兴安落叶松不同生长时期诱导防御基因表达谱的变化
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摘要
兴安落叶松(Larix gmelinii)是中国东北地区最具经济意义和生态价值的重要树种之一。目前,对兴安落叶松生长发育及抗性相关基因知之甚少。为此,采用喷雾法对松苗进行非离体处理,分别喷施0.1mM的茉莉酸和茉莉酸甲酯水溶液,诱导6h后,剪取相距松苗顶端30cm处的针叶用CTAB法进行总RNA提取,应用短读序测序技术—-Illumina测序技术对兴安落叶松进行转录组de novo测序、组装；分别构建茉莉酸和茉莉酸甲酯诱导6h后兴安落叶松的数字基因表达谱,分析不同生长时期经由茉莉酸和茉莉酸甲酯诱导的兴安落叶松基因表达谱的变化。结果如下：
转录组通过单次运行测序得到25,977,782条短读序列,相互缀连成545,211个叠连群,锚定出92,511个框架和平均读长为517nt的51,157个Unigene,其中包含了脂氧合酶基因、苯丙氨酸解氨酶基因、丝氨酸蛋白酶抑制剂基因、半胱氨酸蛋白酶抑制剂基因和几丁质酶基因等若干与抗虫、抗病相关的基因。把组装得到的Unigene在不同的数据库中进行比对,有32,445个独特基因序列与Nr数据库中蛋白相似；与COG数据库中的序列同源的Unigene9,920个,分为25种功能；基于与GO数据库中序列的同源性,把13,317个Unigene分为44个功能类群；在KEGG(?)库中14,462个Unigene进行Pathway注释,涉及到的Pathway有119个,有36.76%的Unigene参与到代谢途径、次生代谢产物的生物合成途径中。基于测序结果,经Blastx有32,047个Unigene得到编码区核酸序列和氨基酸序列,为进一步研究相关基因的功能提供了大量的本底数据。
数字基因表达谱测序有5个样本,分别得到350万到590万数量不等的原始序列标签,去冗余后获得了52,040个参考基因；差异表达基因中孤儿序列数量低于30%；多数差异表达基因显著富集于分子功能Ontology中的氧化还原酶活性功能。从总体上研究不同诱导处理后,生长时期不同的兴安落叶松mRNA的表达变化情况,对样品DGE数据库间的差异表达基因进行分析,茉莉酸与茉莉酸甲酯诱导处理后针叶差异表达基因数量相近,多数为下调表达；抽芽后120天的兴安落叶松针叶诱导处理后上调表达和下调表达基因数量均多于相同处理后抽芽60天的针叶。
兴安落叶松经茉莉酸和茉莉酸甲酯诱导后,代谢相关基因差异表达变化的数量约为次生代谢相关基因变化数量的2倍。分别对相同生长时期不同诱导处理和不同生长时期相同诱导处理的兴安落叶松差异表达基因进行分析,且着重分析与抗虫或抗病相关的苯丙氨酸、酪氨酸和色氨酸的生物合成,苯丙酸类化合物生物合成、芥子油苷生物合成和α-亚麻酸代谢途径中的关键酶基因的差异表达。
抽芽后60天的兴安落叶松经茉莉酸和茉莉酸甲酯分别诱导处理后,天冬氨酸解氨酶、苯丙氨酸解氨酶、反式肉桂酸4-单加氧酶、松柏醛脱氢酶、转移酶活性、糖基转移酶和脂氧合酶基因表达量变化趋势相同,表达量均明显高于对照；茉莉酸诱导3-脱氢奎尼酸脱水酶、莽草酸脱氢酶和香豆酸3-羟化酶基因下调表达,而茉莉酸甲酯诱导其上调表达。
抽芽后120天的兴安落叶松经茉莉酸和茉莉酸甲酯分别诱导处理后,3-脱氢奎尼酸脱水酶、莽草酸脱氢酶、天冬氨酸解氨酶、香豆酸3-羟化酶、松柏醛脱氢酶、转移酶活性、糖基转移酶和脂氧合酶的基因表达量变化趋势相同,表达量明显高于对照；茉莉酸诱导的苯丙氨酸解氨酶和反式肉桂酸4-单加氧酶的基因上调表达,而茉莉酸甲酯诱导其下调表达。
对不同生长时期相同诱导处理后差异表达基因分析显示,抽芽后120天的兴安落叶松经茉莉酸诱导后与相同诱导处理抽芽后60天的兴安落叶松相比更侧重于能量合成与代谢,而经茉莉酸甲酯诱导后则侧重于诱导植物化学防御。无论是茉莉酸诱导还是茉莉酸甲酯诱导,抽芽后120天的兴安落叶松,苯丙氨酸解氨酶和脂氧合酶基因相较于抽芽后60天的兴安落叶松基因表达量明显上调。
对丝氨酸蛋白酶抑制剂基因、半胱氨酸蛋白酶抑制剂基因、病原相关蛋白基因和几丁质酶基因等抗性相关基因进行差异表达分析,茉莉酸和茉莉酸甲酯的诱导处理都可以使丝氨酸蛋白酶抑制剂基因表达量发生明显差异,而半胱氨酸蛋白酶抑制剂基因和磺基转移酶基因均无差异表达。
转录组和数字基因表达谱所获得的数据为进一步研究落叶松生长发育、生理代谢及抗性相关基因结构和功能提供了重要的本底资源。兴安落叶松经茉莉酸、茉莉酸甲酯诱导处理后,应用数字基因表达谱分析抗病虫基因的差异表达变化,抽芽后60天喷施茉莉酸和茉莉酸甲酯均可使抗病虫基因显著差异表达,而抽芽后120天茉莉酸甲酯对抗病虫基因诱导效果优于茉莉酸；为生产实践中植物抗虫诱导剂的选择及诱导剂的作用机理研究提供理论依据。
Larix gmelinii is one of the most economically and ecologically important tree species in Northeast China, however, little is understood about its genes involved in growth, development, and resistance of the species. In this study, we performed the de novo assembly of Larix gmelinii transcriptome using a short read sequencing technology (Illumina) and analyzed the transcript differences between Larix gmelinii of different phase induced by jasmonic acid and by methyl jasmonate respectively for6h using a tag-based digital gene expression system. Sample seedlings were treated non in vitro with0.1mM jasmonic acid,0.1mM methyl jasmonate, or0.1%aqueous acetone solution (as control) separately using a handheld sprayer. Tree needles from upper part of the seedling (circa30cm from the top) were sampled for total RNA isolation6h after being sprayed, total RNA isolation following the CTAB method protocol. The following are the results of this study.
In a single run,25,977,782short reads were produced, which were assembled into545,211contigs assembled further into92,511scaffolds. After filling gaps in scaffolds by using paired-end reads,51,157unigenes were obtained with mean unigene size being517nt, including many disease/insect-resistance related genes, such as lipoxygenase (LOX) gene, phenylalanine ammonialyase (PAL) gene, serine protease inhibitor (serpin) gene, cysteine protease inhibitor (cystatin) gene and chitinase gene. We matched unigene sequences against Nr protein databases obtaining32,445unigenes from which9,920sequences had a COG classification and were divided into25COG categories. Further, we obtained the Gene Ontology (GO) functional annotation with Nr annotation. Based on the sequence homology,13,317sequences were categorized into44functional groups. We assigned14,462sequences to119KEGG pathways,36.76%of these unigenes involving in metabolic pathways and the biosynthesis of secondary metabolites. In total,32,047unigenes were predicted by using Blastx based on sequencing results and we use blast results information to extract CDS from Unigene sequences and translate them into peptide sequencs, providing a lot of fundamental data for further researching related genes functions.
We sequenced5digital gene expression libraries and generated between3.5and5.9million raw tags for each of the5samples, obtained52,040reference genes after removal of redundancy and found that less than30%of the differentially expressed genes are orphan sequences. We found that oxidoreductase activity is the most significantly enriched GO-term of molecular functions in5digital gene expression libraries. The mRNA expression changes at different growth phase of Larix gmelinii inducing by different elicitors in general. The number of differentially expressed genes in the tree needles induced by jasmonic acid and methyl jasmonate is similar, with the majority are down-regulated. The number of differentially expressed genes,whether up-regulated or down-regulated, induced by elicitors in the120-day needles of Larix gmelinii are more than in the60-day needles.
The number of differentially expressed genes of metabolism-related is twice as much as secondary metabolism-related in Larix gmelinii induced by jasmonic acid and methyl jasmonate. The differentially expressed genes of Larix gmelinii in one growth phase induced by different elicitors and in different growth phases induced by the same elicitor were analyzed putting emphasis on the analysis of differentially expressed about the disease/insect-resistance related key enzyme genes in the pathways of phenylalanine, tyrosine and tryptophan biosynthesis, phenylpropanoid biosynthesis, glucosinolate biosynthesis and alpha-Linolenic acid metabolism.
Among the samples of Larix gmelinii sprout after60days, the expression of aspartate transaminase gene, phenylalanine ammonialyase gene, trans-cinnamate4-monooxygenase gene, coniferyl-aldehyde dehydrogenase gene, transferase activity gene, glucosyl transferase gene and lipoxygenase gene which treated by jasmonic acid or methyl jasmonate was significantly higher than the control. The expression of3-dehydroquinate dehydratase gene, shikimate dehydrogenase gene and coumarate3-hydroxylase gene was significantly different, and the result showed that the gene expression was down-regulated among jasmonic acid treatment samples, whereas up-regulated among methyl jasmonate samples.
Among the samples of120-day needles, treated by jasmonic acid or methyl jasmonate, the expression of3-dehydroquinate dehydratase gene, shikimate dehydrogenase gene, aspartate transaminase gene, coumarate3-hydroxylase gene, coniferyl-aldehyde dehydrogenase gene, transferase activity gene, glucosyl transferase gene and lipoxygenase gene was significantly higher than the control. The expression of phenylalanine ammonialyase gene and trans-cinnamate4-monooxygenase gene was significantly different, showing that the gene expression was up-regulated among jasmonic acid treatment samples, whereas down-regulated among methyl jasmonate samples.
The analysis of differentially expressed genes was conducted by the same elicitor treatment to the needles of different growth phases. The result showed that the120-day needles induced by jasmonic acid were focused on energy synthesis and metabolism more than the60-day needles that, induced by methyl jasmonate, however, were more focused on plant chemical defense. Whether the samples were induced by jasmonic acid or methyl jasmonate, the expression of phenylalanine ammonialyase gene and lipoxygenase gene for the120-day needles were significantly higher than that of60-day needles.
The analysis was conducted for the differentially expressed resistance related genes, such as serine protease inhibitor gene, cysteine protease inhibitor gene, pathogenesis-related protein gene and chitinase gene, indicating that serine protease inhibitor gene, treated by jasmonic acid or methyl jasmonate, was significantly changed than the control, but cysteine protease inhibitor gene and sulfotransferase gene were not significantly changed.
The data of transcriptome and digital gene expression libraries obtained in this study provide important fundamental resources for further researching on growth, development, physiological metabolism and structures and functions of resistance related genes of Larix gmelinii. The analysis of differentially expressed disease/insect-resistance related genes was conducted using digital gene expression libraries sequencing for Larix gmelinii induced by jasmonic acid or methyl jasmonate. The result showed that the disease/insect-resistance related genes was significantly changed for the60-day needles than the control, and methyl jasmonate was better than jasmonic acid in induction of disease/insect-resistance related genes for the120-day needles. The results provide important theoretical foundations for selection of elicitors related to plant resistance to insects in industry practices and further research on mechanism of elicitors.
转录组通过单次运行测序得到25,977,782条短读序列,相互缀连成545,211个叠连群,锚定出92,511个框架和平均读长为517nt的51,157个Unigene,其中包含了脂氧合酶基因、苯丙氨酸解氨酶基因、丝氨酸蛋白酶抑制剂基因、半胱氨酸蛋白酶抑制剂基因和几丁质酶基因等若干与抗虫、抗病相关的基因。把组装得到的Unigene在不同的数据库中进行比对,有32,445个独特基因序列与Nr数据库中蛋白相似；与COG数据库中的序列同源的Unigene9,920个,分为25种功能；基于与GO数据库中序列的同源性,把13,317个Unigene分为44个功能类群；在KEGG(?)库中14,462个Unigene进行Pathway注释,涉及到的Pathway有119个,有36.76%的Unigene参与到代谢途径、次生代谢产物的生物合成途径中。基于测序结果,经Blastx有32,047个Unigene得到编码区核酸序列和氨基酸序列,为进一步研究相关基因的功能提供了大量的本底数据。
数字基因表达谱测序有5个样本,分别得到350万到590万数量不等的原始序列标签,去冗余后获得了52,040个参考基因；差异表达基因中孤儿序列数量低于30%；多数差异表达基因显著富集于分子功能Ontology中的氧化还原酶活性功能。从总体上研究不同诱导处理后,生长时期不同的兴安落叶松mRNA的表达变化情况,对样品DGE数据库间的差异表达基因进行分析,茉莉酸与茉莉酸甲酯诱导处理后针叶差异表达基因数量相近,多数为下调表达；抽芽后120天的兴安落叶松针叶诱导处理后上调表达和下调表达基因数量均多于相同处理后抽芽60天的针叶。
兴安落叶松经茉莉酸和茉莉酸甲酯诱导后,代谢相关基因差异表达变化的数量约为次生代谢相关基因变化数量的2倍。分别对相同生长时期不同诱导处理和不同生长时期相同诱导处理的兴安落叶松差异表达基因进行分析,且着重分析与抗虫或抗病相关的苯丙氨酸、酪氨酸和色氨酸的生物合成,苯丙酸类化合物生物合成、芥子油苷生物合成和α-亚麻酸代谢途径中的关键酶基因的差异表达。
抽芽后60天的兴安落叶松经茉莉酸和茉莉酸甲酯分别诱导处理后,天冬氨酸解氨酶、苯丙氨酸解氨酶、反式肉桂酸4-单加氧酶、松柏醛脱氢酶、转移酶活性、糖基转移酶和脂氧合酶基因表达量变化趋势相同,表达量均明显高于对照；茉莉酸诱导3-脱氢奎尼酸脱水酶、莽草酸脱氢酶和香豆酸3-羟化酶基因下调表达,而茉莉酸甲酯诱导其上调表达。
抽芽后120天的兴安落叶松经茉莉酸和茉莉酸甲酯分别诱导处理后,3-脱氢奎尼酸脱水酶、莽草酸脱氢酶、天冬氨酸解氨酶、香豆酸3-羟化酶、松柏醛脱氢酶、转移酶活性、糖基转移酶和脂氧合酶的基因表达量变化趋势相同,表达量明显高于对照；茉莉酸诱导的苯丙氨酸解氨酶和反式肉桂酸4-单加氧酶的基因上调表达,而茉莉酸甲酯诱导其下调表达。
对不同生长时期相同诱导处理后差异表达基因分析显示,抽芽后120天的兴安落叶松经茉莉酸诱导后与相同诱导处理抽芽后60天的兴安落叶松相比更侧重于能量合成与代谢,而经茉莉酸甲酯诱导后则侧重于诱导植物化学防御。无论是茉莉酸诱导还是茉莉酸甲酯诱导,抽芽后120天的兴安落叶松,苯丙氨酸解氨酶和脂氧合酶基因相较于抽芽后60天的兴安落叶松基因表达量明显上调。
对丝氨酸蛋白酶抑制剂基因、半胱氨酸蛋白酶抑制剂基因、病原相关蛋白基因和几丁质酶基因等抗性相关基因进行差异表达分析,茉莉酸和茉莉酸甲酯的诱导处理都可以使丝氨酸蛋白酶抑制剂基因表达量发生明显差异,而半胱氨酸蛋白酶抑制剂基因和磺基转移酶基因均无差异表达。
转录组和数字基因表达谱所获得的数据为进一步研究落叶松生长发育、生理代谢及抗性相关基因结构和功能提供了重要的本底资源。兴安落叶松经茉莉酸、茉莉酸甲酯诱导处理后,应用数字基因表达谱分析抗病虫基因的差异表达变化,抽芽后60天喷施茉莉酸和茉莉酸甲酯均可使抗病虫基因显著差异表达,而抽芽后120天茉莉酸甲酯对抗病虫基因诱导效果优于茉莉酸；为生产实践中植物抗虫诱导剂的选择及诱导剂的作用机理研究提供理论依据。
Larix gmelinii is one of the most economically and ecologically important tree species in Northeast China, however, little is understood about its genes involved in growth, development, and resistance of the species. In this study, we performed the de novo assembly of Larix gmelinii transcriptome using a short read sequencing technology (Illumina) and analyzed the transcript differences between Larix gmelinii of different phase induced by jasmonic acid and by methyl jasmonate respectively for6h using a tag-based digital gene expression system. Sample seedlings were treated non in vitro with0.1mM jasmonic acid,0.1mM methyl jasmonate, or0.1%aqueous acetone solution (as control) separately using a handheld sprayer. Tree needles from upper part of the seedling (circa30cm from the top) were sampled for total RNA isolation6h after being sprayed, total RNA isolation following the CTAB method protocol. The following are the results of this study.
In a single run,25,977,782short reads were produced, which were assembled into545,211contigs assembled further into92,511scaffolds. After filling gaps in scaffolds by using paired-end reads,51,157unigenes were obtained with mean unigene size being517nt, including many disease/insect-resistance related genes, such as lipoxygenase (LOX) gene, phenylalanine ammonialyase (PAL) gene, serine protease inhibitor (serpin) gene, cysteine protease inhibitor (cystatin) gene and chitinase gene. We matched unigene sequences against Nr protein databases obtaining32,445unigenes from which9,920sequences had a COG classification and were divided into25COG categories. Further, we obtained the Gene Ontology (GO) functional annotation with Nr annotation. Based on the sequence homology,13,317sequences were categorized into44functional groups. We assigned14,462sequences to119KEGG pathways,36.76%of these unigenes involving in metabolic pathways and the biosynthesis of secondary metabolites. In total,32,047unigenes were predicted by using Blastx based on sequencing results and we use blast results information to extract CDS from Unigene sequences and translate them into peptide sequencs, providing a lot of fundamental data for further researching related genes functions.
We sequenced5digital gene expression libraries and generated between3.5and5.9million raw tags for each of the5samples, obtained52,040reference genes after removal of redundancy and found that less than30%of the differentially expressed genes are orphan sequences. We found that oxidoreductase activity is the most significantly enriched GO-term of molecular functions in5digital gene expression libraries. The mRNA expression changes at different growth phase of Larix gmelinii inducing by different elicitors in general. The number of differentially expressed genes in the tree needles induced by jasmonic acid and methyl jasmonate is similar, with the majority are down-regulated. The number of differentially expressed genes,whether up-regulated or down-regulated, induced by elicitors in the120-day needles of Larix gmelinii are more than in the60-day needles.
The number of differentially expressed genes of metabolism-related is twice as much as secondary metabolism-related in Larix gmelinii induced by jasmonic acid and methyl jasmonate. The differentially expressed genes of Larix gmelinii in one growth phase induced by different elicitors and in different growth phases induced by the same elicitor were analyzed putting emphasis on the analysis of differentially expressed about the disease/insect-resistance related key enzyme genes in the pathways of phenylalanine, tyrosine and tryptophan biosynthesis, phenylpropanoid biosynthesis, glucosinolate biosynthesis and alpha-Linolenic acid metabolism.
Among the samples of Larix gmelinii sprout after60days, the expression of aspartate transaminase gene, phenylalanine ammonialyase gene, trans-cinnamate4-monooxygenase gene, coniferyl-aldehyde dehydrogenase gene, transferase activity gene, glucosyl transferase gene and lipoxygenase gene which treated by jasmonic acid or methyl jasmonate was significantly higher than the control. The expression of3-dehydroquinate dehydratase gene, shikimate dehydrogenase gene and coumarate3-hydroxylase gene was significantly different, and the result showed that the gene expression was down-regulated among jasmonic acid treatment samples, whereas up-regulated among methyl jasmonate samples.
Among the samples of120-day needles, treated by jasmonic acid or methyl jasmonate, the expression of3-dehydroquinate dehydratase gene, shikimate dehydrogenase gene, aspartate transaminase gene, coumarate3-hydroxylase gene, coniferyl-aldehyde dehydrogenase gene, transferase activity gene, glucosyl transferase gene and lipoxygenase gene was significantly higher than the control. The expression of phenylalanine ammonialyase gene and trans-cinnamate4-monooxygenase gene was significantly different, showing that the gene expression was up-regulated among jasmonic acid treatment samples, whereas down-regulated among methyl jasmonate samples.
The analysis of differentially expressed genes was conducted by the same elicitor treatment to the needles of different growth phases. The result showed that the120-day needles induced by jasmonic acid were focused on energy synthesis and metabolism more than the60-day needles that, induced by methyl jasmonate, however, were more focused on plant chemical defense. Whether the samples were induced by jasmonic acid or methyl jasmonate, the expression of phenylalanine ammonialyase gene and lipoxygenase gene for the120-day needles were significantly higher than that of60-day needles.
The analysis was conducted for the differentially expressed resistance related genes, such as serine protease inhibitor gene, cysteine protease inhibitor gene, pathogenesis-related protein gene and chitinase gene, indicating that serine protease inhibitor gene, treated by jasmonic acid or methyl jasmonate, was significantly changed than the control, but cysteine protease inhibitor gene and sulfotransferase gene were not significantly changed.
The data of transcriptome and digital gene expression libraries obtained in this study provide important fundamental resources for further researching on growth, development, physiological metabolism and structures and functions of resistance related genes of Larix gmelinii. The analysis of differentially expressed disease/insect-resistance related genes was conducted using digital gene expression libraries sequencing for Larix gmelinii induced by jasmonic acid or methyl jasmonate. The result showed that the disease/insect-resistance related genes was significantly changed for the60-day needles than the control, and methyl jasmonate was better than jasmonic acid in induction of disease/insect-resistance related genes for the120-day needles. The results provide important theoretical foundations for selection of elicitors related to plant resistance to insects in industry practices and further research on mechanism of elicitors.
引文
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