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| 甘蔗耐寒相关miRNA的生物信息学分析及其靶基因预测 |
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朱鹏锦, 宋奇琦, 谭秦亮, 程 琴, 李佳慧, 庞新华, 周全光,吕 平, 欧克纬, 卢业飞, 农泽梅, 唐桓伟, 龙盛风*
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广西壮族自治区亚热带作物研究所, 南宁 530001
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| 摘要: |
| 为了解不同基因型甘蔗(Saccharum officinarum)响应低温胁迫的分子机制,该研究以低温胁迫4 ℃处理 24 h 后的3个不同耐寒性甘蔗品种的叶片为材料进行Illumina HiSeqTM 2000 高通量测序,构建了18个低温胁迫前后sRNA文库。结果表明:(1)共获得分属于84个家族的322个已知miRNA及预测得到110个新miRNA,并在已知miRNA中筛选出100个差异表达miRNA(61个上调,39个下调),新miRNA中筛选出37个差异表达 miRNA(15个上调, 22个下调)。(2)利用psRNATarget、TargetFinder、Tapirhybrid软件对所获得的差异表达miRNA进行靶基因预测,得到1 844个靶基因并进行GO分析揭示其主要功能类别,即分子功能、细胞组分与生物过程。(3)为验证高通量测序数据的可靠性,筛选14个miRNA及其靶基因进行qRT-PCR验证,结果显示这些miRNA均被检测发现且大多表达结果与测序结果一致。(4)鉴定出部分差异表达miRNA的靶基因,这些基因参与植物生长、发育及低温胁迫反应。综上认为,耐寒型甘蔗体内miRNA直接或间接作用靶基因实现表达调控相关代谢途径,对其重要农艺性状均起着关键的调控作用。 |
| 关键词: 甘蔗, 低温胁迫, 耐寒性, miRNA, 生物信息学 |
| DOI：10.11931/guihaia.gxzw202101060 |
| 分类号:Q943 |
| 文章编号:1000-3142(2022)11-1840-14 |
| Fund project:广西自然科学基金(2017GXNSFBA198054); 广西创新驱动发展专项(桂科AA17202042-5); 广西农业科学院基本科研业务专项(桂农科2021YT151)[Supported by Natural Science Foundation of Guangxi(2017GXNSFBA198054); Special Project of Guangxi Innovation-driven Development Special Project of(Guike AA17202042-5); Basic Scientific Research Project of Guangxi Academy of Agricultural Sciences(Guinongke 2021YT151)]。 |
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| Bioinformatics analysis of microRNAs and prediction of target genes associated with cold tolerance in sugarcane |
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ZHU Pengjin, SONG Qiqi, TAN Qinliang, CHENG Qin, LI Jiahui, PANG Xinhua, ZHOU Quanguang, LÜ Ping, OU Kewei, LU Yefei, NONG Zemei, TANG Huanwei, LONG Shengfeng*
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Guangxi Subtropical Crops Research Institute, Nanning 530001, China
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| Abstract: |
| In order to identify the molecular mechanisms of different sugarcane(Saccharum officinarum )responding to cold stress, the leaves of different sugarcane genotypes with different cold tolerance treated at 4 ℃ for 24 h were sampled as the materials for high-through transcriptome sequencing with Illumina HiSeqTM 2000, and 18 sRNA libraries before and after cold stress were constructed. The results were as follows:(1)A total of 322 known miRNAs of 84 families were discovered, and 110 new miRNAs were predicted. Among the known miRNAs, 100 differentially expressed miRNAs were screened out(61 up-regulated, 39 down-regulated), and 37 differentially expressed miRNAs(15 up-regulated, 22 down-regulated)were screened out from the new miRNAs.(2)A total of 1 844 target genes were predicted by using psRNATarget, TargetFinder and Tapirhybrid software. Three main functional categories of these target genes were revealed via the functional analysis of gene ontology, namely molecular function, cellular component and biological process.(3)In order to verify the reliability of high-throughput sequencing data, 14 miRNAs and their target genes were selected for qRT-PCR analysis, which showed that the 14 miRNAs were detected and most of the expressions were consistent with the sequencing results.(4)Some miRNA target genes were identified, which involved in plant growth, development and cold stress responses. All the above results indicate that miRNA in cold tolerant sugarcane directly or indirectly regulates the expression of target genes to realize the expression regulation of related metabolic pathways, and plays a key role in regulating the important agronomic traits. |
| Key words: sugarcane, cold stress, cold tolerance, miRNAs, bioinformatics |
