大豆逆境胁迫相关microRNA的发掘与验证
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摘要
MicroRNA (miRNA)是植物中广泛存在的、长度约20-25nt的内源单链非编码小分子RNA,在植物的生长发育、应对各种逆境胁迫等方面起着非常重要的调控作用。而目前关于大豆miRNA的研究还非常有限。
为发掘逆境相关的miRNA,对大豆(Glycine max)幼苗进行了干旱、高盐、低温、脱落酸(ABA)和大豆花叶病毒(SMV)胁迫处理,提取你不同组织的小RNA后等量混合构建混合小RNA文库,用Solexa技术进行高通量测序,与生物信息学分析相结合,发掘与大豆逆境相关的miRNA,为大豆小RNA在抗逆研究方面提供有价值的信息。
主要研究结果如下：
1.在逆境胁迫条件下小分子RNA混合文库的Solexa测序共获得3201342条原始小分子RNA序列,经生物信息学分析筛选出338403条候选miRNA (?)序列,占原始序列的10.6%。共鉴定出包括60个已知miRNA家族的228个miRNA,64个新miRNA家族的76个miRNA。
2.利用miRNA芯片筛选出22个逆境胁迫应答miRNA。其中,4个miRNA与高盐胁迫应答相关,miR156a、miR164、miR166a和miR2911;10个miRNA与干旱胁迫应答相关,niR164、 miR166a、miR168、482b-5p、miR2118、miR2911、miR1507b、miR1508a、miR319g和miR1450;8个miRNA与低温胁迫应答相关,miR156a、 miR164、miR166a、miR168、miR159a-3p、miR1508a、 miR1450和niR2911。
3.受干旱胁迫的大豆miR2118至少有4类靶基因。Northern杂交结果显示,大豆miR2118受干旱胁迫诱导表达且表达有时空特异性。miR2118先在根中表达,后在茎和叶中高表达。在根中0.5小时被诱导表达,1小时表达量最高,表达呈先上调后下调,而茎和叶中表达呈上调趋势,而对高盐和低温胁迫无响应。通过5'RACE方法鉴定了miR2118在大豆中的4个功能各异的靶基因,包括一个编码未知功能蛋白的基因,3个分别编码LRR蛋白、信号肽酶Ⅰ和类基因沉默蛋白抑制子3的基因。
4. miR1511与mR1511*共同切割同一靶基因。高通量测序数据分析及Northern杂交结果均证明了niR1511和miR1511的存在。5'RACE方法验证了niR1511的靶基因为一个属于60S核糖体蛋白L4家族(RPL4) Gmrpl4a (Glyma10g05580.1)基因,同时发现miR1511*也切割该靶基因,miR1511*的切割Gmrpl4a的第一个外显子,miR1511的切割Gmrpl4a的第二个外显子。
5.研究结果显示miR1511有等位变异及地域分布特点。不同栽培大豆(Glycine max) MR1511序列是保守的；多年生野生大豆虽有多处Indel和SNP位点,但miR1511及miR1511*位点序列保守；而在一年生野生大豆(Glycine soja)中,存在4种不同的等位变异,其中两种由于片段缺失导致miR1511缺失,Northern杂交结果也验证了这种缺失现象,约1/4的一年生野生大豆不能加工形成miR1511。这些缺失种质主要集中分布在黄河中下游地区,说明MR1511基因的进化经历了自然选择。
MicroRNAs (miRNAs) are a class of20-25nucleotides, endogenous, small noncoding single-strand RNAs that play critical regulatory roles in plants growth and development, as well as responses to different environmental stresses. But limited researches have been done on the soybean miRNAs.
In order to cloning with stress-related miRNAs in soybean, the soybean seedlings were treated with various stresses, including drought, high salinity, low temperature, abscisic acid (ABA) and soybean mosaic virus (SMV). A mixed small RNA library was constructed and sequenced by Solexa technology. These results provide inprotant clues for the research of soybean stress tolerance.
The major results are as following:
1. A total of3201342raw sequence reads were obtained by solexa high-troughtput sequencing technology including338403candidate miRNA reads were generated from stress-treated soybean small RNA library. Fanally,228known miRNAs and76putative novel miRNAs were found by bioinformatic analysis, which belongs to60and64miRNA families, respectively.
2. A total of22stress-responsive miRNAs were identified using miRNA microarray screenings, including4salinity-responsive miRNAs (miR156a, miR164, miR166a and peu-miR2911),10drought-responsive miRNAs (miR164, miR166a, miR168,482b-5p, miR2118, miR2911, miR1507b, miR1508a, miR319g and miR1450), and8low temperature-responsive miRNAs (miR156a, miR164, miR166a, miR168, miR159a-3p, miR1508a, miR1450and miR2911).
3. miR2118expression were upregulated by drought stress, the expression was induced firstly from root, then in root and leaf, the expression was induced in0.5h reached high in1h then declined, while continued increasing expression in shoot and leaf. miR2118expression was not induced by high silinity and low temperature. Using5'RACE (Rapidd amplification of cDNA ends)-PCR, we have identified4target genes of of which coding leucine-rich repeat-containing protein, signal peptidase I, suppressor gene silencing3-like and one unkown protein, respectively
4. miRNA1511and miRNA1511were cooperated to cleave the same target gene. miR1511*was validated by analyzing high-troughtput sequencing data and Northern blotting. Using5'RACE-PCR, we identified one target gene belonged to60S ribosomal protein L4family gene Gmrpl4a (Glyma10g05580.1), which were cleaved by both miR1511and miR1511*. The target cleavage site of the miR1511was identified in the first exon of Gmrpl4a, and the miR1511target in second exon of Gmrpl4a.
5. Allelic variation of miR1511gene were identified on geographical distribution in China. The MIR1511were conserved in cultivated soybean (Glycine max), but there were several Indels and SNPs in MR1511for perennial wild soybean, though conserved miR1511and miR1511*sequences. There were4allelic variations in MIR1511,2of them were absent of miR1511in annual wild soybeans (Glycine soja), which were confirmed by Northern blotting. One fouth of annual wild soybean accessions were absent of miR1511. We have found with absent of miR1511in Glycine soja, Which were mainly came from lower and middle reaches Yellow River. These results indicated the evolution of MIR1511gene undergo natural selection.
为发掘逆境相关的miRNA,对大豆(Glycine max)幼苗进行了干旱、高盐、低温、脱落酸(ABA)和大豆花叶病毒(SMV)胁迫处理,提取你不同组织的小RNA后等量混合构建混合小RNA文库,用Solexa技术进行高通量测序,与生物信息学分析相结合,发掘与大豆逆境相关的miRNA,为大豆小RNA在抗逆研究方面提供有价值的信息。
主要研究结果如下：
1.在逆境胁迫条件下小分子RNA混合文库的Solexa测序共获得3201342条原始小分子RNA序列,经生物信息学分析筛选出338403条候选miRNA (?)序列,占原始序列的10.6%。共鉴定出包括60个已知miRNA家族的228个miRNA,64个新miRNA家族的76个miRNA。
2.利用miRNA芯片筛选出22个逆境胁迫应答miRNA。其中,4个miRNA与高盐胁迫应答相关,miR156a、miR164、miR166a和miR2911;10个miRNA与干旱胁迫应答相关,niR164、 miR166a、miR168、482b-5p、miR2118、miR2911、miR1507b、miR1508a、miR319g和miR1450;8个miRNA与低温胁迫应答相关,miR156a、 miR164、miR166a、miR168、miR159a-3p、miR1508a、 miR1450和niR2911。
3.受干旱胁迫的大豆miR2118至少有4类靶基因。Northern杂交结果显示,大豆miR2118受干旱胁迫诱导表达且表达有时空特异性。miR2118先在根中表达,后在茎和叶中高表达。在根中0.5小时被诱导表达,1小时表达量最高,表达呈先上调后下调,而茎和叶中表达呈上调趋势,而对高盐和低温胁迫无响应。通过5'RACE方法鉴定了miR2118在大豆中的4个功能各异的靶基因,包括一个编码未知功能蛋白的基因,3个分别编码LRR蛋白、信号肽酶Ⅰ和类基因沉默蛋白抑制子3的基因。
4. miR1511与mR1511*共同切割同一靶基因。高通量测序数据分析及Northern杂交结果均证明了niR1511和miR1511的存在。5'RACE方法验证了niR1511的靶基因为一个属于60S核糖体蛋白L4家族(RPL4) Gmrpl4a (Glyma10g05580.1)基因,同时发现miR1511*也切割该靶基因,miR1511*的切割Gmrpl4a的第一个外显子,miR1511的切割Gmrpl4a的第二个外显子。
5.研究结果显示miR1511有等位变异及地域分布特点。不同栽培大豆(Glycine max) MR1511序列是保守的；多年生野生大豆虽有多处Indel和SNP位点,但miR1511及miR1511*位点序列保守；而在一年生野生大豆(Glycine soja)中,存在4种不同的等位变异,其中两种由于片段缺失导致miR1511缺失,Northern杂交结果也验证了这种缺失现象,约1/4的一年生野生大豆不能加工形成miR1511。这些缺失种质主要集中分布在黄河中下游地区,说明MR1511基因的进化经历了自然选择。
MicroRNAs (miRNAs) are a class of20-25nucleotides, endogenous, small noncoding single-strand RNAs that play critical regulatory roles in plants growth and development, as well as responses to different environmental stresses. But limited researches have been done on the soybean miRNAs.
In order to cloning with stress-related miRNAs in soybean, the soybean seedlings were treated with various stresses, including drought, high salinity, low temperature, abscisic acid (ABA) and soybean mosaic virus (SMV). A mixed small RNA library was constructed and sequenced by Solexa technology. These results provide inprotant clues for the research of soybean stress tolerance.
The major results are as following:
1. A total of3201342raw sequence reads were obtained by solexa high-troughtput sequencing technology including338403candidate miRNA reads were generated from stress-treated soybean small RNA library. Fanally,228known miRNAs and76putative novel miRNAs were found by bioinformatic analysis, which belongs to60and64miRNA families, respectively.
2. A total of22stress-responsive miRNAs were identified using miRNA microarray screenings, including4salinity-responsive miRNAs (miR156a, miR164, miR166a and peu-miR2911),10drought-responsive miRNAs (miR164, miR166a, miR168,482b-5p, miR2118, miR2911, miR1507b, miR1508a, miR319g and miR1450), and8low temperature-responsive miRNAs (miR156a, miR164, miR166a, miR168, miR159a-3p, miR1508a, miR1450and miR2911).
3. miR2118expression were upregulated by drought stress, the expression was induced firstly from root, then in root and leaf, the expression was induced in0.5h reached high in1h then declined, while continued increasing expression in shoot and leaf. miR2118expression was not induced by high silinity and low temperature. Using5'RACE (Rapidd amplification of cDNA ends)-PCR, we have identified4target genes of of which coding leucine-rich repeat-containing protein, signal peptidase I, suppressor gene silencing3-like and one unkown protein, respectively
4. miRNA1511and miRNA1511were cooperated to cleave the same target gene. miR1511*was validated by analyzing high-troughtput sequencing data and Northern blotting. Using5'RACE-PCR, we identified one target gene belonged to60S ribosomal protein L4family gene Gmrpl4a (Glyma10g05580.1), which were cleaved by both miR1511and miR1511*. The target cleavage site of the miR1511was identified in the first exon of Gmrpl4a, and the miR1511target in second exon of Gmrpl4a.
5. Allelic variation of miR1511gene were identified on geographical distribution in China. The MIR1511were conserved in cultivated soybean (Glycine max), but there were several Indels and SNPs in MR1511for perennial wild soybean, though conserved miR1511and miR1511*sequences. There were4allelic variations in MIR1511,2of them were absent of miR1511in annual wild soybeans (Glycine soja), which were confirmed by Northern blotting. One fouth of annual wild soybean accessions were absent of miR1511. We have found with absent of miR1511in Glycine soja, Which were mainly came from lower and middle reaches Yellow River. These results indicated the evolution of MIR1511gene undergo natural selection.
引文
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