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Leafy spurge (Euphorbia esula L.) is an invasive perennial weed infesting range and recreational lands of North America. Previous research and omics projects with E. esula have helped develop it as a model for studying many aspects of perennial plant development and response to abiotic stress. However, the lack of an assembled genome for E. esula has limited the power of previous transcriptomics studies to identify functional promoter elements and transcription factor binding sites. An assembled genome for E. esula would enhance our understanding of signaling processes controlling plant development and responses to environmental stress and provide a better understanding of genetic factors impacting weediness traits, evolution, and herbicide resistance. A comprehensive transcriptome database would also assist in analyzing future RNA-seq studies and is needed to annotate and assess genomic sequence assemblies. Here, we assembled and annotated 56,234 unigenes from an assembly of 589,235 RNA-seq-derived contigs and a previously published Sanger-sequenced expressed sequence tag collection. The resulting data indicate that we now have sequence for >90% of the expressed E. esula protein-coding genes. We also assembled the gene space of E. esula by using a limited coverage (18X) genomic sequence database. In this study, the programs Velvet and Trinity produced the best gene-space assemblies based on representation of expressed and conserved eukaryotic genes. The results indicate that E. esula contains as much as 23% repetitive sequences, of which 11% are unique. Our sequence data were also sufficient for assembling a full chloroplast and partial mitochondrial genome. Further, marker analysis identified more than 150,000 high-quality variants in our E. esula L-RNA–scaffolded, whole-genome, Trinity-assembled genome. Based on these results, E. esula appears to have limited heterozygosity. This study provides a blueprint for low-cost genomic assemblies in weed species and new resources for identifying conserved and novel promoter regions among coordinately expressed genes of E. esula.
The evolution of glyphosate resistance in weedy species places an environmentally benign herbicide in peril. The first report of a dicot plant with evolved glyphosate resistance was horseweed, which occurred in 2001. Since then, several species have evolved glyphosate resistance and genomic information about nontarget resistance mechanisms in any of them ranges from none to little. Here, we report a study combining iGentifier transcriptome analysis, cDNA sequencing, and a heterologous microarray analysis to explore potential molecular and transcriptomic mechanisms of nontarget glyphosate resistance of horseweed. The results indicate that similar molecular mechanisms might exist for nontarget herbicide resistance across multiple resistant plants from different locations, even though resistance among these resistant plants likely evolved independently and available evidence suggests resistance has evolved at least four separate times. In addition, both the microarray and sequence analyses identified non–target-site resistance candidate genes for follow-on functional genomics analysis.
Crop allelopathy has seldom been used effectively by farmers in weed management. Traditional breeding methods have not been successful in producing highly allelopathic crops with good yields. Genetic engineering may have the potential for overcoming this impasse. Crops have been made resistant to insects, pathogens, and herbicides with transgenes, but biotechnology has not produced crops that control weeds with allelochemicals. The strategies for producing allelopathic crops by biotechnology are relatively complex, usually involving multiple genes. One can choose to enhance production of allelochemicals already present in a crop or to impart the production of new compounds. The first strategy involves identification of the allelochemical(s), determination of the enzymes and genes encoding them, and the use of genetic engineering to enhance their production. The latter strategy employs altering existing biochemical pathways by insertions of transgenes to produce new allelochemicals. With either strategy, there are potential problems with tissue-specific promoters, autotoxicity, metabolic imbalances, and proper movement of the allelopathic compound to the rhizosphere.
Hydro-distilled essential oils from fruits, aerial parts (without fruits) and roots of Pimpinellaspecies native to Turkey and their phylogenetic relationships to one another were examined. Phytochemical investigation of the essential oils of 19 species resulted in isolation of 16 phenylpropanoids, four sesquiterpenes and two azulene-type norsesquiterpenes. The structures of the isolated compounds were determined primarily from 1D- and 2D-NMR experiments as well as liquid chromatography–mass spectrometry and gas chromatography–mass spectrometry. Phylogenetic relationships among 26 species were evaluated using ITS 1, ITS 4 nuclear rDNA and psbA-trnH cpDNA sequences. In this study, significance and occurrence of phenylpropanoids, azulenes and geijerenes are discussed from a phylogenetic, chemical and biosynthetic perspective. The distribution of different classes of compounds and their putative associations with one another as per current knowledge of their biosynthetic pathways indicates that this information, in conjunction with the phylogeny, could provide valuable information regarding the presence and perhaps evolution of the different classes of compounds. Analysis of the phenylpropanoid components indicates that (E)-anethole is an obligatory intermediate of this pathway. The various Pimpinellaspecies differ primarily in their ability to acylate anethole, suggesting that while the pathway leading to anethole is common to this genus, species differ in their enzymatic machinery leading to acylate. The relationship between azulenes and geijerenes is not as intuitive, but all Pimpinellaspecies analysed in this study have the biochemical machinery required to synthesize these chemical classes.
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