Sequencing of Non-model Plants for Understanding the Physiological Responses in Plants

From a genomic point of view, plants are complex organisms. Plants adapt to the environment, by developing different physiological and genetic properties, changing their genomic and expression profiles of adaptive factors, as exemplified by polyploidy studies. These characteristics along with the presence of duplicated genes/genomes make sequencing with early low-throughput DNA sequencing technologies in plants a challenging task. With the development of new technologies for molecular analysis, including transcriptome, proteome or microarray profiling, a new perspective in the genomic analysis was open, making possible to programs in species without genomic maps. The opportunity to extend molecular studies from laboratory model scale toward naturally occurring plant populations made it possible to precisely answer the longstanding important ecological and evolutionary questions. Some plant species have unique properties that could help to understand their adaptability to environment, crop production, pest protection or other biological processes. Molecular studies on non-model plants, including algae, mosses, ferns and plants with very specific characteristics are ongoing

MicroRNAs Sequencing for Understanding the Genetic Regulation of Plant Genomes

MicroRNAs (miRNAs) are endogenous non-coding RNAs that play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. Small RNAs are classified into different types by their biogenesis and mode of action, such as miRNAs, siRNAs, piRNAs, and snoRNAs. In the case of miRNAs, this specific type regulates gene expression in plants and animals by targeting mRNAs for cleavage and translational repression, respectively. Diverse miRNAs regulate plant development, metabolism, and responses to biotic and abiotic stresses. The identification of miRNAs has been accomplished in diverse species, organs and developmental or diverse biotic and abiotic stress conditions. Novel massive sequencing techniques and further bioinformatics analysis have allowed the identification of hundreds of miRNAs in Arabidopsis thaliana, Oryza sativa, Malus domestica, Zea mays, Solanum lycopersicum, and other plants. Functional characterization of a given miRNA in a specific biological context has shown their role in the fine-tuning mechanisms of posttranscriptional gene regulation. In this chapter, besides making a summary of genome-wide miRNA profiling in plants, we describe how gain and loss of function approaches influence plant phenotypes that affect development, physiology or stress responses, pointing to miRNAs as effective tools for the generation of new plant phenotypes that improve plant productivity and conservation