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Small RNAs: what makes a plant, a plant

Small RNAs: what makes a plant, a plant
ARC | Federation Fellowships
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  • De novo transcriptome sequence assembly and analysis of RNA silencing genes of Nicotiana benthamiana.

    Kenlee Nakasugi; Ross N Crowhurst; Julia Bally; Craig C Wood; Roger P Hellens; Peter M Waterhouse
    Projects: ARC | Small RNAs: what makes a plant, a plant (FF0776510)
    BACKGROUND: Nicotiana benthamiana has been widely used for transient gene expression assays and as a model plant in the study of plant-microbe interactions, lipid engineering and RNA silencing pathways. Assembling the sequence of its transcriptome provides information that, in conjunction with the genome sequence, will facilitate gaining insight into the plant's capacity for high-level transient transgene expression, generation of mobile gene silencing signals, and hyper-susceptibility to vir...

    Advanced Engineering of Lipid Metabolism in Nicotiana benthamiana Using a Draft Genome and the V2 Viral Silencing-Suppressor Protein

    Naim, Fatima; Nakasugi, Kenlee; Crowhurst, Ross N.; Hilario, Elena; Zwart, Alexander B.; Hellens, Roger P.; Taylor, Jennifer M.; Waterhouse, Peter M.; Wood, Craig C. (2012)
    Projects: ARC | Small RNAs: what makes a plant, a plant (FF0776510)
    The transient leaf assay in Nicotiana benthamiana is widely used in plant sciences, with one application being the rapid assembly of complex multigene pathways that produce new fatty acid profiles. This rapid and facile assay would be further improved if it were possible to simultaneously overexpress transgenes while accurately silencing endogenes. Here, we report a draft genome resource for N. benthamiana spanning over 75% of the 3.1 Gb haploid genome. This resource revealed a two-member NbF...

    Combining Transcriptome Assemblies from Multiple De Novo Assemblers in the Allo-Tetraploid Plant Nicotiana benthamiana

    Nakasugi, Kenlee; Crowhurst, Ross; Bally, Julia; Waterhouse, Peter (2014)
    Projects: ARC | Small RNAs: what makes a plant, a plant (FF0776510)
    Background Nicotiana benthamiana is an allo-tetraploid plant, which can be challenging for de novo transcriptome assemblies due to homeologous and duplicated gene copies. Transcripts generated from such genes can be distinct yet highly similar in sequence, with markedly differing expression levels. This can lead to unassembled, partially assembled or mis-assembled contigs. Due to the different properties of de novo assemblers, no one assembler with any one given parameter space can re-assembl...

    Chimeric DCL1-partnering proteins provide insights into the microRNA pathway

    Rodrigo eS. Reis; Andrew eEamens; Thomas eRoberts; Peter eWaterhouse (2016)
    Projects: ARC | Small RNAs: what makes a plant, a plant (FF0776510), ARC | Discovery Projects - Grant ID: DP130103697 (DP130103697)
    In Arabidopsis thaliana, efficient microRNA (miRNA) production requires DICER-LIKE1 (DCL1) with the assistance of a partnering protein, DOUBLE-STRANDED RNA BINDING1 (DRB1) or DRB2. The presence of either of these DRB proteins is crucial to determine the mode of action of a miRNA; i.e. cleavage or translation inhibition. Here we studied the structural determinants for the role of DRB1 and DRB2 in the miRNA pathway. We developed a series of chimeric vectors encoding different functional domains...
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