烟草靶斑病菌（Rhizoctonia solani AG-3）遗传多样性、定量检测技术及转录组学分析
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摘要
烟草靶斑病(Rhizoctonia solani Kuhn)是一种严重影响烟草产量和品质的叶部病害,在许多国家造成了巨大的经济损失,国内2006年首次报道了该病害在丹东等地发生,迄今,国内外对烟草靶斑病菌相关研究较少,仅见本研究室对烟草靶斑病菌的生物学特性、遗传分化和致病机制等开展了基础性研究。为进一步探明烟草靶斑病菌的分子致病机制及病害流行规律,以期为该病害的防治提供理论依据,本文针对烟草靶斑病菌的致病类型、遗传多样性、定量检测和转录组学进行了系统深入研究,研究成果报道如下：
1.明确了辽宁省烟草靶斑病菌存在着明显的生理分化现象,可划分为三个致病类型,即致病类型Ⅰ(强致病类型)、Ⅱ(中等致病类型)及Ⅲ(弱致病类型),以致病类型Ⅱ为优势种群,分析认为致病类型与菌株地区来源间没有明显相关性。
对来源于不同地区的烟草靶斑病菌基因组ITS序列区进行了聚类分析,结果表各菌株间存在一定的差异,可将测试菌株分为两个ITS类群,进一步分析表明该类群划分与致病类型无明显相关性。
2.建立并优化了适用于烟草靶斑病菌遗传多样性分析的SRAP反应体系,并对SRAP分组与菌株地区来源及致病类型间的关系进行了研究。选取多态性良好的初筛引物及优化后的反应体系对辽宁省烟草靶斑病菌进行PCR扩增,获得多态性条带743条,多态性百分比为98.4%,可将烟草靶斑病菌株划分为3个SGs类群；经分析SGs类群所表现出来的菌株基因组之间的多态性与菌株致病力相关,其中强致病类型菌株YC-9、YMC-2、LJT-8和DB-3都被聚合在SG I类群中,占SGI类群总数的66.7%；而弱致病力菌株LF-2、QYS-5和QYS-7都被聚合在SG Ⅱ类群。这表明SRAP分组与致病类型划分存在明显相关性,而与地区来源没有相关性；与不同融合群标准菌株分析比较表明,SRAP分组与融合群划分无明显相关性。国内外文献无此方面报道,本文为首次采用SRAP技术对烟草靶斑病菌致病类型及遗传多样性进行的研究。
3.建立了烟草靶斑病菌的Real-time PCR定量检测体系,并应用该体系对烟草靶斑病进行早期定量检测,在接种侵染6h后便可检出YC-9菌株DNA,该体系也可以实时监测烟草靶斑病原菌在土壤中动态变化情况。参考NCBI数据库中R. solani不同融合群的ITS序列,设计了对R. solani AG-3特异的引物Rs TqF1/R4和探针QTqF1,并分别建立了适于检测烟草组织和土壤样品的Real-time PCR反应体系。应用该体系对接种烟草靶斑病菌的烟草叶片进行检测结果表明：在接种后6h后即可检测到烟草靶斑病菌,远早于接种36h后观察到可见病原菌子实体结构；采用该体系对各月发病烟田土壤样品定量结果表明：烟草靶斑病菌的群体随不同月份呈现动态变化趋势。自5月中下旬土壤中烟草靶斑病菌拷贝数逐渐升高,到6月28日达到最高,此后开始下降,到8月9日降到最低,8月末烟草靶斑病菌在土壤中拷贝数开始增加,直到1月21日达到最高,此后烟草靶斑病菌下降至4月份达到最低水平。本文为国内外首次建立并应用Real-time PCR技术对烟草靶斑病菌进行的定量检测研究。
4.首次建立了烟草靶斑病菌转录组数据库,为分析烟草靶斑病菌的基因结构及其功能奠定了基础。采用转录组测序以及短序列组装,与烟草互作的T1靶斑病菌样品和未互作的T2对照样品经组装分别获得630125和562259个Contigs,N50值分别为96nt和104nt；经Transcripts组装后,T1和T2分别获得21206和20400条转录本序列,N50分别为1213bp和1247bp；最终共获得21779条Unigenes,平均长度为873nt,N50值为1339nt,较全面的获得了烟草靶斑病菌转录组数据库。
5.通过对上述获得的烟草靶斑病菌转录组数据库的分析,首次对其Unigenes和差异表达基因进行了功能信息注释及代谢途径分析,进而从转录组水平阐明了烟草靶斑病菌的分子致病机理。
采用Blastx软件比对全部Unigenes,其中14389条Unigenes被注释,与担子菌同源最高,其中包含植物病原担子菌T. cucumeris和R. solani等；经GO功能分类分析,共有5976条Unigenes被归类到48个功能类别中,其中生物代谢过程及催化活性和结合作用的分子功能最多；通过COG功能分类,共有5458条Unigenes被归类到25个功能类别中,其中预测功能,复制、重组和修复功能,碳水化合物运输和代谢功能的基因最多；经过KEGG代谢通路的分析,共有3820条基因被注释到158个信号通路中,其中注释到染色体通路、DNA修复和重组蛋白通路、剪接体通路、肽酶通路、泛素系统代谢通路和DNA复制蛋白中的基因较多。
采用RPKM法进行差异表达基因分析,共获得827条差异表达基因,得到注释的有730条。通过GO和COG功能分类以及KEGG通路富集分析,差异表达基因多是参与蛋白质合成过程的相关基因,其中包括核糖体蛋白、转录因子、翻译因子、延伸因子等相关功能基因。
Tobacco target spot caused by Rhizoctonia solani AG-3was one of the most economically important diseases of tobacco leaf and occurs in many countries. It was first reported at Dandong city of China in2006. There was a little report about the biological characteristics, genetic differentiation and pathogen mechanism of the pathogen. In this dissertation, the genetic diversity, quantitative detection technique and transcriptome analysis of R. solani AG-3were systematically and intensively studied, the results were as follows:
1. There were an obvious physiological differentiation among R. solani AG-3from Liaoning province, and three pathotypes, which contain pathotype I, II and III with strong, medium and weak pathogenicity respectively, were determined.
Some differences of ITS region of R. solani AG-3are founded. There was no correlation between the difference group and pathotypes of R. solani AG-3from tobacco.
2. SRAP reaction system of R. solani AG-3from tobacco was firstly established, and genetic diversity of the R. solani AG-3from Liaoning province is analyzed by SRAP reaction system, and the relationships between SRAP groups (SGs) and the locality source of R. solani AG-3were elaborated. Using optimum reaction system and primarily screened SRAP primers which have a good polymorphism, a PCR amplication is performed, and743polymorphism DNA fragements were acquired, percentage of polymorphic loci was98.4%. R. solani AG-3strains from tobacco were divided into three SGs according to SRAP polymorphism between R. solani strains genom from tobacco. All strains with strong pathogenicity containing YC-9, YMC-2, LJT-8and DB-3strains were clusted in SG I, accouting for66.7%of the SG I; and all strains with weak pathogenicity clusted in SG II. The results showed that it is an obvious correlation between SGs and pathotype of strains but not between SGs and the locality source. Further more, there was no correlation between SGs and the anastomosis group. At present, the paper was firstly report relationship between pathotype and genetic diversity of R. solani AG-3from tobacco in the literature at home and abroad.
3. Quantitative detection systems of R. solani AG-3from tobacco firstly established could be applied to early detect in tobacco tissue and determin dynamic changes in soil, and can fastly detect YC-9strain DNA post inoculation6h, and could also be used to montoring dynamic change of R. solani AG-3from tobacco in soil. Basing on ITS sequence of different anamosis group from NCBI, the specific primer Rs TqF1/R4and probe QTqFl were designed; Real-time PCR systems were respectively established to detece the pathogen from tobacco tissue and soil. The detection resulted show that DNA of R. solani YC-9strain from tobacco tissue was deteced post inoculation6h, and it was far earlier than post inoculation48h by observing the lesions. It was suggested the system was fit to early detect R. solani AG-3from tobacco. The quantitative results showed that R. solani AG-3from tobacco in soil has a dynamic change trend according to different monthly. The copies of R. solani AG-3from tobacco in soil had begun to increase since the mid to late May, and reach to the highest on June28; then it was decline until August9reach to the lowest. It reached the highest on January21, since then R. solani AG-3from tobacco began to decrease and reach to the lowest level in April.
4. The firstly established transcriptome database of R. solani AG-3from tobacco could be as a foundation for analyzing its genes structure and function. Using the transcriptome sequencing and short sequence assembly, a total of630125and562259Contigs were respectively obtained from T1and T2samples, and N50is96and104nt, respectively. There were21206transcript sequences from T1with N501213bp and20400transcript sequences from T2with N501247bp, the average fragment length to836bp.21779Unigenes were received, and the average length was873nt with N50value1339nt. a comprehensive transcriptome database of R. solani AG-3from tobacco was established.
5. Information of function of Unigenes is annotated and differentially expressed gene and these pathways related to pathogenicity of R. solani AG-3from tobacco were analyzed, and pathogenesis were illuminated in level of transcriptom. Through Blastx comparation, a total of14389unigenes were annotated its function. All annoated Unigenes were homology with basidiomycete's fungi containing the pathogens T. cucumeris and R. solani. Unigenes in the category of48kinds of Gene Ontology (GO) function, the most function is metabolic process in the biological process and the catalytic activity in molecular function and cell precess and binding functional genes. Unigenes were classified in the25clusters of orthologous groups (COGs), including prediction, replication, recombination and repair function, carbohydrate transport and metabolism. Through KEGG metabolic pathway analysis, a total of3820genes were annotated in158pathways. Among them, there were more genes annotated to the chromosomes, recombinant proteins and DNA repair pathways, splicing pathway, peptides, enzymes, metabolic pathway and DNA replication proteins of ubiquitin system.
Through the analysis on transcriptomes of R. solani AG-3from tobacco by the RPKM method, the results showed that827differentially expressed genes (DEGs) were acquired and730genes were annoated. The GO and COG functional entaintment and KEGG pathway enrichment analysis of the expression pattern were performed, most of differentially expressed genes were involved in protein synthesis process, including ribosomal proteins, transcription factors, translation factor and elongtation factor, etc. These genes played important roles in pathogensis process of R. solani AG-3.
1.明确了辽宁省烟草靶斑病菌存在着明显的生理分化现象,可划分为三个致病类型,即致病类型Ⅰ(强致病类型)、Ⅱ(中等致病类型)及Ⅲ(弱致病类型),以致病类型Ⅱ为优势种群,分析认为致病类型与菌株地区来源间没有明显相关性。
对来源于不同地区的烟草靶斑病菌基因组ITS序列区进行了聚类分析,结果表各菌株间存在一定的差异,可将测试菌株分为两个ITS类群,进一步分析表明该类群划分与致病类型无明显相关性。
2.建立并优化了适用于烟草靶斑病菌遗传多样性分析的SRAP反应体系,并对SRAP分组与菌株地区来源及致病类型间的关系进行了研究。选取多态性良好的初筛引物及优化后的反应体系对辽宁省烟草靶斑病菌进行PCR扩增,获得多态性条带743条,多态性百分比为98.4%,可将烟草靶斑病菌株划分为3个SGs类群；经分析SGs类群所表现出来的菌株基因组之间的多态性与菌株致病力相关,其中强致病类型菌株YC-9、YMC-2、LJT-8和DB-3都被聚合在SG I类群中,占SGI类群总数的66.7%；而弱致病力菌株LF-2、QYS-5和QYS-7都被聚合在SG Ⅱ类群。这表明SRAP分组与致病类型划分存在明显相关性,而与地区来源没有相关性；与不同融合群标准菌株分析比较表明,SRAP分组与融合群划分无明显相关性。国内外文献无此方面报道,本文为首次采用SRAP技术对烟草靶斑病菌致病类型及遗传多样性进行的研究。
3.建立了烟草靶斑病菌的Real-time PCR定量检测体系,并应用该体系对烟草靶斑病进行早期定量检测,在接种侵染6h后便可检出YC-9菌株DNA,该体系也可以实时监测烟草靶斑病原菌在土壤中动态变化情况。参考NCBI数据库中R. solani不同融合群的ITS序列,设计了对R. solani AG-3特异的引物Rs TqF1/R4和探针QTqF1,并分别建立了适于检测烟草组织和土壤样品的Real-time PCR反应体系。应用该体系对接种烟草靶斑病菌的烟草叶片进行检测结果表明：在接种后6h后即可检测到烟草靶斑病菌,远早于接种36h后观察到可见病原菌子实体结构；采用该体系对各月发病烟田土壤样品定量结果表明：烟草靶斑病菌的群体随不同月份呈现动态变化趋势。自5月中下旬土壤中烟草靶斑病菌拷贝数逐渐升高,到6月28日达到最高,此后开始下降,到8月9日降到最低,8月末烟草靶斑病菌在土壤中拷贝数开始增加,直到1月21日达到最高,此后烟草靶斑病菌下降至4月份达到最低水平。本文为国内外首次建立并应用Real-time PCR技术对烟草靶斑病菌进行的定量检测研究。
4.首次建立了烟草靶斑病菌转录组数据库,为分析烟草靶斑病菌的基因结构及其功能奠定了基础。采用转录组测序以及短序列组装,与烟草互作的T1靶斑病菌样品和未互作的T2对照样品经组装分别获得630125和562259个Contigs,N50值分别为96nt和104nt；经Transcripts组装后,T1和T2分别获得21206和20400条转录本序列,N50分别为1213bp和1247bp；最终共获得21779条Unigenes,平均长度为873nt,N50值为1339nt,较全面的获得了烟草靶斑病菌转录组数据库。
5.通过对上述获得的烟草靶斑病菌转录组数据库的分析,首次对其Unigenes和差异表达基因进行了功能信息注释及代谢途径分析,进而从转录组水平阐明了烟草靶斑病菌的分子致病机理。
采用Blastx软件比对全部Unigenes,其中14389条Unigenes被注释,与担子菌同源最高,其中包含植物病原担子菌T. cucumeris和R. solani等；经GO功能分类分析,共有5976条Unigenes被归类到48个功能类别中,其中生物代谢过程及催化活性和结合作用的分子功能最多；通过COG功能分类,共有5458条Unigenes被归类到25个功能类别中,其中预测功能,复制、重组和修复功能,碳水化合物运输和代谢功能的基因最多；经过KEGG代谢通路的分析,共有3820条基因被注释到158个信号通路中,其中注释到染色体通路、DNA修复和重组蛋白通路、剪接体通路、肽酶通路、泛素系统代谢通路和DNA复制蛋白中的基因较多。
采用RPKM法进行差异表达基因分析,共获得827条差异表达基因,得到注释的有730条。通过GO和COG功能分类以及KEGG通路富集分析,差异表达基因多是参与蛋白质合成过程的相关基因,其中包括核糖体蛋白、转录因子、翻译因子、延伸因子等相关功能基因。
Tobacco target spot caused by Rhizoctonia solani AG-3was one of the most economically important diseases of tobacco leaf and occurs in many countries. It was first reported at Dandong city of China in2006. There was a little report about the biological characteristics, genetic differentiation and pathogen mechanism of the pathogen. In this dissertation, the genetic diversity, quantitative detection technique and transcriptome analysis of R. solani AG-3were systematically and intensively studied, the results were as follows:
1. There were an obvious physiological differentiation among R. solani AG-3from Liaoning province, and three pathotypes, which contain pathotype I, II and III with strong, medium and weak pathogenicity respectively, were determined.
Some differences of ITS region of R. solani AG-3are founded. There was no correlation between the difference group and pathotypes of R. solani AG-3from tobacco.
2. SRAP reaction system of R. solani AG-3from tobacco was firstly established, and genetic diversity of the R. solani AG-3from Liaoning province is analyzed by SRAP reaction system, and the relationships between SRAP groups (SGs) and the locality source of R. solani AG-3were elaborated. Using optimum reaction system and primarily screened SRAP primers which have a good polymorphism, a PCR amplication is performed, and743polymorphism DNA fragements were acquired, percentage of polymorphic loci was98.4%. R. solani AG-3strains from tobacco were divided into three SGs according to SRAP polymorphism between R. solani strains genom from tobacco. All strains with strong pathogenicity containing YC-9, YMC-2, LJT-8and DB-3strains were clusted in SG I, accouting for66.7%of the SG I; and all strains with weak pathogenicity clusted in SG II. The results showed that it is an obvious correlation between SGs and pathotype of strains but not between SGs and the locality source. Further more, there was no correlation between SGs and the anastomosis group. At present, the paper was firstly report relationship between pathotype and genetic diversity of R. solani AG-3from tobacco in the literature at home and abroad.
3. Quantitative detection systems of R. solani AG-3from tobacco firstly established could be applied to early detect in tobacco tissue and determin dynamic changes in soil, and can fastly detect YC-9strain DNA post inoculation6h, and could also be used to montoring dynamic change of R. solani AG-3from tobacco in soil. Basing on ITS sequence of different anamosis group from NCBI, the specific primer Rs TqF1/R4and probe QTqFl were designed; Real-time PCR systems were respectively established to detece the pathogen from tobacco tissue and soil. The detection resulted show that DNA of R. solani YC-9strain from tobacco tissue was deteced post inoculation6h, and it was far earlier than post inoculation48h by observing the lesions. It was suggested the system was fit to early detect R. solani AG-3from tobacco. The quantitative results showed that R. solani AG-3from tobacco in soil has a dynamic change trend according to different monthly. The copies of R. solani AG-3from tobacco in soil had begun to increase since the mid to late May, and reach to the highest on June28; then it was decline until August9reach to the lowest. It reached the highest on January21, since then R. solani AG-3from tobacco began to decrease and reach to the lowest level in April.
4. The firstly established transcriptome database of R. solani AG-3from tobacco could be as a foundation for analyzing its genes structure and function. Using the transcriptome sequencing and short sequence assembly, a total of630125and562259Contigs were respectively obtained from T1and T2samples, and N50is96and104nt, respectively. There were21206transcript sequences from T1with N501213bp and20400transcript sequences from T2with N501247bp, the average fragment length to836bp.21779Unigenes were received, and the average length was873nt with N50value1339nt. a comprehensive transcriptome database of R. solani AG-3from tobacco was established.
5. Information of function of Unigenes is annotated and differentially expressed gene and these pathways related to pathogenicity of R. solani AG-3from tobacco were analyzed, and pathogenesis were illuminated in level of transcriptom. Through Blastx comparation, a total of14389unigenes were annotated its function. All annoated Unigenes were homology with basidiomycete's fungi containing the pathogens T. cucumeris and R. solani. Unigenes in the category of48kinds of Gene Ontology (GO) function, the most function is metabolic process in the biological process and the catalytic activity in molecular function and cell precess and binding functional genes. Unigenes were classified in the25clusters of orthologous groups (COGs), including prediction, replication, recombination and repair function, carbohydrate transport and metabolism. Through KEGG metabolic pathway analysis, a total of3820genes were annotated in158pathways. Among them, there were more genes annotated to the chromosomes, recombinant proteins and DNA repair pathways, splicing pathway, peptides, enzymes, metabolic pathway and DNA replication proteins of ubiquitin system.
Through the analysis on transcriptomes of R. solani AG-3from tobacco by the RPKM method, the results showed that827differentially expressed genes (DEGs) were acquired and730genes were annoated. The GO and COG functional entaintment and KEGG pathway enrichment analysis of the expression pattern were performed, most of differentially expressed genes were involved in protein synthesis process, including ribosomal proteins, transcription factors, translation factor and elongtation factor, etc. These genes played important roles in pathogensis process of R. solani AG-3.
引文
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