RNA-Sequencing analysis of reproduction/meiosis in Selaginella moellendorffii

To investigate global gene expression during meiosis in S. moellendorfii, digital gene-expression profiling of a series of sporangia at different developmental stages was performed by Illumina HiSeq™ 2000 sequencing platforms, with young leaves being used as a control. The samples were collected from South Mountain, Chongqing (29°33'44.18"N; 106°37'35.62"E) and stored in RNAlater solution. Total RNAs were extracted using the TRIzol solution. The clean reads were aligned to the genome sequence of S. moellendorfii at JGI database by SOAP2. Gene expression levels were calculated from the number of uniquely aligned clean reads and then normalized into units of Reads Per Kilobase per Million reads mapped (RPKM). Genes were considered to be differentially expressed if they had an FDR < 0.05, P-value < 0.05, and the absolute value of log2Ratio = 1 between reproductive and vegetative samples. As a result, 5416 genes were found to be up-regulated in reproductive/meiotic samples. Overall design: Gene expression patterns of a series of sporangia at different developmental stages was detected by Illumina HiSeq™ 2000 sequencing platforms, with young leaves being used as a control.