GSE97978
Small RNA (sRNA), mRNA and SMRT sequencing data from pre-meiotic and meiotic anthers of Lilium Maculatum
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 Lilium anthers. Overall design: The L. maculatum plants were purchased from Home Depot (Newark, 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, so as to compensate for the lack of Lilium genome.  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” (v3) provided by Pacific Biosciences. Phased siRNA precursors were identified using “PHASIS" software package, and transcripts for protein-coding genes were identified using “Trinotate” (https://trinotate.github.io/).