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Background <p><i>Chrysanthemum morifolium</i> is one of the ten traditional famous flowers in China and the four major cut flowers in the world, with high ornamental and economic value. However, low temperature stress impedes its annual production and mining cold-tolerance genes could provide key genetic resources for breeding chrysanthemums with improved cold tolerance. <i>Chrysanthemum indicum</i> L. as a wild species closely related to cultivated chrysanthemum, is a native diploid plant with simple genetic background. Therefore, we used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze <i>Chrysanthemum indicum</i> transcription response to low temperature.</p> Results <p>Illumina sequencing technology was used for the transcriptome sequencing of 12 samples, and at least 45,668,468 clean reads and 62,199 de novo genes were generated from four libraries: T01, controls; T02, -4℃ freezing treatments for 4&#xa0;h; T03, -4℃ freezing treatments for 4&#xa0;h with prior cold acclimation (CA); T04, 4℃ CA for 4&#xa0;h. In total, 20,690 differentially expressed genes (DEGs) were identified, including 11,670 up-regulated genes and 9020 down-regulated genes. We performed KEGG pathway enrichment analyses, and found that cold-responsive genes play a significant role in the plant hormone signaling pathway and phenylpropanoid biosynthesis pathway. Correlation analysis suggests that the expression of the 1R-MYB transcription factor shows a correlation with genes involved in the ABA signaling and anthocyanin biosynthesis pathways. We also verified expression levels of 16 DEGs using quantitative real-time polymerase chain reaction (qRT-PCR), and the results were basically consistent with Illumina sequencing results.</p> Conclusion <p>In summary, our study provides a genome-wide transcript profile of <i>Chrysanthemum indicum</i>. By predicting potential cold-tolerance genes in <i>Chrysanthemum indicum</i>, it provides an effective gene reserve for cultivating new varieties of low temperature resistant chrysanthemum. At the same time, it provides a new theoretical basis for cultivating new cold-tolerant chrysanthemum varieties.</p>

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Transcriptome analysis and gene mining of chrysanthemum(Chrysanthemum indicum)in response to low temperature stress

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年8月5日

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  • Siyu Feng,
  • Yuzhi Song,
  • Shuheng Wang,
  • Xuanlu Liu,
  • Jiayi Yin,
  • Yuan Meng,
  • Yun Bai,
  • Xue Yang,
  • Yunwei Zhou

摘要

Background

Chrysanthemum morifolium is one of the ten traditional famous flowers in China and the four major cut flowers in the world, with high ornamental and economic value. However, low temperature stress impedes its annual production and mining cold-tolerance genes could provide key genetic resources for breeding chrysanthemums with improved cold tolerance. Chrysanthemum indicum L. as a wild species closely related to cultivated chrysanthemum, is a native diploid plant with simple genetic background. Therefore, we used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze Chrysanthemum indicum transcription response to low temperature.

Results

Illumina sequencing technology was used for the transcriptome sequencing of 12 samples, and at least 45,668,468 clean reads and 62,199 de novo genes were generated from four libraries: T01, controls; T02, -4℃ freezing treatments for 4 h; T03, -4℃ freezing treatments for 4 h with prior cold acclimation (CA); T04, 4℃ CA for 4 h. In total, 20,690 differentially expressed genes (DEGs) were identified, including 11,670 up-regulated genes and 9020 down-regulated genes. We performed KEGG pathway enrichment analyses, and found that cold-responsive genes play a significant role in the plant hormone signaling pathway and phenylpropanoid biosynthesis pathway. Correlation analysis suggests that the expression of the 1R-MYB transcription factor shows a correlation with genes involved in the ABA signaling and anthocyanin biosynthesis pathways. We also verified expression levels of 16 DEGs using quantitative real-time polymerase chain reaction (qRT-PCR), and the results were basically consistent with Illumina sequencing results.

Conclusion

In summary, our study provides a genome-wide transcript profile of Chrysanthemum indicum. By predicting potential cold-tolerance genes in Chrysanthemum indicum, it provides an effective gene reserve for cultivating new varieties of low temperature resistant chrysanthemum. At the same time, it provides a new theoretical basis for cultivating new cold-tolerant chrysanthemum varieties.