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Systematic identification and characterization of long non-coding RNAs involved in cytoplasmic male sterility in pepper (Capsicum annuum L.)

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Abstract

Long non-coding RNAs (lncRNAs) participate in many biological processes and play extremely important regulatory roles in animals and plants. However, little is known about lncRNAs and their functions in cytoplasmic male sterility (CMS) during the developmental process of floral buds in pepper. In the present study, we systematically identified lncRNAs in the pepper CMS line (9704A) and maintainer line (9704B) using high-throughput sequencing and bioinformatic analyses. A total of 10,655 putative lncRNAs were identified during the developmental process of floral buds, and 262, 298 and 905 differentially expressed lncRNAs (DELs) were obtained in three stages, respectively. Moreover, 1137 unique DELs were identified between 9704A and 9704B, and their cis and trans target protein-coding genes were predicted. We used Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses to decipher the potential functions of DELs. The cell and cellular process GO terms were significantly enriched, and KEGG pathway analysis showed enrichments in the pathways for starch and sucrose metabolism genes, pentose and glucuronate interconversions, all of which were highly associated with pollen development. Besides, a regulatory network about the lncRNAs and the protein-coding genes involved in the formation of CMS was constructed. Our findings laid a foundation for further studies on the function of lncRNAs in pollen development and provided valuable insights into the regulatory mechanism underlying CMS.

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Data Availability

All of the RNA-Seq data generated in this study is available from the SRA-Archive (http://www.ncbi.nlm.nih.gov/sra) under the study accession number: SRP186136. The other supporting data are included as Additional files.

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Acknowledgements

This work was financially supported by the China Agriculture Research System (Grant No. CARS-24-A-05) and the National Natural Science Foundation of China (31760575). The funding bodies themselves did not participate in the design of the study or the collection, analysis, and interpretation of data, or in writing the manuscript.

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

    Junheng Lv, Zhoubin Liu, Jing Wang, Yuhua Liu & Xuexiao Zou

  2. Vegetable Institution of Hunan Academy of Agricultural Science, Changsha, 410125, Hunan, China

    Bozhi Yang, Zhuqing Zhang, Yanqing Ma, Wenchao Chen, Lijun Ou & Xuexiao Zou

  3. College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, China

    Minghua Deng

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  1. Junheng Lv
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Contributions

ZXX, OLJ and CWC conceived and designed the experiments. LJH wrote the manuscript. LJH, LZB, and YBZ performed the experiments. DMH, LYH and WJ analyzed the data. ZZQ and MYQ revised the manuscript for the language. All authors read and approved the final manuscript.

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Correspondence to Wenchao Chen, Lijun Ou or Xuexiao Zou.

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Junheng Lv and Zhoubin Liu contributed equally to this work and should be considered as co-first authors.

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10725_2020_605_MOESM1_ESM.tif

Supplementary material 1 (TIF 554.3 kb) Fig. S1. GO enrichment analysis for differentially expressed target protein-coding genes in cis between 9704A and 9704B

10725_2020_605_MOESM2_ESM.tif

Supplementary material 2 (TIF 902.1 kb) Fig. S2. GO enrichment analysis for differentially expressed target protein-coding genes in trans between 9704A and 9704B

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Lv, J., Liu, Z., Yang, B. et al. Systematic identification and characterization of long non-coding RNAs involved in cytoplasmic male sterility in pepper (Capsicum annuum L.). Plant Growth Regul 91, 277–288 (2020). https://doi.org/10.1007/s10725-020-00605-4

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