RNA-seq transcriptome profiling of young gametophytes and capsules at different developmental stages of Pogonatum aloides

To investigate global gene expression during development in Pogonatum aloides, digital gene-expression profiling of capsules at different developmental stages was performed by Illumina HiSeq™ 2000 sequencing platforms, with the young gametophyte being used as a control. The samples of P. aloides were collected from Jiming Mountain, Ningde (26°56'39.34"N; 118°57'21.45"E, and stored in RNAlater solution. Total RNAs were extracted using the TRIzol reagent. The RNA-Seq reads were assembled into transcripts using SOAPdenovo v1.04. 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, 4007 genes were found to be up-regulated in reproductive/meiotic samples. Overall design: Gene expression patterns of capsules at different developmental stages of P. aloides were detected by Illumina HiSeq™ 2000 sequencing platforms, with the young gametophyte being used as a control.