Coconut Transcriptome Profiling
We used TruSeq RNA Sample Preparation kit for cDNA library construction (Illumina, San Diego, CA). First, poly-T oligo-attached magnetic beads were used to isolate mRNA from total RNA. The isolated mRNA was fragmented and reverse transcribed to single-stranded cDNA with random primers, forming a mixture of DNA/RNA hybrid. The second-stranded cDNA was then synthesized and purified. During the synthesis of the second stranded cDNA, deoxythymidine triphosphate (dTTP) was substituted with deoxyuridine triphosphate (dUTP), which helped enforce strand-specificity (Wang et al. 2011). The resulting double-stranded cDNA was end-repaired and adenylated, followed by poly A tailing, paired-end Y-adaptor ligation, and then treated with uracil-DNA glucosylase (UDG) to digest the dUTP-marked strand. The selected strand was amplified and screened through agarose gel electrophoresis. Fragments ranging from 350 bp to 520 bp were selected for later sequencing.