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Noncoding and coding transcriptome analysis reveals the regulation roles of long noncoding RNAs in fruit development of hot pepper (Capsicum annuum L.)

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Abstract

Long non-coding RNAs (lncRNAs) have been shown to play critical regulatory roles in diverse biological processes in plants. However, the presence of lncRNAs and their potential functions in hot pepper are still unknown. Using strand-specific RNA-sequencing, a total of 2505 putative lncRNAs were identified in the fruits of hot pepper. The lncRNAs were transcribed from all pepper chromosomes and 95.37% of them originated from intergenic regions. And 1066 lncRNAs were differentially expressed among the four samples during pepper fruit development. Many potential protein-coding (PC) genes targeted by lncRNAs with cis or trans-acting were also identified. Six of them and their target genes were further validated by quantitative RT-PCR. Some of these target genes were involved in plant hormone signal transduction, cell wall formation and carotenoid biosynthesis, indicating the roles of lncRNAs in the regulation of fruit development and quality. This study identified a large number of lncRNAs in hot pepper, thereby providing some insights into the fruit development of hot pepper.

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Acknowledgements

This research is financially supported by China Agriculture Research System (CARS-25-A-8).

Author Contributions

XZ, YM and LO conceived and designed the experiments. LO, ZL, ZZ, GW, YZ, LK and BY performed the experiments. SY, JL, YL, WC, XD, XL, and SZ analyzed the data. XZ, YM supervised the progress of the project. LO and ZL wrote the paper.

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  1. Lijun Ou, Zhoubin Liu, Zhuqing Zhang, Ge Wei, Yuping Zhang have contributed equally.

Authors and Affiliations

  1. Hunan Vegetable Research Institute, Changsha, 410125, China

    Lijun Ou, Zhoubin Liu, Zhuqing Zhang, Ge Wei, Linyu Kang, Bozhi Yang, Sha Yang, Junheng Lv, Yuhua Liu, Wenchao Chen, Xiongze Dai, Xuefeng Li, Shudong Zhou, Yanqing Ma & Xuexiao Zou

  2. Longping Branch, Graduate School of Hunan University, Changsha, 410125, China

    Zhoubin Liu, Linyu Kang, Junheng Lv, Yuhua Liu & Xuexiao Zou

  3. College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, China

    Yuping Zhang

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10725_2017_290_MOESM1_ESM.tiff

Fig. S1 Expression levels as determined by RNA-seq and qRT-PCR are highly correlated. The log2 of the values in the RNA-seq and the qRT-PCR data were plotted along with the linear fit line to examine the correlation relationship between the two methods (R2=0.773, p<0.001) (TIFF 237 KB)

10725_2017_290_MOESM2_ESM.tiff

Fig. S2 Venn diagrams showing the number of differentially expressed (DE) lncRNAs among the four samples. (A, B, C) Venn diagram showing the overlap of DE lncRNAs between adjacent stages (A1 vs A2, A2 vs A3 and A1vs A3). (D) Venn diagram showing the overlap of DE lncRNAs among the four samples (TIFF 431 KB)

10725_2017_290_MOESM3_ESM.jpg

Fig. S3 GO enrichment analysis of the differentially expressed lncRNA and genes (DEGs) of the pepper variety ‘Luosijiao’ during the fruit development (JPG 620 KB)

10725_2017_290_MOESM4_ESM.tiff

Fig. S4 KEGG pathway of the differentially expressed genes (DEGs) in all the samples. A1, 30 DAA of ‘Luosijiao’, A2, 40 DAA of ‘Luosijiao’, A3, 50 DAA of ‘Luosijiao’, B1, 30 DAA of ‘06J19-1-1-1-2’ (TIFF 1801 KB)

10725_2017_290_MOESM5_ESM.tif

Fig. S5 The lncRNAs (TCONS_00030795) acts as a can-miR399a target mimic in pepper. Capana03g002858 (phytol kinase 1) was the target gene of can-miR399a (TIF 479 KB)

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Ou, L., Liu, Z., Zhang, Z. et al. Noncoding and coding transcriptome analysis reveals the regulation roles of long noncoding RNAs in fruit development of hot pepper (Capsicum annuum L.). Plant Growth Regul 83, 141–156 (2017). https://doi.org/10.1007/s10725-017-0290-3

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