A protocol for Laser Microdissection (LMD) followed by transcriptome analysis of plant reproductive tissue in phylogenetically distant angiosperms

Here we describe a protocol for plant tissue preparation, cryoprotection, cryo-sectioning, laser microdissection and RNA sample preparation for Illumina sequencing of complex plant organs from three phyletically distant plant species: Arabidopsis thaliana (Brassicaceae), Eschscholzia californica (Papaveraceae), and Oryza sativa (Poaceae). We are confident that this approach is widely applicable to other plant species to enable phylotranscriptomics with high spatial resolution. The protocol is rapid, produces high quality sections of complex organs and well suited for RNA-seq approaches. We provide detailed description of each stage of sample preparation with the quality and quantity measurements as well as a detailed analysis of generated transcriptomes.