GSE112800
Small RNA (sRNA) sequencing data from pre-meiotic and meiotic anthers of Asparagus
Purpose: To study pre-meiotic (21-nt) and meiotic (24-nt) phasiRNA pathways in non-grass monocots Methods: Anthers were dissected using a 2 mm stage micrometer in a stereo microscope, and immediately frozen in liquid nitrogen until total RNA isolation was performed. Small RNA, mRNA libraries were generated using short-read (Illumina) and Single Molecule Real Time SMRT (PacBio) sequencing approaches. Stages were assigned based on the morphology of archesporial (AR) and tapetal cells of A. officinalis (Asparagus) anthers. Overall design: Flowering Asparagus plants were harvested from T.S. Smith and Sons Farms (Bridgeville, Delaware). Buds corresponding to pre-meiotic and meiotic stages were used to generate mRNA, full-length and sRNA libraries. Data from mRNA-seq and SMRT-seq were used for de novo transcriptome assemblies.  These assemblies were then used along with sRNA data to identify phased-siRNA precursor transcripts and other protein factors that play a role in reproductive phasiRNA pathways. mRNA-seq assembly was performed using “Trinity RNA-Seq assembler”, full-length transcript assembly was prepared using “SMRT-tools” (v2.3) provided by Pacific Biosciences. Phased siRNA precursors were identified using “PHASIS suite” (https://github.com/atulkakrana/PHASIS/wiki), and transcripts sfor protein-coding genes were identified using “Trinotate” (https://trinotate.github.io/).