东农冬麦1号越冬期间的microRNA高通量测序及生物信息学分析
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摘要
东农冬麦1号作为黑龙江省唯一能安全过冬的栽培品种,有着重要抗寒miRNA和miRNA相关靶基因资源。本研究旨在挖掘东农冬麦1号的优良抗寒miRNA资源。一方面揭示“东农冬麦1号”强抗寒机理,拓宽冬小麦抗寒遗传基础,为栽培冬小麦转基因研究提供优良抗寒miRNA靶基因源,从而最终为北方地区栽培冬小麦的改良做出重要贡献；另一方面也为miRNA代谢机制的深入研究提供重要信息。
本研究以东农冬麦1号分为试验材料,在大田自然降温条件下,分别于5℃、-15℃和-25℃三个不同低温下取材分蘖节,采用HiSeq技术进行高通量测序,测序片段长度经统计分析进行Rfam(10.1)、Genbank数据库和重复序列筛选,最后把所有的得到的片段进行注释分类,找到三个温度点的所有miRNA,包括已知和未知miRNA。对已知miRNA进行分析,首先进行碱基偏向性分析,构建三个温度时间点miRNA表达谱,然后进行miRNA差异分析,并构建miRNA差异表达谱,然后对已知的miRNA进行表达差异分析和家族分析：对未知的miRNA进行预测分析,包括碱基偏向性分析和二级结构预测,未知miRNA的表达差异分析和靶基因预测,最后预测其未知miRNA的功能。主要研究结果如下：
1.小麦Small RNA测序数据处理及统计分析
采用Solexa测序得到序列长度为10-35nt的小RNA片段,其中文库中数量最多的小RNA是24nt和21nt,最终在5℃、-15℃、-25℃三个温度条件下获得的洁净reads总量分别是10024183、9448982和10868683。
将reads片段与Rfam(10.1)和Genbank数据库比对,去除其中可能的rRNA、scRNA、 snoRNA、snRNA和tRNA。剩下的reads片段通过重复序列比对去除不同类型的重复序列,最后经sRNA分类注释筛选,获得三个不同温度下筛选出的miRNA总数分别为1299843、1167152和1544325。
2.在冷诱导下小麦中已知miRNA鉴定及差异表达分析
构建小麦已知miRNA表达谱。在小麦miRBase中的已知miRNA有44个,在东农冬麦1号三个样品中(分别为5℃、-15℃、-25℃下取样分蘖节)分别发现有35、29和31个,分析小麦保守miRNA阅读框的数量后,发现这些miRNA的表达频率差异很大,其中11个miRNA出现的序列次数相对较高。在差异分析中发现5个与冷诱导有关的miRNA,分别是tae-miR156、tae-miR398、tae-miR160、tae-miR444和tae-miR444b。tae-miR156的表达丰度最高,有下调表达趋势；tae-miR398明显上调表达且差异显著；tae-miR160显著下调表达;tae-miR444和tae-miR444b皆为显著下调表达。根据差异表达分析和已有报道的靶基因分析,本研究推测以上五个miRNA与东农冬麦1号抗寒有关。
3.东农冬麦1号中的部分已知miRNA鉴定及差异表达分析
东农冬麦1号在冷诱导下发现了567个已知miRNA,其中发生显著或极显著差异表达的共164个,我们选择其中的30个miRNA进行差异表达分析,在东农冬麦1号中筛选获得了14个差异表达的已知miRNA,其中3个与花发育有关,分别是Tae-miR166、 Tae-miR172;5个与冷诱导有关,分别是Tae-miR393、Tae-miR169, Tae-miR397、Tae-miR319和Tae-miR165;6个功能未知miRNA,但由冷诱导产生、丰度高,且差异显著的已知的miRNA,分别是Tae-miR5565、Tae-miR5029、Tae-miR5070、Tae-miR5139、Tae-miR5218和Tae-miR3704。
4.预测新的miRNA
本研究在三个低温时间点上共发掘出378个新的小麦miRNA,其中5℃下获得124个,-15℃下获得96个,-25℃下获得125个。三个低温点分别预测到的靶基因数分别是89个、7个8和99个。在预测miRNA数据库中挑选表达量大、均一化处理后表达差极显著的miRNA,最终在东农冬麦1号中筛选出了14个新miRNA。通过建立预测新miRNA表达谱,并利用Mireap软件预测,发现这14个miRNA都具有代表性的二级茎环结构。对选择的14个新miRNA进行靶基因预测,其中7个预测到了靶基因,另7个没有预测到靶基因。本研究对感兴趣的3个新miRNA进行了靶基因分析,初步预测了这3个新miRNA的功能是与低温有关。
Dongnongdongmai1is the uniqueness cultivated wheat variety which can survive in Heilongjiang province (overwinter survival rate more than85%), and it has important cold resistant miRNA and relevant resources of target genes. This study is aimed at exploring the important stress resistant miRNA resources of Dongnongdongmai1. On one hand, it will reveal strong cold resistance mechanism of Dongnongdongmai1, widen the cold resistant hereditary basis of wheat, provide useful traits and sources of cold resistant miRNA genes to wheat genetically modified cultivation, and make an important contribution to the improvement of cultivation in winter wheat in the north of China. On the other hand, it will also supply important information for the deep research of miRNA metabolism.
In this study, tillering nodes of Dongnongdongmai1in three different growing periods were adopted as materials, depth sequencing was conducted through HiSeq technology in three different growing periods, the sequencing results were statistically analysed, then the sequencing fragments were screened by Rfam(10.1), Genbank database, and repeat sequence, finally, all the fragments were classified, and all miRNAs were found in three different period including known and unknown miRNA. Known miRNAs were analysed, first of all, base bias analysis was adopted, and miRNA expression profiling was build in three temperature points, then different analysis was conduced in miRNA, meanwhile, miRNA differential expression profiling was build. Differential expression analysis and family analysis were adopted on known miRNA, and unknown miRNAs were predicted and analyzed in including base bias analysis, secondary structure prediction, unknown miRNA differential expression analysis and target gene prediction and functions prediction. The results are as follows:
1. Wheat Small RNA sequencing data processing and Statistics Analysis
The largest numbers of the small RNA we have got were24nt and21nt among the fragments of the length between10nt and35nt by adopting Solexa Sequencing. At last, clean reads accounts (10024183,9448982,10868683) were obtained at3different temperature points.
The possible rRNA, scRNA, snoRNA, snRNA, tRNA from reads fragments were erased by the comparison between Rfam(10.1) and Genbanak database. The rest of the Different respective sequences were erased by repetitive sequences comparison, at last, sRNA categories and selection were conducted, the total accounts we selected at3different temperatures of miRNA are1299843,1167152,1544325.
2. Identification and Difference Expressions of the Known miRNA under Cold Induction
The known miRNA expression profile was built.of the wheat. There are44known miRNA in wheat miRBase, but35,29and31known miRNA in each3samples (tillering nodes under5℃、-15℃and-25℃) were found in Dongnongdongmai1. The accounts of wheat conservative reading frame were analysed, and a big difference was found in express frequency of miRNA. Among them, the higher frequency of11miRNA was found,5miRNAs were referring to cold inducement in the difference analysis, they are tae-miR156,tae-miR398, tae-miR160and tae-miR444and tae-miR444b, and tae miR156expression was in the highest abundance, it had a downregulated trend, and tae-miR398was significantly up-regulated expressed, while tae-miR.160taemiR444and tae-miR444b significantly were significantly down-regulated expressed. Based on the difference analysis and reported target genetic analysis, we infer that above5miRNA have something to do with the cold resistance of Dongnongdongmai1.
3. The Identification of a Part of Known miRNA and Difference Analysis of Dongnongdongmai1
567known miRNA were found in Dongnongdongmai1under the cold induction, among them,164known miRNA were in OEG analysis. Among the selected14known miRNA in OEG analysis,3miRNAs were connected with flower development, they are Tae-miR168, Tae-miR166, Tae-miR172.5miRNAs were connected with cold induction, they are Tae-miR169, Tae-miR397, Tae-miR319, Tae-miR165,6unknown were from cold induction and significant in OEG known miRNA. They are Tae-miR5565,Tae-miR5029, Tae-miR5070、Tae-miR5139, Tae-miR5218,Tae-miR3704.
4. Predicting the New miRNA
378new wheat miRNAs were discovered on the three low temperature points in this study. The number of the new wheat miRNA on each low temperature point are124,96and125, and the predicted accounts of target genes are89,78and99. Among the predicted miRNA database, fully expressed and significant in OEG analysis ones were choosed. Finally,14new miRNA among "Dongnongdongmai1" were choosed and new miRNA expression profile was built and predicted, take advantage of the Mineap software,14miRNAs were predicted which had typical secondary stem-loop structure. Furthermore, the selected14new miRNA were predicted in target genes, seven of them were predicted in target genes, while another seven did not. In this study, the3interesting new miRNAs were analysed, the function of the3new miRNA was predicted by analysing the target genes.
本研究以东农冬麦1号分为试验材料,在大田自然降温条件下,分别于5℃、-15℃和-25℃三个不同低温下取材分蘖节,采用HiSeq技术进行高通量测序,测序片段长度经统计分析进行Rfam(10.1)、Genbank数据库和重复序列筛选,最后把所有的得到的片段进行注释分类,找到三个温度点的所有miRNA,包括已知和未知miRNA。对已知miRNA进行分析,首先进行碱基偏向性分析,构建三个温度时间点miRNA表达谱,然后进行miRNA差异分析,并构建miRNA差异表达谱,然后对已知的miRNA进行表达差异分析和家族分析：对未知的miRNA进行预测分析,包括碱基偏向性分析和二级结构预测,未知miRNA的表达差异分析和靶基因预测,最后预测其未知miRNA的功能。主要研究结果如下：
1.小麦Small RNA测序数据处理及统计分析
采用Solexa测序得到序列长度为10-35nt的小RNA片段,其中文库中数量最多的小RNA是24nt和21nt,最终在5℃、-15℃、-25℃三个温度条件下获得的洁净reads总量分别是10024183、9448982和10868683。
将reads片段与Rfam(10.1)和Genbank数据库比对,去除其中可能的rRNA、scRNA、 snoRNA、snRNA和tRNA。剩下的reads片段通过重复序列比对去除不同类型的重复序列,最后经sRNA分类注释筛选,获得三个不同温度下筛选出的miRNA总数分别为1299843、1167152和1544325。
2.在冷诱导下小麦中已知miRNA鉴定及差异表达分析
构建小麦已知miRNA表达谱。在小麦miRBase中的已知miRNA有44个,在东农冬麦1号三个样品中(分别为5℃、-15℃、-25℃下取样分蘖节)分别发现有35、29和31个,分析小麦保守miRNA阅读框的数量后,发现这些miRNA的表达频率差异很大,其中11个miRNA出现的序列次数相对较高。在差异分析中发现5个与冷诱导有关的miRNA,分别是tae-miR156、tae-miR398、tae-miR160、tae-miR444和tae-miR444b。tae-miR156的表达丰度最高,有下调表达趋势；tae-miR398明显上调表达且差异显著；tae-miR160显著下调表达;tae-miR444和tae-miR444b皆为显著下调表达。根据差异表达分析和已有报道的靶基因分析,本研究推测以上五个miRNA与东农冬麦1号抗寒有关。
3.东农冬麦1号中的部分已知miRNA鉴定及差异表达分析
东农冬麦1号在冷诱导下发现了567个已知miRNA,其中发生显著或极显著差异表达的共164个,我们选择其中的30个miRNA进行差异表达分析,在东农冬麦1号中筛选获得了14个差异表达的已知miRNA,其中3个与花发育有关,分别是Tae-miR166、 Tae-miR172;5个与冷诱导有关,分别是Tae-miR393、Tae-miR169, Tae-miR397、Tae-miR319和Tae-miR165;6个功能未知miRNA,但由冷诱导产生、丰度高,且差异显著的已知的miRNA,分别是Tae-miR5565、Tae-miR5029、Tae-miR5070、Tae-miR5139、Tae-miR5218和Tae-miR3704。
4.预测新的miRNA
本研究在三个低温时间点上共发掘出378个新的小麦miRNA,其中5℃下获得124个,-15℃下获得96个,-25℃下获得125个。三个低温点分别预测到的靶基因数分别是89个、7个8和99个。在预测miRNA数据库中挑选表达量大、均一化处理后表达差极显著的miRNA,最终在东农冬麦1号中筛选出了14个新miRNA。通过建立预测新miRNA表达谱,并利用Mireap软件预测,发现这14个miRNA都具有代表性的二级茎环结构。对选择的14个新miRNA进行靶基因预测,其中7个预测到了靶基因,另7个没有预测到靶基因。本研究对感兴趣的3个新miRNA进行了靶基因分析,初步预测了这3个新miRNA的功能是与低温有关。
Dongnongdongmai1is the uniqueness cultivated wheat variety which can survive in Heilongjiang province (overwinter survival rate more than85%), and it has important cold resistant miRNA and relevant resources of target genes. This study is aimed at exploring the important stress resistant miRNA resources of Dongnongdongmai1. On one hand, it will reveal strong cold resistance mechanism of Dongnongdongmai1, widen the cold resistant hereditary basis of wheat, provide useful traits and sources of cold resistant miRNA genes to wheat genetically modified cultivation, and make an important contribution to the improvement of cultivation in winter wheat in the north of China. On the other hand, it will also supply important information for the deep research of miRNA metabolism.
In this study, tillering nodes of Dongnongdongmai1in three different growing periods were adopted as materials, depth sequencing was conducted through HiSeq technology in three different growing periods, the sequencing results were statistically analysed, then the sequencing fragments were screened by Rfam(10.1), Genbank database, and repeat sequence, finally, all the fragments were classified, and all miRNAs were found in three different period including known and unknown miRNA. Known miRNAs were analysed, first of all, base bias analysis was adopted, and miRNA expression profiling was build in three temperature points, then different analysis was conduced in miRNA, meanwhile, miRNA differential expression profiling was build. Differential expression analysis and family analysis were adopted on known miRNA, and unknown miRNAs were predicted and analyzed in including base bias analysis, secondary structure prediction, unknown miRNA differential expression analysis and target gene prediction and functions prediction. The results are as follows:
1. Wheat Small RNA sequencing data processing and Statistics Analysis
The largest numbers of the small RNA we have got were24nt and21nt among the fragments of the length between10nt and35nt by adopting Solexa Sequencing. At last, clean reads accounts (10024183,9448982,10868683) were obtained at3different temperature points.
The possible rRNA, scRNA, snoRNA, snRNA, tRNA from reads fragments were erased by the comparison between Rfam(10.1) and Genbanak database. The rest of the Different respective sequences were erased by repetitive sequences comparison, at last, sRNA categories and selection were conducted, the total accounts we selected at3different temperatures of miRNA are1299843,1167152,1544325.
2. Identification and Difference Expressions of the Known miRNA under Cold Induction
The known miRNA expression profile was built.of the wheat. There are44known miRNA in wheat miRBase, but35,29and31known miRNA in each3samples (tillering nodes under5℃、-15℃and-25℃) were found in Dongnongdongmai1. The accounts of wheat conservative reading frame were analysed, and a big difference was found in express frequency of miRNA. Among them, the higher frequency of11miRNA was found,5miRNAs were referring to cold inducement in the difference analysis, they are tae-miR156,tae-miR398, tae-miR160and tae-miR444and tae-miR444b, and tae miR156expression was in the highest abundance, it had a downregulated trend, and tae-miR398was significantly up-regulated expressed, while tae-miR.160taemiR444and tae-miR444b significantly were significantly down-regulated expressed. Based on the difference analysis and reported target genetic analysis, we infer that above5miRNA have something to do with the cold resistance of Dongnongdongmai1.
3. The Identification of a Part of Known miRNA and Difference Analysis of Dongnongdongmai1
567known miRNA were found in Dongnongdongmai1under the cold induction, among them,164known miRNA were in OEG analysis. Among the selected14known miRNA in OEG analysis,3miRNAs were connected with flower development, they are Tae-miR168, Tae-miR166, Tae-miR172.5miRNAs were connected with cold induction, they are Tae-miR169, Tae-miR397, Tae-miR319, Tae-miR165,6unknown were from cold induction and significant in OEG known miRNA. They are Tae-miR5565,Tae-miR5029, Tae-miR5070、Tae-miR5139, Tae-miR5218,Tae-miR3704.
4. Predicting the New miRNA
378new wheat miRNAs were discovered on the three low temperature points in this study. The number of the new wheat miRNA on each low temperature point are124,96and125, and the predicted accounts of target genes are89,78and99. Among the predicted miRNA database, fully expressed and significant in OEG analysis ones were choosed. Finally,14new miRNA among "Dongnongdongmai1" were choosed and new miRNA expression profile was built and predicted, take advantage of the Mineap software,14miRNAs were predicted which had typical secondary stem-loop structure. Furthermore, the selected14new miRNA were predicted in target genes, seven of them were predicted in target genes, while another seven did not. In this study, the3interesting new miRNAs were analysed, the function of the3new miRNA was predicted by analysing the target genes.
引文
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