reviewed in plants. Here, we summarize the evolution, biogenesis, and structure of miRNAs, as well as their interactions with mRNAs and computational models for predicting target genes. In addition, we review current advances in CRISPR/Cas for functional analysis and for modulating miRNA genes in plants. Extending our knowledge of miRNAs and their manipulation with CRISPR will provide fundamental understanding of the functions of plant miRNAs and facilitate more sustainable and publicly acceptable genetic engineering of crops.

The Multiverse of Plant Small RNAs: How Can We Explore It?

Plant small RNAs (sRNAs) are a heterogeneous group of noncoding RNAs with a length of 20–24 nucleotides that are widely studied due to their importance as major regulators in various biological processes. sRNAs are divided into two main classes—microRNAs (miRNAs) and small interfering RNAs (siRNAs)—which differ in their biogenesis and functional pathways. Their identification and enrichment with new structural variants would not be possible without the use of various high-throughput sequencing (NGS) techniques, allowing for the detection of the total population of sRNAs in plants. Classifying sRNAs and predicting their functional role based on such high-performance datasets is a nontrivial bioinformatics task, as plants can generate millions of sRNAs from a variety of biosynthetic pathways. Over the years, many computing tools have been developed to meet this challenge. Here, we review more than 35 tools developed specifically for plant sRNAs over the past few years and explore some of their basic algorithms for performing tasks related to predicting, identifying, categorizing, and quantifying individual sRNAs in plant samples, as well as visualizing the results of these analyzes. We believe that this review will be practical for biologists who want to analyze their plant sRNA datasets but are overwhelmed by the number of tools available, thus answering the basic question of how to choose the right one for a particular study.

Creating and maintaining a high-confidence microRNA repository for crop research: A brief review and re-examination of the current crop microRNA registries

miRBase was established as an authoritative microRNA (miRNA) database with a uniform nomenclature system and a searchable web interface. Recent popularization of the next-generation sequencing technology in small RNA cloning led to an explosive growth of the miRNA repository. Although a specific definition system has been proposed for the plant miRNAs, the quality of the plant miRNA registries deposited in miRBase is largely dependent on the submitters. With the growing concerns over the annotation quality, a set of criteria for identification of the high-confidence (HC) miRNAs was recently developed by miRBase. Since miRNAs could serve as a powerful tool for crop genetic improvement and breeding, we present a brief overview of the miRBase-registered crop miRNAs in this study. A total of 54 plants were identified from the 82 Viridiplantae species in the current version of miRBase, and were regarded as the crops. A total of 6316 precursors encoding 7422 mature miRNAs (miRBase release 22.1) were included in our survey. Based on the HC annotation criteria, we performed structure- and sequencing data-based analyses of the confidence of the crop miRNAs. According to the results, we propose suggestions for improvements of the HC annotation system and, moreover, discuss strategies for creating and maintaining an HC miRNA repository of crops. Finally, we hope that this study inspires more efforts devoted to HC miRNA discoveries for crop research.