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

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Abstract

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.

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Acknowledgements

This work was financially supported by Hainan Provincial Natural Science Foundation of China (318MS098), the National Key Research and Development Program of China (2018YFD1000504), the Innovation Team Project Funds for Chinese Academy of Tropical Agricultural Sciences (1630062017027, 17CXTD-10) and the President’s Fund of Minnan Normal University (KJ2020004).

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Authors and Affiliations

  1. College of Horticulture, Hainan University, Haikou, 570228, China

    Min Liu & Hong-Na Zhang

  2. Key Laboratory of Landscape Plants With Fujian and Taiwan Characteristics, Fujian Province University, School of Biological Science and Biotechnology, Minnan Normal University, No.36, Xianqian Street, Zhangzhou, 363099, China

    Min Liu & Yun-He Li

  3. Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China

    Min Liu, Qing-Song Wu, Sheng-Hui Liu, Hong-Na Zhang, Wen-Qiu Lin, Xiu-Mei Zhang & Yun-He Li

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  1. Min Liu
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Contributions

YL and QW conceived and designed the experiments. YL performed histological observation and wrote the manuscript. ML performed plant treating, qRT-PCR, PCR validation of AS and fusion gene. ML, SL, HZ, WL, XZ and QW participated in the preparation of the plant materials. YL and ML performed the data analysis. All authors of this study have read and approved the manuscript.

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Correspondence to Yun-He Li.

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Communicated by Xingfeng Shao.

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Liu, M., Wu, QS., Liu, SH. et al. Combining single-molecule sequencing and Illumina RNA sequencing to elucidate flowering induction of pineapple (Ananas comosus (L.) Merr.) treated with exogenous ethylene. Plant Growth Regul 94, 303–321 (2021). https://doi.org/10.1007/s10725-021-00720-w

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