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Transcriptional profiling of long noncoding RNAs associated with flower color formation in Ipomoea nil

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Abstract

Main conclusion

LncRNAs regulate flower color formation in Ipomoea nil via vacuolar pH, TCA cycle, and oxidative phosphorylation pathways.

Abstract

The significance of long noncoding RNA (lncRNA) in diverse biological processes is crucial in plant kingdoms. Although study on lncRNAs has been extensive in mammals and model plants, lncRNAs have not been identified in Ipomoea nil (I. nil). In this study, we employed whole transcriptome strand-specific RNA sequencing to identify 11,203 expressed lncRNA candidates, including 961 known lncRNA and 10,242 novel lncRNA in the I. nil genome. These lncRNAs in I. nil had fewer exons and were generally shorter in length compared to mRNA genes. Totally, 1141 different expression lncRNAs (DELs) were significantly identified between white and red flowers. The functional analysis indicated that lncRNA-targeted genes were enriched in the TCA cycle, photosynthesis, and oxidative phosphorylation-related pathway, which was also found in differentially expressed genes (DEGs) functional enrichments. LncRNAs can regulate transcriptional levels through cis- or trans-acting mechanisms. LncRNA cis-targeted genes were significantly enriched in potassium and lysosome. For trans-lncRNA, two energy metabolism pathways, TCA cycles and oxidative phosphorylation, were identified from positive association pairs of trans-lncRNA and mRNA. This research advances our understanding of lncRNAs and their role in flower color development, providing valuable insights for future selective breeding of I. nil.

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Data availability

The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive in BIG Data Center, Beijing Institute of Genomics (BIG) (https://bigd.big.ac.cn/gsa/), Chinese Academy of Sciences, under accession numbers CRA008699 that are publicly accessible at https://bigd.big.ac.cn/gsa.

Abbreviations

DEL:

Different expression lncRNA

DEG:

Differentially expressed gene

PCG:

Protein coding gene

lincRNA:

Long intergenic ncRNA

lncNAT:

Natural antisense transcripts

Bi-directional lncRNA:

Opposite strand of a PCG, same promoter.

Sense intergenic upstream lncRNA:

LincRNAs < 5 kb upstream of nearest PCG

Intergenic lncRNA:

LincRNAs > 5 kb upstream of nearest PCG

Antisense exonic lncRNA:

LncNAT of overlapping PCG’s exon

Antisense intronic lncRNA:

LncNAT of overlapping PCG’s intronic

Sense intronic lncRNA:

Within PCG intron

TPM:

Transcript per million reads

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Acknowledgements

We thank Dr. Zongxiu Sun (China Agricultural University) for providing and identifying Ipomoea nil strain at China National Rice Research Institute.

Funding

A fund supported this work from the Open Project of Hubei Key Laboratory of Wudang Local Chinese Medicine Research (Hubei University of Medicine) Grant No. WDCM2022005 (to C.Z.). These funders did not play any roles in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.

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Author notes

  1. Hanlin Zhou, Ruizhi Yan, and Huan He have contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, China Three Gorges University, Yichang, 443002, China

    Hanlin Zhou, Ruizhi Yan, Huan He, Xinlin Wei, Shuangcheng Liu, Bintao Guo, Chao Zhou & Zhengquan He

  2. Hubei Key Laboratory of Wudang Local Chinese Medicine Research, School of Basic Medicine, Biomedical Research Institute, Hubei University of Medicine, Shiyan, 442000, China

    Yonghong Zhang

  3. Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, 430056, China

    Xiaoyun Liu

  4. MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China

    Shafeeq Ur Rahman

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  1. Hanlin Zhou
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  10. Chao Zhou
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Correspondence to Chao Zhou or Zhengquan He.

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Zhou, H., Yan, R., He, H. et al. Transcriptional profiling of long noncoding RNAs associated with flower color formation in Ipomoea nil. Planta 258, 6 (2023). https://doi.org/10.1007/s00425-023-04142-y

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