Combining single-molecule sequencing and Illumina RNA sequencing to elucidate flowering induction of pineapple (Ananas comosus (L.) Merr.) treated with exogenous ethylene

Exogenous ethylene (ethephon) is widely used to induce pineapple ( Ananas comosus (L.) Merr.) flowering. However, economic losses often occur due to inappropriate flower induction, which results in a lower flowering rate or no flowering, and the molecular mechanisms of flowering induction in pineapple remain unclear. To understand the global changes in gene expression during ethylene-induced pineapple flowering, we performed single-molecule real-time (SMRT) sequencing and Illumina RNA sequencing of shoot apexes or inflorescences at six time points (0 d, 8 h, 1 d, 4 d, 7 d, and 14 d after ethephon treatment). In addition, to understand the cellular and physiological processes during flowering, we also observed histological changes and measured the changes in several endogenous plant growth regulators. In this study, we obtained 29,745 polished high-quality isoforms, of which 523 had not yet been annotated within the A. comosus genome. Furthermore, 2049 alternative splicing (AS) events, 78 fusion genes, 139 long-chain non-coding RNAs (lncRNAs), and 11,184 alternative polyadenylation (APA) events were identified by SMRT sequencing. Illumina sequencing of libraries generated from these samples yielded 106.09 Gb clean reads, and the total mapped reads were 86.53%. Comparative analysis of these transcriptome databases revealed 3,690 differentially expressed genes (DEGs) between 0 d and the other time points. Candidate genes that may be involved in pineapple flowering are predicted to encode hormone-related proteins, flowering time proteins, and transcription factors. This study contributes to transcriptome information for A. comosus and will facilitate further exploration of the molecular mechanisms of ethylene-induced pineapple flowering.