RNA-seq of Elaeis guineensis: Isolate OPM4
After the QC procedures, rRNA is removed using the Ribo-Zero kit (Illumina, San Diego) that enriches non-rRNA such as the mRNA according the manufacturers instructions. Then the enriched non-rRNA were processed using NEBNext Ultra II Directional RNA library prep (NEB, Ipwitch, MA). Briefly, the RNA is fragmented randomly followed by cDNA synthesis using random hexamers. The strandedness of the library was achieved during the second strand synthesis step whereby the dUTP was used in place of dTTP. Then, the double stranded cDNA was end-repaired followed by ligation of Illumina adapter. The adapter-ligated DNA was treated with USER enzyme to degrade second-strand Uracil-containing cDNA thus generating the strand-specific cDNA library after the final PCR enrichment. Appropriate amount of the libraries were loaded onto a NovaSEQ6000 (Illumina, San Diego) for 2 x 150 paired-end sequencing generating 100 million paired-end reads per sample.