Transcriptome analysis of developmental stages of cocoa pod borer, Conopomorpha cramerella: A polyphagous insect pest of economic importance in Southeast Asia

The cocoa pod borer, Conopomorpha cramerella (Snellen) is a serious pest in cocoa plantations in Southeast Asia. It causes significant losses in the crop. Unfortunately, genetic resources for this insect is extremely scarce. To improve these resources, we sequenced the transcriptome of C. cramerella representing the three stages of development, larva, pupa and adult moth using Illumina NovaSeq6000. Transcriptome assembly was performed by Trinity for all the samples. A total number of 147,356,088 high quality reads were obtained. Of these, 285,882 contigs were assembled. The mean contig size was 374 bp. Protein coding sequence (CDS) was extracted from the reconstructed transcripts by TransDecoder. Subsequently, BlastX and InterProScan were applied for homology search to make a prediction of the function of CDS in unigene. Additionally, we identified a number of genes that are involved in reproduction and development such as genes involved in general function processes in the insect. Genes found to be involved in reproduction such as porin, dsx, bol and fruitless were associated with sex determination, spermatogenesis and pheromone binding. Furthermore, transcriptome changes during development were analysed. There were 2,843 differentially expressed genes (DEG) detected between the larva and pupa samples. A total of 2,861 DEG were detected between adult and larva stage whereas between adult and pupa stage, 1,953 DEG were found. In conclusion, the transcriptomes could be a valuable genetic resource for identification of genes in C. cramerella and the study will provide putative targets for RNAi pest control.