Transcriptome datasets of control and EgWRI1-overexpressing Elaeis guineensis protoplasts generated by Illumina sequencing

Protoplasts were isolated from immature leaves of Elaeis guineensis plants grown under controlled greenhouse conditions at IRD (Montpellier, France; 27°C and 60% relative humidity). Three independent protoplast transformation experiments were performed using either a plasmid overexpressing EgWRI1-1 or no plasmid DNA (control). Transformations were retained only when the transformation efficiency, assessed by flow cytometry (NovoCyte), reached at least 50%. Protoplasts were harvested 2 and 5 days after transformation for total RNA extraction. Total RNA was extracted from 400,000 protoplasts using the PureLink® RNA Mini Kit (Invitrogen). RNA-seq libraries were prepared using the Universal Plus mRNA-Seq Kit (Tecan, formerly NuGEN) and sequenced on an Illumina NovaSeq 6000 platform (SP flow cell, single-end 100 bp reads) at the MGX platform (Montpellier GenomiX, France). A total of 12 libraries were generated, yielding an average of 38 million reads per library. Low-quality reads were removed using Cutadapt. The resulting high-quality reads were mapped to the oil palm EG5.Genes.V5 reference gene set (51,490 coding sequences; http://genomsawit.mpob.gov.my) using BWA-MEM with default parameters.