张紫阳, 刘艳, 魏瑞研, 等. 基于高通量测序的低温胁迫下赤桉miRNAs的挖掘与分析[J]. 华南农业大学学报, 2021, 42(3): 64-74. DOI: 10.7671/j.issn.1001-411X.202011009
    引用本文: 张紫阳, 刘艳, 魏瑞研, 等. 基于高通量测序的低温胁迫下赤桉miRNAs的挖掘与分析[J]. 华南农业大学学报, 2021, 42(3): 64-74. DOI: 10.7671/j.issn.1001-411X.202011009
    ZHANG Ziyang, LIU Yan, WEI Ruiyan, et al. Mining and analysis of miRNAs from Eucalyptus camaldulensis under low temperature stress based on high-throughput sequencing[J]. Journal of South China Agricultural University, 2021, 42(3): 64-74. DOI: 10.7671/j.issn.1001-411X.202011009
    Citation: ZHANG Ziyang, LIU Yan, WEI Ruiyan, et al. Mining and analysis of miRNAs from Eucalyptus camaldulensis under low temperature stress based on high-throughput sequencing[J]. Journal of South China Agricultural University, 2021, 42(3): 64-74. DOI: 10.7671/j.issn.1001-411X.202011009

    基于高通量测序的低温胁迫下赤桉miRNAs的挖掘与分析

    Mining and analysis of miRNAs from Eucalyptus camaldulensis under low temperature stress based on high-throughput sequencing

    • 摘要:
      目的  预测、挖掘和分析涉及赤桉Eucalyptus camaldulensis低温胁迫应答的miRNA,为研究其调控赤桉低温胁迫应答的分子网络奠定基础。
      方法  采用高通量测序对低温处理组和对照(CK)组的赤桉组培苗茎尖进行小RNA测序。以miRBase21.0、Rfam14.1和巨桉E. grandis基因组为参考数据库,利用Bowtie、miREAP和miRDeep2等软件进行miRNA预测,使用RNAfold对预测到的miRNA前体进行二级结构的折叠;采用psRNATarget预测靶基因,通过DEGSeq包分析差异表达的miRNA,并对它们进行GO注释和KEGG富集分析。
      结果  在赤桉中,共预测到隶属于54个家族的392个已知miRNA和97个新miRNA;其中,CK组共预测到282个已知miRNA,65个新miRNA;低温处理组共预测到329个已知miRNA,51个新miRNA。挖掘到80个在低温处理下显著差异表达的miRNA,包括55个上调和25个下调。GO基因功能注释和KEGG富集分析的结果表明,这些差异表达miRNA可能通过参与代谢通路、次生代谢物的生物合成、细胞膜的改变、信号转导和生物调节等响应低温胁迫。此外,还挖掘到25个可能与ICE1-CBFs-COR通路有关的miRNA。
      结论  借助高通量测序和生物信息学软件初步得到了低温胁迫下差异表达的赤桉miRNA,为进一步分析这些miRNA在赤桉低温胁迫中的分子功能提供一些参考。

       

      Abstract:
      Objective  To predict, mine and analyze the miRNAs involved in low temperature stress response of Eucalyptus camaldulensis, and lay a foundation for further study of the molecular network of regulating low temperature stress response.
      Method  Small RNAs were sequenced by high-throughput sequencing using the shoot tips of the tissue cultured seedlings of E. camaldulensis from the low temperature treatment group and the control group (CK). The miRBase21.0, Rfam14.1 and E. grandis genome were taken as reference databases. Bowtie, miREAP as well as miRDeep2 software were used for miRNA prediction. RNAfold was used to fold the secondary structure of the predicted miRNA precursors. psRNATarget was used to predict target genes. The miRNAs with differential expression were analyzed through DEGSeq package, and GO annotation and KEGG enrichment analysis were further performed.
      Result  A total of 392 known miRNAs and 97 novel miRNAs belonging to 54 families were predicted in E. camaldulensis. The 282 known miRNAs and 65 novel miRNAs were predicted in CK, while 329 known miRNAs and 51 novel miRNAs were predicted in the low temperature treatment group. At the same time, 80 significantly differentially expressed miRNAs in low temperature treatment group were mined, including 55 up-regulated and 25 down-regulated. The results of GO annotation and KEGG enrichment analysis indicated that these differentially expressed miRNAs might respond to low temperature stress by participating in metabolic pathways, biosynthesis of secondary metabolites, cell membrane changes, signal transduction, and biological regulation. In addition, we found 25 miRNAs that might be associated with the ICE1-CBFs-COR pathway.
      Conclusion  The differentially expressed miRNAs are initially obtained by high-throughput sequencing and bioinformatics software under low temperature stress, which can provide some references for further analysis of the molecular functions of these miRNAs in E. camaldulensis under low temperature stress.

       

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