COMPARATIVE TRANSCRIPTOME PROFILING OF MOMORDICA COCHINCHINENSIS (LOUR.) SPRENG. ARIL USING OXFORD NANOPORE AND ILLUMINA SEQUENCING TECHNOLOGIES

Gac (Momordica cochinchinensis (Lour.) Spreng.) is a tropical fruit recognized for its exceptionally high carotenoid content, particularly lycopene and β‑carotene. Although Gac possesses significant nutritional and pharmacological value, genomic and transcriptomic resources for this species are limited. Previous studies utilizing Illumina RNA‑Seq established the first de novo transcriptome of Gac aril, identifying over 81,000 unigenes and key enzymes involved in carotenoid biosynthesis. In this study, we generated a transcriptome of Gac aril using Oxford Nanopore Technologies (ONT) direct RNA sequencing and compared its assembly and annotation with the published Illumina dataset. ONT sequencing produced over 13 million long reads, resulting in 52,755 unigenes with an average length of 777 bp and an N50 of 922 bp, which are substantially longer than those generated using Illumina sequencing (average 388 bp, N50 450 bp). Functional annotation identified 33,235 unigenes with significant matches, including full-length carotenoid-related unigenes, e.g., phytoene synthase (PSY), phytoene desaturase (PDS), zeta-carotene desaturase (ZDS), zeta-carotene isomerase (Z-ISO), prolycopene isomerase (CRISTO), lycopene ß-cyclase (LCYB), and lycopene ε-cyclase (LCYE). Long-read ONT sequencing enabled the recovery of full-length transcripts, reducing assembly fragmentation and redundancy and yielding a more compact, biologically representative unigene set. While Illumina technology remains superior in sequencing accuracy and quantitative profiling, ONT offers enhanced structural resolution, isoform discovery, and the potential to detect RNA modifications. Recent advances in ONT chemistry, flow cell design, and bioinformatic pipelines are rapidly improving accuracy and throughput, establishing ONT as a credible stand‑alone approach for transcriptome analysis in non‑model plants. These findings demonstrate that ONT sequencing can reveal novel regulatory features of carotenoid biosynthesis in Gac, providing valuable resources for functional genomics and metabolic engineering in carotenoid‑rich crops.