Transcriptome analysis and gene mining of chrysanthemum(Chrysanthemum indicum)in response to low temperature stress.
- 1College of Horticulture, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- 2College of Horticulture, Jilin Agricultural University, Changchun, Jilin, 130118, China. [email protected].
- 3College of Horticulture, Jilin Agricultural University, Changchun, Jilin, 130118, China. [email protected].
Abstract
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.
Related
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BibTeX
@article{feng2026transcriptome,
title = {{Transcriptome analysis and gene mining of chrysanthemum(Chrysanthemum indicum)in response to low temperature stress.}},
author = {Siyu Feng and Yuzhi Song and Shuheng Wang and Xuanlu Liu and Jiayi Yin and Yuan Meng and Yun Bai and Xue Yang and Yunwei Zhou},
journal = {BMC plant biology},
year = {2026},
month = aug,
doi = {10.1186/s12870-026-09615-2},
url = {https://europepmc.org/article/MED/42972524},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Transcriptome analysis and gene mining of chrysanthemum(Chrysanthemum indicum)in response to low temperature stress.
AU - Siyu Feng
AU - Yuzhi Song
AU - Shuheng Wang
AU - Xuanlu Liu
AU - Jiayi Yin
AU - Yuan Meng
AU - Yun Bai
AU - Xue Yang
AU - Yunwei Zhou
PY - 2026
DA - 2026/08/05
JO - BMC plant biology
DO - 10.1186/s12870-026-09615-2
UR - https://europepmc.org/article/MED/42972524
AB - 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.
SN - 1471-2229
ER -