RNA-Seq of cacao: Infected with Cocoa Pod Borer
RNA was extracted from 8 plant tissue samples and assessed for quality using QiaXpert (Qiagen) and an Agilent Bioanalyzer RNA Nano chip to determine RNA integrity (RIN). Only samples with a RIN  7 and RNA quantity of at least 1 g were selected for sequencing. To focus on messenger RNA (mRNA), poly(A) selection was performed using the NEBNext Ultra RNA Library Prep Kit for Illumina. The enriched mRNA was then converted into complementary DNA (cDNA) and quantified using a Qubit 2.0 DNA Broad Range Assay (Invitrogen, USA). A minimum of 10 ng of cDNA was fragmented to a target size of 200300 bp using a Covaris S220. The fragmented cDNA underwent end repair, adapter ligation, and PCR enrichment following the NEBNext Ultra RNA Library Prep Kit protocol. The final sequencing libraries were validated with an Agilent Bioanalyzer High Sensitivity DNA Chip and quantified using the KAPA kit on an Agilent Stratagene Mx-3005p qPCR system. Sequencing was performed on an Illumina HiSeq 2000 platform.