The Plant Cell · 2015 · 48 citations · 47 references
Life SciencesPlant BiologyPlant SciencesCrop PhysiologyPlant GeneticsPlant Molecular BiologyAmino Acid Biosynthesis InhibitionJasmonate BiologyDefense Responses Mediated By JasmonatesJasmonate BiosynthesisJasmonate-induced Gene ExpressionJasmonic Acid BiosynthesisJasmonic Acid Signaling PathwayPlant Defense MechanismsPlant Defense MetabolitesTyrosine Biosynthesis
Non-protein amino acids, often isomers of the standard 20 protein amino acids, have defense-related functions in many plant species. A targeted search for jasmonate-induced metabolites in cultivated rice (Oryza sativa) identified (R)-β-tyrosine, an isomer of the common amino acid (S)-α-tyrosine in the seeds, leaves, roots, and root exudates of the Nipponbare cultivar. Assays with 119 diverse cultivars showed a distinct presence/absence polymorphism, with β-tyrosine being most prevalent in temperate japonica cultivars. Genetic mapping identified a candidate gene on chromosome 12, which was confirmed to encode a tyrosine aminomutase (TAM1) by transient expression in Nicotiana benthamiana and in vitro enzyme assays. A point mutation in TAM1 eliminated β-tyrosine production in Nipponbare. Rice cultivars that do not produce β-tyrosine have a chromosome 12 deletion that encompasses TAM1. Although β-tyrosine accumulation was induced by the plant defense signaling molecule jasmonic acid, bioassays with hemipteran and lepidopteran herbivores showed no negative effects at physiologically relevant β-tyrosine concentrations. In contrast, root growth of Arabidopsis thaliana and other tested dicot plants was inhibited by concentrations as low as 1 μM. As β-tyrosine is exuded into hydroponic medium at higher concentrations, it may contribute to the allelopathic potential of rice.
47
Fast gapped-read alignment with Bowtie 2
Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan, Ira M. Hall · Bioinformatics · 2010 · 30.4K citations · Full text
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
Robert J. Elshire, Jeffrey C. Glaubitz, Qi Sun et al. · PLoS ONE · 2011 · 6.8K citations · Full text
The map-based sequence of the rice genome